Package 'terra'

Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Authors: Robert J. Hijmans [cre, aut] , Roger Bivand [ctb] , Krzysztof Dyba [ctb], Edzer Pebesma [ctb] , Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <[email protected]>
License: GPL (>=3)
Version: 1.7-74
Built: 2024-03-31 23:22:00 UTC
Source: https://github.com/rspatial/terra

Help Index


Description of the methods in the terra package

Description

terra provides methods to manipulate geographic (spatial) data in "raster" and "vector" form. Raster data divide space into rectangular grid cells and they are commonly used to represent spatially continuous phenomena, such as elevation or the weather. Satellite images also have this data structure, and in that context grid cells are often referred to as pixels. In contrast, "vector" spatial data (points, lines, polygons) are typically used to represent discrete spatial entities, such as a road, country, or bus stop.

The package implements two main classes (data types): SpatRaster and SpatVector. SpatRaster supports handling large raster files that cannot be loaded into memory; local, focal, zonal, and global raster operations; polygon, line and point to raster conversion; integration with modeling methods to make spatial predictions; and more. SpatVector supports all types of geometric operations such as intersections.

Additional classes include SpatExtent, which is used to define a spatial extent (bounding box); SpatRasterDataset, which represents a collection of sub-datasets for the same area. Each sub-dataset is a SpatRaster with possibly many layers, and may, for example, represent different weather variables; and SpatRasterCollection and SpatVectorCollection that are equivalent to lists of SpatRaster or SpatVector objects. There is also a SpatGraticule class to assist in adding a longitude/latitude lines and labels to a map with another coordinate reference system.

These classes hold a C++ pointer to the data "reference class" and that creates some limitations. They cannot be recovered from a saved R session either or directly passed to nodes on a computer cluster. Generally, you should use writeRaster to save SpatRaster objects to disk (and pass a filename or cell values to cluster nodes). Also see wrap. Also, package developers should not directly access this pointer, as its user-interface is not stable.

The terra package is conceived as a replacement of the raster package. terra has a very similar, but simpler, interface, and it is faster than raster. At the bottom of this page there is a table that shows differences in the methods between the two packages.

Below is a list of some of the most important methods grouped by theme.

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SpatRaster

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I. Creating, combining and sub-setting

rast Create a SpatRaster from scratch, file, or another object
c Combine SpatRasters (multiple layers)
add<- Add a SpatRaster to another one
subset or [[, or $ Select layers of a SpatRaster
selectRange Select cell values from different layers using an index layer
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II. Changing the spatial extent or resolution

Also see the methods in section VIII

merge Combine SpatRasters with different extents (but same origin and resolution)
mosaic Combine SpatRasters with different extents using a function for overlapping cells
crop Select a geographic subset of a SpatRaster
extend Add rows and/or columns to a SpatRaster
trim Trim a SpatRaster by removing exterior rows and/or columns that only have NAs
aggregate Combine cells of a SpatRaster to create larger cells
disagg Subdivide cells
resample Resample (warp) values to a SpatRaster with a different origin and/or resolution
project Project (warp) values to a SpatRaster with a different coordinate reference system
shift Adjust the location of SpatRaster
flip Flip values horizontally or vertically
rotate Rotate values around the date-line (for lon/lat data)
t Transpose a SpatRaster
--------------------------- ------------------------------------------------------------------------------------------

III. Local (cell based) methods

Apply-like methods

app Apply a function to all cells, across layers, typically to summarize (as in base::apply)
tapp Apply a function to groups of layers (as in base::tapply and stats::aggregate)
lapp Apply a function to using the layers of a SpatRaster as variables
sapp Apply a function to each layer
rapp Apply a function to a spatially variable range of layers
--------------------------- ------------------------------------------------------------------------------------------

Arithmetic, logical, and standard math methods

Arith-methods Standard arithmetic methods (+, -, *, ^, %%, %/%, /)
Compare-methods Comparison methods for SpatRaster (==, !=, >, <, <=, >=m is.na, is.finite)
not.na a one-step equivalent to !is.na
Summary-methods mean, max, min, median, sum, range, prod,
any, all, stdev, which.min, which.max, anyNA, noNA, allNA
Logic-methods Boolean methods (!, &, |)
Math-methods abs, sign, sqrt, ceiling, floor, trunc, cummax, cummin, cumprod,
cumsum, log, log10, log2, log1p, acos, acosh, asin, asinh, atan, atanh,
exp, expm1, cos, cosh, sin, sinh, tan, tanh, round, signif
as.bool create a Boolean (logical) SpatRaster
as.int create an integer (whole numbers) SpatRaster
--------------------------- ------------------------------------------------------------------------------------------

Other methods

approximate Compute missing values for cells by interpolation across layers
roll Rolling functions such as the rolling mean
cellSize Compute the area of cells
classify (Re-)classify values
subst Substitute (replace) cell values
cover First layer covers second layer except where the first layer is NA
init Initialize cells with new values
mask Replace values in a SpatRaster based on values in another SpatRaster
which.lyr which is the first layer that is TRUE?
segregate Make a 0/1 layer for each unique value
rangeFill Make a 0/1 SpatRaster for a time series
regress Cell-based regression models
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IV. Zonal and global methods

expanse Compute the summed area of cells
crosstab Cross-tabulate two SpatRasters
freq Frequency table of SpatRaster cell values
global Summarize SpatRaster cell values with a function
quantile Quantiles
layerCor Correlation between layers
stretch Stretch values
scale Scale values
summary Summary of the values of a SpatRaster (quartiles and mean)
unique Get the unique values in a SpatRaster
zonal Summarize a SpatRaster by zones in another SpatRaster
--------------------------- ------------------------------------------------------------------------------------------

V. Situation (spatial context) based methods

adjacent Identify cells that are adjacent to a set of cells of a SpatRaster
boundaries Detection of boundaries (edges)
distance Shortest distance to a cell that is not NA or to or from a vector object
gridDist Shortest distance through adjacent grid cells
costDist Shortest distance considering cell-varying friction
direction Direction (azimuth) to or from cells that are not NA
focal Focal (neighborhood; moving window) functions
focal3D Three dimensional (row, col, lyr) focal functions
focalCpp Faster focal by using custom C++ functions
focalReg Regression between layers for focal areas
focalPairs Apply a function (e.g. a correlation coefficient) to focal values for pairs of layers
patches Find patches (clumps)
sieve Sieve filter to remove small patches
terrain Compute slope, aspect and other terrain characteristics from elevation data
viewshed Compute viewshed (showing areas that are visible from a particular location
shade Compute hill shade from slope and aspect layers
autocor Compute global or local spatial autocorrelation
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VI. Model predictions

predict Predict a non-spatial (regression or classification) model to a SpatRaster
interpolate Predict a spatial model to a SpatRaster
interpIDW Inverse-distance-weighted interpolation
interpNear Nearest neighbor interpolation
k_means k-means clustering of SpatRaster data
princomp and prcomp Principal Component Analysis (PCA) with raster data
--------------------------- ------------------------------------------------------------------------------------------

VII. Accessing cell values

Apart from the function listed below, you can also use indexing with [ with cell numbers, and row and/or column numbers

values cell values (fails with very large rasters)
values<- Set new values to the cells of a SpatRaster
setValues Set new values to the cells of a SpatRaster
as.matrix Get cell values as a matrix
as.array Get cell values as an array
extract Extract cell values from a SpatRaster (with cell numbers, coordinates, points, lines, or polygons)
extractAlong Extract cell values along a line such that the values are in the right order
spatSample Regular or random sample
minmax Get the minimum and maximum value of the cells of a SpatRaster (if known)
setMinMax Compute the minimum and maximum value of a SpatRaster if these are not known
extract spatial queries of a SpatRaster with a SpatVector
--------------------------- ------------------------------------------------------------------------------------------

VIII. Getting and setting dimensions

Get or set basic parameters of SpatRasters. If there are values associated with a SpatRaster (either in memory or via a link to a file) these are lost when you change the number of columns or rows or the resolution. This is not the case when the extent is changed (as the number of columns and rows will not be affected). Similarly, with crs you can set the coordinate reference system, but this does not transform the data (see project for that).

ncol The number of columns
nrow The number of rows
ncell The number of cells (can not be set directly, only via ncol or nrow)
res The resolution (x and y)
nlyr Get or set the number of layers
names Get or set the layer names
xres The x resolution (can be set with res)
yres The y resolution (can be set with res)
xmin The minimum x coordinate (or longitude)
xmax The maximum x coordinate (or longitude)
ymin The minimum y coordinate (or latitude)
ymax The maximum y coordinate (or latitude)
ext Get or set the extent (minimum and maximum x and y coordinates ("bounding box")
origin The origin of a SpatRaster
crs The coordinate reference system (map projection)
is.lonlat Test if an object has (or may have) a longitude/latitude coordinate reference system
sources Get the filename(s) to which a SpatRaster is linked
inMemory Are the data sources in memory (or on disk)?
compareGeom Compare the geometry of SpatRasters
NAflag Set the NA value (for reading from a file with insufficient metadata)
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IX. Computing row, column, cell numbers and coordinates

Cell numbers start at 1 in the upper-left corner. They increase within rows, from left to right, and then row by row from top to bottom. Likewise, row numbers start at 1 at the top of the raster, and column numbers start at 1 at the left side of the raster.

xFromCol x-coordinates from column numbers
yFromRow y-coordinates from row numbers
xFromCell x-coordinates from row numbers
yFromCell y-coordinates from cell numbers
xyFromCell x and y coordinates from cell numbers
colFromX Column numbers from x-coordinates (or longitude)
rowFromY Row numbers from y-coordinates (or latitude)
rowColFromCell Row and column numbers from cell numbers
cellFromXY Cell numbers from x and y coordinates
cellFromRowCol Cell numbers from row and column numbers
cellFromRowColCombine Cell numbers from all combinations of row and column numbers
cells Cell numbers from an SpatVector or SpatExtent
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X. Time related methods

time Get or set time
fillTime can add empty layers in between existing layers to assure that the time step between layers is constant
mergeTime combine multiple rasters, perhaps partly overlapping in time, into a single time series
--------------------------- ------------------------------------------------------------------------------------------

XI. Methods for categorical rasters

is.factor Are there categorical layers?
levels Get active categories, or set categories
activeCat Get or set the active category
cats Get categories (active and inactive)
set.cats Set categories in place
concats Combine SpatRasters with different categories
catalyze Create a layer for each category
as.numeric use the active category to create a non-categorical SpatRaster
as.factor Make the layers of a SpatRaster categorical
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XII. Writing SpatRaster files

Basic

writeRaster Write all values of SpatRaster to disk. You can set the filetype, datatype, compression.
writeCDF Write SpatRaster data to a netCDF file
--------------------------- ------------------------------------------------------------------------------------------

Advanced

readStart Open file connections for efficient multi-chunk reading
readStop Close file connections
writeStart Open a file for writing
writeValues Write some values
writeStop Close the file after writing
blocks Get blocksize for reading files (when not writing)
--------------------------- ------------------------------------------------------------------------------------------

XIII. Miscellaneous SpatRaster methods

terraOptions Show, set, or get session options, mostly to control memory use and to set write options
sources Show the data sources of a SpatRaster
tmpFiles Show or remove temporary files
mem_info memory needs and availability
inMemory Are the cell values in memory?
--------------------------- ------------------------------------------------------------------------------------------

XIV. SpatRasterDataset

A SpatRasterDataset contains SpatRasters that represent sub-datasets for the same area. They all have the same extent and resolution.

sds Create a SpatRasterDataset from a file with subdatasets (ncdf or hdf) or from SpatRasters
[ or $ Extract a SpatRaster
names Get the names of the sub-datasets
--------------------------- ------------------------------------------------------------------------------------------

XV. SpatRasterCollections

A SpatRasterCollection is a vector of SpatRaster objects. Unlike for a SpatRasterDataset, there the extent and resolution of the SpatRasters do not need to match each other.

sprc create a SpatRasterCollection from (a list of) SpatRasters
length how many SpatRasters does the SpatRasterCollection have?
crop crop a SpatRasterCollection
impose force the members of SpatRasterCollection to the same geometry
merge merge the members of a SpatRasterCollection
mosaic mosaic (merge with a function for overlapping areas) the members of a SpatRasterCollection
[ extract a SpatRaster
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SpatVector

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XVI. Create SpatVector objects

vect Create a SpatVector from a file (for example a "shapefile") or from another object
vector_layers list or delete layers in a vector database such as GPGK
rbind append SpatVectors of the same geometry type
unique remove duplicates
na.omit remove empty geometries and/or fields that are NA
project Project a SpatVector to a different coordinate reference system
writeVector Write SpatVector data to disk
centroids Get the centroids of a SpatVector
voronoi Voronoi diagram
delaunay Delaunay triangles
convHull Compute the convex hull of a SpatVector
minRect Compute the minimum minimal bounding rotated rectangle of a SpatVector
minCircle Compute the minimal bounding circle of a SpatVector
fillHoles Remove or extract holes from polygons
--------------------------- ------------------------------------------------------------------------------------------

XVII. Properties of SpatVector objects

geom returns the geometries as matrix or WKT
crds returns the coordinates as a matrix
linearUnits returns the linear units of the crs (in meter)
ncol The number of columns (of the attributes)
nrow The number of rows (of the geometries and attributes)
names Get or set the layer names
ext Get the extent (minimum and maximum x and y coordinates ("bounding box")
crs The coordinate reference system (map projection)
is.lonlat Test if an object has (or may have) a longitude/latitude coordinate reference system
--------------------------- ------------------------------------------------------------------------------------------

XVIII. Geometric queries

adjacent find adjacent polygons
expanse computes the area covered by polygons
nearby find nearby geometries
nearest find the nearest geometries
relate geometric relationships such as "intersects", "overlaps", and "touches"
perim computes the length of the perimeter of polygons, and the length of lines
--------------------------- ------------------------------------------------------------------------------------------

XIX. Geometric operations

erase or "-" erase (parts of) geometries
intersect or "*" intersect geometries
union or "+" Merge geometries
cover update polygons
symdif symmetrical difference of two polygons
aggregate dissolve smaller polygons into larger ones
buffer buffer geometries
disagg split multi-geometries into separate geometries
crop clip geometries using a rectangle (SpatExtent) or SpatVector
--------------------------- ------------------------------------------------------------------------------------------

XX. SpatVector attributes

We use the term "attributes" for the tabular data (data.frame) associated with vector geometries.

extract spatial queries between SpatVector and SpatVector (e.g. point in polygons)
sel select - interactively select geometries
click identify attributes by clicking on a map
merge Join a table with a SpatVector
as.data.frame get attributes as a data.frame
as.list get attributes as a list
values Get the attributes of a SpatVector
values<- Set new attributes to the geometries of a SpatRaster
sort sort SpatVector by the values in a field
--------------------------- ------------------------------------------------------------------------------------------

XXI. Change geometries (for display, experimentation)

shift change the position geometries by shifting their coordinates in horizontal and/or vertical direction
spin rotate geometries around an origin
rescale shrink (or expand) geometries, for example to make an inset map
flip flip geometries vertically or horizontally
t transpose geometries (switch x and y)
--------------------------- ------------------------------------------------------------------------------------------

XXII. Geometry properties and topology

width the minimum diameter of the geometries
clearance the minimum clearance of the geometries
sharedPaths shared paths (arcs) between line or polygon geometries
simplifyGeom simplify geometries
gaps find gaps between polygon geometries
fillHoles get or remove the polygon holes
makeNodes create nodes on lines
mergeLines connect lines to form polygons
removeDupNodes remove duplicate nodes in geometries and optionally rounds the coordinates
is.valid check if geometries are valid
makeValid attempt to repair invalid geometries
snap make boundaries of geometries identical if they are very close to each other
erase (single argument) remove parts of geometries that overlap
union (single argument) create new polygons such that there are no overlapping polygons
rotate rotate to (dis-) connect them across the date-line
normalize.longitude move geometries that are outside of the -180 to 180 degrees range.
elongate make lines longer by extending both sides
combineGeoms combine geometries that overlap, share a border, or are within a minimum distance of each other
forceCCW force counter-clockwise polygon winding
--------------------------- ------------------------------------------------------------------------------------------

XXIII. SpatVectorCollections

A SpatVectorCollection is a vector of SpatVector objects.

svc create a SpatVectorCollection from (a list of) SpatVector objects
length how many SpatRasters does the SpatRasterCollection have?
[ extract a SpatVector
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Other classes

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XXIV. SpatExtent

ext Create a SpatExtent object. For example to crop a Spatial dataset
intersect Intersect two SpatExtent objects, same as -
union Combine two SpatExtent objects, same as +
Math-methods round/floor/ceiling of a SpatExtent
align Align a SpatExtent with a SpatRaster
draw Create a SpatExtent by drawing it on top of a map (plot)
--------------------------- ------------------------------------------------------------------------------------------

XXV. SpatGraticule

graticule Create a graticule
crop crop a graticule
plot<SpatGraticule> plot a graticule
--------------------------- ------------------------------------------------------------------------------------------

General methods

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XXVI. Conversion between spatial data objects from different packages

You can coerce SpatRasters to Raster* objects, after loading the raster package, with as(object, "Raster"), or raster(object) or brick(object) or stack(object)

rast SpatRaster from matrix and other objects
vect SpatVector from sf or Spatial* vector data
sf::st_as_sf sf object from SpatVector
rasterize Rasterizing points, lines or polygons
rasterizeWin Rasterize points with a moving window
rasterizeGeom Rasterize attributes of geometries such as "count", "area", or "length"
as.points Create points from a SpatRaster or SpatVector
as.lines Create lines from a SpatRaster or SpatVector
as.polygons Create polygons from a SpatRaster
as.contour Contour lines from a SpatRaster
--------------------------- ------------------------------------------------------------------------------------------

XXVII. Plotting

Maps

plot Plot a SpatRaster or SpatVector. The main method to create a map
panel Combine multiple plots
points Add points to a map
lines Add lines to a map
polys Add polygons to a map
text Add text (such as the values of a SpatRaster or SpatVector) to a map
halo Add text with a halo to a map
image Alternative to plot to make a map with a SpatRaster
plotRGB Combine three layers (red, green, blue channels) into a single "real color" plot
plot<SpatGraticule> plot a graticule
sbar Add a scale bar to a map
north Add a north arrow to a map
inset Add a small inset (overview) map
dots Make a dot-density map
cartogram Make a cartogram
persp Perspective plot of a SpatRaster
contour Contour plot or filled-contour plot of a SpatRaster
colorize Combine three layers (red, green, blue channels) into a single layer with a color-table
--------------------------- ------------------------------------------------------------------------------------------

Interacting with a map

zoom Zoom in to a part of a map by drawing a bounding box on it
click Query values of SpatRaster or SpatVector by clicking on a map
sel Select a spatial subset of a SpatRaster or SpatVector by drawing on a map
draw Create a SpatExtent or SpatVector by drawing on a map
--------------------------- ------------------------------------------------------------------------------------------

Other plots

plot x-y scatter plot of the values of (a sample of) the layers of two SpatRaster objects
hist Histogram of SpatRaster values
barplot Bar plot of a SpatRaster
density Density plot of SpatRaster values
pairs Pairs plot for layers in a SpatRaster
boxplot Box plot of the values of a SpatRaster
--------------------------- ------------------------------------------------------------------------------------------

Comparison with the raster package

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XXVIII. New method names

terra has a single class SpatRaster for which raster has three (RasterLayer, RasterStack, RasterBrick). Likewise there is a single class for vector data SpatVector that replaces six Spatial* classes. Most method names are the same, but note the following important differences in methods names with the raster package

raster package terra package
raster, brick, stack rast
rasterFromXYZ rast( , type="xyz")
stack, addLayer c
addLayer add<-
area cellSize or expanse
approxNA approximate
calc app
cellFromLine, cellFromPolygon, cells
cellsFromExtent cells
cellStats global
clump patches
compareRaster compareGeom
corLocal focalPairs
coordinates crds
couldBeLonLat is.lonlat
disaggregate disagg
distanceFromPoints distance
drawExtent, drawPoly, drawLine draw
dropLayer subset
extent ext
getValues values
isLonLat, isGlobalLonLat is.lonlat
layerize segregate
layerStats layerCor
movingFun roll
NAvalue NAflag
nlayers nlyr
overlay lapp
unstack as.list
projectRaster project
rasterToPoints as.points
rasterToPolygons as.polygons
reclassify, subs, cut classify
sampleRandom, sampleRegular spatSample
shapefile vect
stackApply tapp
stackSelect selectRange

XXIX. Changed behavior

Also note that even if function names are the same in terra and raster, their output can be different. In most cases this was done to get more consistency in the returned values (and thus fewer errors in the downstream code that uses them). In other cases it simply seemed better. Here are some examples:

as.polygons By default, terra returns dissolved polygons
quantile computes by cell, across layers instead of the other way around
extract By default, terra returns a matrix, with the first column the sequential ID of the vectors.
raster returns a list (for lines or polygons) or a matrix (for points, but without the ID
column. You can use list=TRUE to get the results as a list
values terra always returns a matrix. raster returns a vector for a RasterLayer
Summary-methods With raster, mean(x, y) and mean(stack(x, y) return the same result, a single
layer with the mean of all cell values. This is also what terra returns with
mean(c(x, y)), but with mean(x, y) the parallel mean is returned -- that is, the
computation is done layer-wise, and the number of layers in the output is the same as
that of x and y (or the larger of the two if they are not the same). This affects
all summary functions (sum, mean, median, which.min, which.max, min, max,
prod, any, all, stdev), except range, which is not implemented for this case
(you can use min and max instead)
--------------------------- ------------------------------------------------------------------------------------------

Authors

Except where indicated otherwise, the methods and functions in this package were written by Robert Hijmans. The configuration scripts were written by Roger Bivand. Some of code using the GEOS library was adapted from code by Edzer Pebesma for sf. Michael Sumner contributed various bits and pieces.

Acknowledgments

This package is an attempt to climb on the shoulders of giants (GDAL, PROJ, GEOS, NCDF, GeographicLib, Rcpp, R). Many people have contributed by asking questions or raising issues. Feedback and suggestions by Márcia Barbosa, Kendon Bell, Andrew Gene Brown, Jean-Luc Dupouey, Krzysztof Dyba, Sarah Endicott, Derek Friend, Alex Ilich, Gerald Nelson, Jakub Nowosad, and Monika Tomaszewska have been especially helpful.


Active category

Description

Get or set the active category of a multi-categorical SpatRaster layer

Usage

## S4 method for signature 'SpatRaster'
activeCat(x, layer=1)
## S4 replacement method for signature 'SpatRaster'
activeCat(x, layer=1)<-value

Arguments

x

SpatRaster

layer

positive integer, the layer number or name

value

positive integer or character, indicating which column in the categories to use. Note that when a number is used this index is zero based, and "1" refers to the second column. This is because the first column of the categories has the cell values, not categorical labels

Value

integer

See Also

levels, cats

Examples

set.seed(0)
r <- rast(nrows=10, ncols=10)
values(r) <- sample(3, ncell(r), replace=TRUE) + 10
d <- data.frame(id=11:13, cover=c("forest", "water", "urban"), letters=letters[1:3], value=10:12)
levels(r) <- d

activeCat(r)
activeCat(r) <- 3
activeCat(r)

Add (in place) a SpatRaster to another SpatRaster or to a SpatRasterDataset or SpatRasterCollection

Description

Add (in place) a SpatRaster to another SpatRaster. Comparable with c, but without copying the object.

Usage

## S4 replacement method for signature 'SpatRaster,SpatRaster'
add(x)<-value

## S4 replacement method for signature 'SpatRasterDataset,SpatRaster'
add(x)<-value

## S4 replacement method for signature 'SpatRasterCollection,SpatRaster'
add(x)<-value

Arguments

x

SpatRaster, SpatRasterDataset or SpatRasterCollection

value

SpatRaster

Value

SpatRaster

See Also

c

Examples

r <- rast(nrows=5, ncols=9, vals=1:45)
x <- c(r, r*2)
add(x) <- r*3
x

draw a box

Description

Similar to box allowing adding a box around a map. This function will place the legend in the locations within the mapped area as delineated by the axes.

Usage

add_box(...)

Arguments

...

arguments passed to lines

Examples

v <- vect(system.file("ex/lux.shp", package="terra"))
plot(v)
add_box(col="red", lwd=3, xpd=TRUE)

add a custom legend

Description

Wrapper around legend that allows adding a custom legend to a map using a keyword such as "topleft" or "bottomright". This function will place the legend in the locations within the mapped area as delineated by the axes.

Usage

add_legend(x, y, ...)

Arguments

x

The keyword to be used to position the legend (or the x coordinate)

y

The y coordinate to be used to position the legend (is x is also a coordinate)

...

arguments passed to legend

Examples

v <- vect(system.file("ex/lux.shp", package="terra"))
plot(v)
points(centroids(v), col="red")
legend("topleft", legend = "centroids", pch = 20, xpd=NA, bg="white", col="red")
add_legend("topright", legend = "centroids", pch = 20, col="red")

Adjacent cells

Description

Identify cells that are adjacent to a set of raster cells. Or identify adjacent polygons

Usage

## S4 method for signature 'SpatRaster'
adjacent(x, cells, directions="rook", pairs=FALSE, include=FALSE, symmetrical=FALSE)

## S4 method for signature 'SpatVector'
adjacent(x, type="rook", pairs=TRUE, symmetrical=FALSE)

Arguments

x

SpatRaster

cells

vector of cell numbers for which adjacent cells should be found. Cell numbers start with 1 in the upper-left corner and increase from left to right and from top to bottom

directions

character or matrix to indicated the directions in which cells are considered connected. The following character values are allowed: "rook" or "4" for the horizontal and vertical neighbors; "bishop" to get the diagonal neighbors; "queen" or "8" to get the vertical, horizontal and diagonal neighbors; or "16" for knight and one-cell queen move neighbors. If directions is a matrix it should have odd dimensions and have logical (or 0, 1) values

pairs

logical. If TRUE, a two-column matrix of pairs of adjacent cells is returned. If x is a SpatRaster and pairs is FALSE, an n*m matrix is returned where the number of rows n is length(cells) and the number of columns m is the number of neighbors requested with directions

include

logical. Should the focal cells be included in the result?

type

character. One of "rook", "queen", "touches", or "intersects". "queen" and "touches" are synonyms. "rook" exclude polygons that touch at a single node only. "intersects" includes polygons that touch or overlap

symmetrical

logical. If TRUE and pairs=TRUE, an adjacent pair is only included once. For example, if polygon 1 is adjacent to polygon 3, the implied adjacency between 3 and 1 is not reported

Value

matrix

Note

When using global lon/lat rasters, adjacent cells at the other side of the date-line are included.

See Also

relate, nearby

Examples

r <- rast(nrows=10, ncols=10)
adjacent(r, cells=c(1, 5, 55), directions="queen") 
r <- rast(nrows=10, ncols=10, crs="+proj=utm +zone=1 +datum=WGS84")
adjacent(r, cells=11, directions="rook") 

#same as 
rk <- matrix(c(0,1,0,1,0,1,0,1,0), 3, 3)
adjacent(r, cells=11, directions=rk) 

## note that with global lat/lon data the E and W connect
r <- rast(nrows=10, ncols=10, crs="+proj=longlat +datum=WGS84")
adjacent(r, cells=11, directions="rook") 

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
a <- adjacent(v, symmetrical=TRUE)
head(a)

Aggregate raster or vector data

Description

Aggregate a SpatRaster to create a new SpatRaster with a lower resolution (larger cells). Aggregation groups rectangular areas to create larger cells. The value for the resulting cells is computed with a user-specified function.

You can also aggregate ("dissolve") a SpatVector. This either combines all geometries into one geometry, or it combines the geometries that have the same value for the variable(s) specified with argument by.

Usage

## S4 method for signature 'SpatRaster'
aggregate(x, fact=2, fun="mean", ..., cores=1, filename="", overwrite=FALSE, wopt=list())

## S4 method for signature 'SpatVector'
aggregate(x, by=NULL, dissolve=TRUE, fun="mean", count=TRUE, ...)

Arguments

x

SpatRaster

fact

positive integer. Aggregation factor expressed as number of cells in each direction (horizontally and vertically). Or two integers (horizontal and vertical aggregation factor) or three integers (when also aggregating over layers)

fun

function used to aggregate values. Either an actual function, or for the following, their name: "mean", "max", "min", "median", "sum", "modal", "any", "all", "prod", "which.min", "which.max", "sd" (sample standard deviation) and "std" (population standard deviation)

...

additional arguments passed to fun, such as na.rm=TRUE

cores

positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created. Ignored for C++ level implemented functions that are listed under fun

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

by

character. The variable(s) used to group the geometries

dissolve

logical. Should borders between aggregated geometries be dissolved?

count

logical. If TRUE and by is not NULL, a variable "agg_n" is included that shows the number of input geometries for each output geometry

Details

Aggregation starts at the upper-left end of a SpatRaster. If a division of the number of columns or rows with factor does not return an integer, the extent of the resulting SpatRaster will be somewhat larger then that of the original SpatRaster. For example, if an input SpatRaster has 100 columns, and fact=12, the output SpatRaster will have 9 columns and the maximum x coordinate of the output SpatRaster is also adjusted.

The function fun should take multiple numbers, and return a single number. For example mean, modal, min or max.

It should also accept a na.rm argument (or ignore it as one of the 'dots' arguments).

Value

SpatRaster

See Also

disagg to disaggregate

Examples

r <- rast()
# aggregated SpatRaster, no values
ra <- aggregate(r, fact=10)

values(r) <- runif(ncell(r))
# aggregated raster, max of the values
ra <- aggregate(r, fact=10, fun=max)

# multiple layers
s <- c(r, r*2)
x <- aggregate(s, 20)


## SpatVector 
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
va <- aggregate(v, "ID_1")

plot(va, "NAME_1", lwd=5, plg=list(x="topright"), mar=rep(2,4))
lines(v, lwd=3, col="light gray")
lines(va)
text(v, "ID_1", halo=TRUE)

Align a SpatExtent

Description

Align an SpatExtent with a SpatRaster This can be useful to create a new SpatRaster with the same origin and resolution as an existing SpatRaster. Do not use this to force data to match that really does not match (use e.g. resample or (dis)aggregate for this).

It is also possible to align a SpatExtent to a clean divisor.

Usage

## S4 method for signature 'SpatExtent,SpatRaster'
align(x, y, snap="near")

## S4 method for signature 'SpatExtent,numeric'
align(x, y)

Arguments

x

SpatExtent

y

SpatRaster or numeric

snap

Character. One of "near", "in", or "out", to determine in which direction the extent should be aligned. To the nearest border, inwards or outwards

Value

SpatExtent

See Also

ext, draw

Examples

r <- rast()
e <- ext(-10.1, 9.9, -20.1, 19.9)
ea <- align(e, r)
e
ext(r)
ea

align(e, 0.5)

Compare two SpatRasters for equality

Description

Compare two SpatRasters for (near) equality.

First the attributes of the objects are compared. If these are the same, a (perhaps small) sample of the raster cells is compared as well.

The sample size used can be increased with the maxcell argument. You can set it to Inf, but for large rasters your computer may not have sufficient memory. See the examples for a safe way to compare all values.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
all.equal(target, current, maxcell=100000, ...)

Arguments

target

SpatRaster

current

SpatRaster

maxcell

positive integer. The size of the regular sample used to compare cell values

...

additional arguments passed to all.equal.numeric to compare cell values

Value

Either TRUE or a character vector describing the differences between target and current.

See Also

identical, compareGeom

Examples

x <- sqrt(1:100)
mat <- matrix(x, 10, 10)
r1 <- rast(nrows=10, ncols=10, xmin=0, vals = x)
r2 <- rast(nrows=10, ncols=10, xmin=0, vals = mat)

all.equal(r1, r2)
all.equal(r1, r1*1)
all.equal(rast(r1), rast(r2))

# compare geometries 
compareGeom(r1, r2)

# Compare all cell values for near equality
# as floating point number imprecision can be a problem
m <- minmax(r1 - r2)
all(abs(m) < 1e-7)

# comparison of cell values to create new SpatRaster
e <- r1 == r2

Animate a SpatRaster

Description

Animate (sequentially plot) the layers of a SpatRaster to create a movie.

This does not work with R-Studio.

Usage

## S4 method for signature 'SpatRaster'
animate(x, pause=0.25, main, range, maxcell=50000, n=1, ...)

Arguments

x

SpatRaster

pause

numeric. How long should be the pause be between layers?

main

title for each layer. If not supplied the z-value is used if available. Otherwise the names are used.

range

numeric vector of length 2. Range of values to plot

maxcell

positive integer. Maximum number of cells to use for the plot. If maxcell < ncell(x), spatSample(type="regular") is used before plotting

n

integer > 0. Number of loops

...

Additional arguments passed to plot

Value

None

See Also

plot

Examples

s <- rast(system.file("ex/logo.tif", package="terra"))   
animate(s, n=1)

Apply a function to the cells of a SpatRaster

Description

Apply a function to the values of each cell of a SpatRaster. Similar to apply – think of each layer in a SpatRaster as a column (or row) in a matrix.

This is generally used to summarize the values of multiple layers into one layer; but this is not required.

app calls function fun with the raster data as first argument. Depending on the function supplied, the raster data is represented as either a matrix in which each layer is a column, or a vector representing a cell. The function should return a vector or matrix that is divisible by ncell(x). Thus, both "sum" and "rowSums" can be used, but "colSums" cannot be used.

You can also apply a function fun across datasets by layer of a SpatRasterDataset. In that case, summarization is by layer across SpatRasters.

Usage

## S4 method for signature 'SpatRaster'
app(x, fun, ..., cores=1, filename="", overwrite=FALSE, wopt=list())

## S4 method for signature 'SpatRasterDataset'
app(x, fun, ..., cores=1, filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster or SpatRasterDataset

fun

a function that operates on a vector or matrix. This can be a function that is defined in base-R or in a package, or a function you write yourself (see examples). Functions that return complex output (e.g. a list) may need to be wrapped in your own function to simplify the output to a vector or matrix. The following functions have been re-implemented in C++ for speed: "sum", "mean", "median", "modal", "which", "which.min", "which.max", "min", "max", "prod", "any", "all", "sd", "std", "first". To use the base-R function for say, "min", you could use something like fun=function(i) min(i) or the equivalent fun = \(i) min(i)

...

additional arguments for fun. These are typically numerical constants. They should *never* be another SpatRaster

cores

positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used. You can also supply a cluster object. Ignored for functions that are implemented by terra in C++ (see under fun)

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

Details

To speed things up, parallelization is supported, but this is often not helpful, and it may actually be slower. There is only a speed gain if you have many cores (> 8) and/or a very complex (slow) function fun. If you write fun yourself, consider supplying a cppFunction made with the Rcpp package instead (or go have a cup of tea while the computer works for you).

Value

SpatRaster

See Also

lapp, tapp, Math-methods, roll

Examples

r <- rast(ncols=10, nrows=10)
values(r) <- 1:ncell(r)
x <- c(r, sqrt(r), r+50)
s <- app(x, fun=sum)
s
# for a few generic functions like 
# "sum", "mean", and "max" you can also do
sum(x)

## SpatRasterDataset
sd <- sds(x, x*2, x/3)
a <- app(sd, max)
a
# same as 
max(x, x*2, x/3)
# and as (but slower)
b <- app(sd, function(i) max(i))


## also works for a single layer
f <- function(i) (i+1) * 2 * i + sqrt(i)
s <- app(r, f)
# same as above, but that is not memory-safe
# and has no filename argument 
s <- f(r)

## Not run: 
#### multiple cores 
test0 <- app(x, sqrt) 
test1 <- app(x, sqrt, cores=2)

testfun <- function(i) { 2 * sqrt(i) }
test2 <- app(x, fun=testfun, cores =2)

## this fails because testfun is not exported to the nodes
# test3 <- app(x, fun=function(i) testfun(i), cores=2)
## to export it, add it as argument to fun
test3 <- app(x, fun=function(i, ff) ff(i), cores =3, ff=testfun)

## End(Not run)

Estimate values for cell values that are NA by interpolating between layers

Description

approximate uses the stats function approx to estimate values for cells that are NA by interpolation across layers. Layers are considered equidistant, unless argument z is used, or time(x) returns values that are not NA, in which case these values are used to determine distance between layers.

For estimation based on neighboring cells see focal

Usage

## S4 method for signature 'SpatRaster'
approximate(x, method="linear", yleft, yright,
            rule=1, f=0, ties=mean, z=NULL, NArule=1,filename="",  ...)

Arguments

x

SpatRaster

method

specifies the interpolation method to be used. Choices are "linear" or "constant" (step function; see the example in approx

yleft

the value to be returned before a non-NA value is encountered. The default is defined by the value of rule given below

yright

the value to be returned after the last non-NA value is encountered. The default is defined by the value of rule given below

rule

an integer (of length 1 or 2) describing how interpolation is to take place at for the first and last cells (before or after any non-NA values are encountered). If rule is 1 then NAs are returned for such points and if it is 2, the value at the closest data extreme is used. Use, e.g., rule = 2:1, if the left and right side extrapolation should differ

f

for method = "constant" a number between 0 and 1 inclusive, indicating a compromise between left- and right-continuous step functions. If y0 and y1 are the values to the left and right of the point then the value is y0*(1-f)+y1*f so that f = 0) is right-continuous and f = 1 is left-continuous

ties

Handling of tied 'z' values. Either a function with a single vector argument returning a single number result or the string "ordered"

z

numeric vector to indicate the distance between layers (e.g., depth). The default is time(x) if these are not NA or else 1:nlys(x)

NArule

single integer used to determine what to do when only a single layer with a non-NA value is encountered (and linear interpolation is not possible). The default value of 1 indicates that all layers will get this value for that cell; all other values do not change the cell values

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

focal, fillTime

Examples

r <- rast(ncols=5, nrows=5)
r1 <- setValues(r, runif(ncell(r)))
r2 <- setValues(r, runif(ncell(r)))
r3 <- setValues(r, runif(ncell(r)))
r4 <- setValues(r, runif(ncell(r)))
r5 <- setValues(r, NA)
r6 <- setValues(r, runif(ncell(r)))
r1[6:10] <- NA
r2[5:15] <- NA
r3[8:25] <- NA
s <- c(r1,r2,r3,r4,r5,r6)
s[1:5] <- NA
x1 <- approximate(s)
x2 <- approximate(s, rule=2)
x3 <- approximate(s, rule=2, z=c(1,2,3,5,14,15))

Arithmetic

Description

Standard arithmetic operators for computations with SpatRasters. Computations are local (applied on a cell by cell basis). If multiple SpatRasters are used, these must have the same geometry (extent and resolution). These operators have been implemented:

+, -, *, /, ^, %%, %/%

You can also use a SpatRaster and a vector or a matrix. If you use a SpatRaster with a vector of multiple numbers, each element in the vector is considered a layer (with a constant value). If you use a SpatRaster with a matrix, the number of columns of the matrix must match the number of layers of the SpatRaster. The rows are used to match the cells. That is, if there are two rows, these match cells 1 and 2, and they are recycled to 3 and 4, etc.

The following methods have been implemented for (SpatExtent, SpatExtent): +, -, and the following for (SpatExtent, numeric): +, -, *, /, %%

Value

SpatRaster or SpatExtent

See Also

ifel to conveniently combine operations and Math-methods or app to use mathematical functions not implemented by the package.

Examples

r1 <- rast(ncols=10, nrows=10)
v <- runif(ncell(r1))
v[10:20] <- NA
values(r1) <- v
r2 <- rast(r1)
values(r2) <- 1:ncell(r2) / ncell(r2)
r3 <- r1 + r2
r2 <- r1 / 10
r3 <- r1 * (r2 - 1 / r2)

b <- c(r1, r2, r3)
b2 <- b * 10

### SpatExtent methods
x <- ext(0.1, 2.2, 0, 3)
y <- ext(-2, 1, -2,2)
# union
x + y
# intersection
x * y

e <- x 
e
e * 2
e / 2
e + 1
e - 1

Create a text representation of (the skeleton of) an object

Description

Create a text representation of (the skeleton of) an object

Usage

## S4 method for signature 'SpatExtent'
as.character(x)

## S4 method for signature 'SpatRaster'
as.character(x)

Arguments

x

SpatRaster

Value

character

Examples

r <- rast()
ext(r)
ext(c(0, 20, 0, 20))

SpatRaster or SpatVector to data.frame

Description

Coerce a SpatRaster or SpatVector to a data.frame

Usage

## S4 method for signature 'SpatVector'
as.data.frame(x, row.names=NULL, optional=FALSE, geom=NULL, ...)

## S4 method for signature 'SpatRaster'
as.data.frame(x, row.names=NULL, optional=FALSE, xy=FALSE, 
	cells=FALSE, time=FALSE, na.rm=NA, wide=TRUE, ...)

Arguments

x

SpatRaster or SpatVector

geom

character or NULL. If not NULL, either "WKT" or "HEX", to get the geometry included in Well-Known-Text or hexadecimal notation. If x has point geometry, it can also be "XY" to add the coordinates of each point

xy

logical. If TRUE, the coordinates of each raster cell are included

time

logical. If TRUE, the time data is included (if available)

na.rm

logical. If TRUE, cells that have a NA value in at least one layer are removed. If the argument is set to NA only cells that have NA values in all layers are removed

cells

logical. If TRUE, the cell numbers of each raster cell are included

wide

logical. If FALSE, the data.frame returned has a "long" format

...

Additional arguments passed to the data.frame

row.names

This argument is ignored

optional

This argument is ignored

Value

data.frame

See Also

as.list, as.matrix. See geom to only extract the geometry of a SpatVector

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
as.data.frame(v)

Conversion to a SpatVector of lines

Description

Conversion of a SpatRaster, SpatVector or SpatExtent to a SpatVector of lines.

Usage

## S4 method for signature 'SpatRaster'
as.lines(x)

## S4 method for signature 'SpatVector'
as.lines(x)

## S4 method for signature 'SpatExtent'
as.lines(x, crs="")

Arguments

x

SpatRaster, SpatVector or SpatExtent

crs

character. The coordinate reference system (see crs)

Value

SpatVector

See Also

as.points, as.polygons

Examples

r <- rast(ncols=2, nrows=2)
values(r) <- 1:ncell(r)

as.lines(r)

as.lines(ext(r), crs=crs(r))

if  (gdal() >= "3.0.0") {
	p <- as.polygons(r)
	as.lines(p)
}

Coerce a Spat* object to a list

Description

Coerce a SpatRaster, SpatRasterCollection, SpatRasterDataset, SpatVector or SpatVectorCollection to a list. With a SpatRaster, each layer becomes a list element. With a SpatRasterCollection or SpatRasterDataset, each SpatRaster becomes a list element. With a SpatVector, each variable (attribute) becomes a list element. With a SpatVectorCollection, each SpatVector becomes a list element.

Usage

## S4 method for signature 'SpatRaster'
as.list(x, geom=NULL, ...)

## S4 method for signature 'SpatRasterCollection'
as.list(x, ...)

## S4 method for signature 'SpatVector'
as.list(x, geom=NULL, ...)

## S4 method for signature 'SpatVectorCollection'
as.list(x, ...)

Arguments

x

SpatRaster, SpatRasterDataset, SpatRasterCollection, or SpatVector

geom

character or NULL. If not NULL, and x is a SpatVector, it should be either "WKT" or "HEX", to get the geometry included in Well-Known-Text or hexadecimal notation. If x has point geometry, it can also bey "XY" to add the coordinates of each point. If x is a SpatRaster, any value that is not NULL will return a list with the the parameters describing the geometry of the SpatRaster are returned

...

additional arguments. These are ignored

Value

list

See Also

see coerce for as.data.frame with a SpatRaster; and geom to only extract the geometry of a SpatVector

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
as.list(v)


s <- rast(system.file("ex/logo.tif", package="terra")) + 1  
as.list(s)

Conversion to a SpatVector of points

Description

Conversion of a SpatRaster, SpatVector or SpatExtent to a SpatVector of points.

Usage

## S4 method for signature 'SpatRaster'
as.points(x, values=TRUE, na.rm=TRUE, na.all=FALSE)

## S4 method for signature 'SpatVector'
as.points(x, multi=FALSE, skiplast=TRUE)

## S4 method for signature 'SpatExtent'
as.points(x, crs="")

Arguments

x

SpatRaster, SpatVector or SpatExtent

values

logical; include cell values as attributes?

multi

logical. If TRUE a multi-point geometry is returned

skiplast

logical. If TRUE the last point of a polygon (which is the same as the first point) is not included

na.rm

logical. If TRUE cells that are NA are ignored

na.all

logical. If TRUE cells are only ignored if na.rm=TRUE and their value is NA for all layers instead of for any layer

crs

character. The coordinate reference system (see crs)

Value

SpatVector

See Also

as.lines, as.points

Examples

r <- rast(ncols=2, nrows=2)
values(r) <- 1:ncell(r)

as.points(r)

if  (gdal() >= "3.0.0") {
	p <- as.polygons(r)
	as.points(p)
}

Conversion to a SpatVector of polygons

Description

Conversion of a SpatRaster, SpatVector or SpatExtent to a SpatVector of polygons.

Usage

## S4 method for signature 'SpatRaster'
as.polygons(x, round=TRUE, aggregate=TRUE, values=TRUE,
		na.rm=TRUE, na.all=FALSE, extent=FALSE, digits=0, ...)

## S4 method for signature 'SpatVector'
as.polygons(x, extent=FALSE)

## S4 method for signature 'SpatExtent'
as.polygons(x, crs="")

Arguments

x

SpatRaster, SpatVector or SpatExtent

round

logical; If TRUE and aggregate=TRUE, values are rounded before aggregation. If this value is FALSE the SpatVector returned can have very many polygons and can be very large

aggregate

logical; combine cells with the same values? If TRUE only the first layer in x is processed

values

logical; include cell values as attributes?

extent

logical. if TRUE, a polygon for the extent of the SpatRaster or SpatVector is returned. If x is a SpatRaster, the polygon has vertices for each row and column, not just the four corners of the raster. This can be useful for more precise projection. If that is not required, it is more efficient to get the extent represented by only the four corners with as.polygons(ext(x), crs=crs(x))

na.rm

logical. If TRUE cells that are NA are ignored

na.all

logical. If TRUE cells are only ignored if na.rm=TRUE and their value is NA for all layers instead of for any layer

digits

integer. The number of digits for rounding (if round=TRUE)

crs

character. The coordinate reference system (see crs)

...

additional arguments. For backward compatibility. Will be removed in the future

Value

SpatVector

See Also

as.lines, as.points

Examples

r <- rast(ncols=2, nrows=2)
values(r) <- 1:ncell(r)

if  (gdal() >= "3.0.0") {
	p <- as.polygons(r)
	p
}

Coerce to a "raster" object

Description

Implementation of the generic as.raster function to create a "raster" (small r) object. Such objects can be used for plotting with the rasterImage function. NOT TO BE CONFUSED with the Raster* (big R) objects defined by the 'raster' package!

Usage

## S4 method for signature 'SpatRaster'
as.raster(x, maxcell=500000, col)

Arguments

x

SpatRaster

maxcell

positive integer. Maximum number of cells to use for the plot

col

vector of colors. Default is col=rev(terrain.colors(255)))

Value

'raster' object

Examples

r <- rast(ncols=3, nrows=3)
values(r) <- 1:ncell(r)
as.raster(r)

Two argument arc-tangent

Description

For SpatRasters x and y, atan2(y, x) returns the angle in radians for the tangent y/x, handling the case when x is zero. See Trig

See Math-methods for other trigonometric and mathematical functions that can be used with SpatRasters.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
atan2(y, x)

## S4 method for signature 'SpatRaster,SpatRaster'
atan_2(y, x, filename, ...)

Arguments

y

SpatRaster

x

SpatRaster

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

See Also

Math-methods

Examples

r1 <- rast(nrows=10, ncols=10)
r2 <- rast(nrows=10, ncols=10)
values(r1) <- (runif(ncell(r1))-0.5) * 10
values(r2) <- (runif(ncell(r1))-0.5) * 10
atan2(r1, r2)

Spatial autocorrelation

Description

Compute spatial autocorrelation for a numeric vector or a SpatRaster. You can compute standard (global) Moran's I or Geary's C, or local indicators of spatial autocorrelation (Anselin, 1995).

Usage

## S4 method for signature 'numeric'
autocor(x, w, method="moran")

## S4 method for signature 'SpatRaster'
autocor(x, w=matrix(c(1,1,1,1,0,1,1,1,1),3), method="moran", global=TRUE)

Arguments

x

numeric or SpatRaster

w

Spatial weights defined by or a rectangular matrix. For a SpatRaster this matrix must the sides must have an odd length (3, 5, ...)

global

logical. If TRUE global autocorrelation is computed instead of local autocorrelation

method

character. If x is numeric or SpatRaster: "moran" for Moran's I and "geary" for Geary's C. If x is numeric also: "Gi", "Gi*" (the Getis-Ord statistics), locmor (local Moran's I) and "mean" (local mean)

Details

The default setting uses a 3x3 neighborhood to compute "Queen's case" indices. You can use a filter (weights matrix) to do other things, such as "Rook's case", or different lags.

Value

numeric or SpatRaster

References

Moran, P.A.P., 1950. Notes on continuous stochastic phenomena. Biometrika 37:17-23

Geary, R.C., 1954. The contiguity ratio and statistical mapping. The Incorporated Statistician 5: 115-145

Anselin, L., 1995. Local indicators of spatial association-LISA. Geographical Analysis 27:93-115

https://en.wikipedia.org/wiki/Indicators_of_spatial_association

See Also

The spdep package for additional and more general approaches for computing spatial autocorrelation

Examples

### raster
r <- rast(nrows=10, ncols=10, xmin=0)
values(r) <- 1:ncell(r)

autocor(r)

# rook's case neighbors
f <- matrix(c(0,1,0,1,0,1,0,1,0), nrow=3)
autocor(r, f)

# local 
rc <- autocor(r, w=f, global=FALSE)

### numeric (for vector data)
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
w <- relate(v, relation="touches")

# global
autocor(v$AREA, w)

# local
v$Gi <- autocor(v$AREA, w, "Gi") 
plot(v, "Gi")

Bar plot of a SpatRaster

Description

Create a barplot of the values of a the first layer of a SpatRaster. For large datasets a regular sample with a size of approximately maxcells is used.

Usage

## S4 method for signature 'SpatRaster'
barplot(height, maxcell=1000000, digits=0, breaks=NULL, col, ...)

Arguments

height

SpatRaster

maxcell

integer. To regularly subsample very large datasets

digits

integer used to determine how to round the values before tabulating. Set to NULL or to a large number if you do not want any rounding

breaks

breaks used to group the data as in cut

col

a color generating function such as rainbow (the default), or a vector of colors

...

additional arguments for plotting as in barplot

Value

A numeric vector (or matrix, when beside = TRUE) of the coordinates of the bar midpoints, useful for adding to the graph. See barplot

See Also

hist, boxplot

Examples

f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
barplot(r, digits=-1, las=2, ylab="Frequency")

op <- par(no.readonly = TRUE)
par(mai = c(1, 2, .5, .5))
barplot(r, breaks=10, col=c("red", "blue"), horiz=TRUE, digits=NULL, las=1)
par(op)

Detect boundaries (edges)

Description

Detect boundaries (edges). Boundaries are cells that have more than one class in the 4 or 8 cells surrounding it, or, if classes=FALSE, cells with values and cells with NA.

Usage

## S4 method for signature 'SpatRaster'
boundaries(x, classes=FALSE, inner=TRUE, 
         directions=8, falseval=0, filename="", ...)

Arguments

x

SpatRaster

inner

logical. If TRUE, "inner" boundaries are returned, else "outer" boundaries are returned

classes

character. Logical. If TRUE all different values are (after rounding) distinguished, as well as NA. If FALSE (the default) only edges between NA and non-NA cells are considered

directions

integer. Which cells are considered adjacent? Should be 8 (Queen's case) or 4 (Rook's case)

falseval

numeric. The value to use for cells that are not a boundary and not NA

filename

character. Output filename

...

options for writing files as in writeRaster

Value

SpatRaster. Cell values are either 1 (a border) or 0 (not a border), or NA

See Also

focal, patches

Examples

r <- rast(nrows=18, ncols=36, xmin=0)
r[150:250] <- 1
r[251:450] <- 2
bi <- boundaries(r)
bo <- boundaries(r, inner=FALSE)
bc <- boundaries(r, classes=TRUE)
#plot(bc)

Box plot of SpatRaster data

Description

Box plot of layers in a SpatRaster

Usage

## S4 method for signature 'SpatRaster'
boxplot(x, y=NULL, maxcell=100000, ...)

Arguments

x

SpatRaster

y

NULL or a SpatRaster. If x is a SpatRaster it used to group the values of x by "zone"

maxcell

Integer. Number of cells to sample from datasets

...

additional arguments passed to graphics::boxplot

Value

boxplot returns a list (invisibly) that can be used with bxp

See Also

pairs, hist

Examples

r1 <- r2 <- r3 <- rast(ncols=10, nrows=10)
set.seed(409)
values(r1) <- rnorm(ncell(r1), 100, 40)
values(r2) <- rnorm(ncell(r1), 80, 10)
values(r3) <- rnorm(ncell(r1), 120, 30)
s <- c(r1, r2, r3)
names(s) <- c("Apple", "Pear", "Cherry")

boxplot(s, notch=TRUE, col=c("red", "blue", "orange"), main="Box plot", ylab="random", las=1)

op <- par(no.readonly = TRUE)
par(mar=c(4,6,2,2))
boxplot(s, horizontal=TRUE, col="lightskyblue", axes=FALSE)
axis(1)
axis(2, at=0:3, labels=c("", names(s)), las=1, cex.axis=.9, lty=0)
par(op)

## boxplot with 2 layers
v <- vect(system.file("ex/lux.shp", package="terra"))
r <- rast(system.file("ex/elev.tif", package="terra"))
y <- rasterize(v, r, "NAME_2")
b <- boxplot(r, y)
bxp(b)

Create a buffer around vector geometries or raster patches

Description

Calculate a buffer around all cells that are not NA in a SpatRaster, or around the geometries of a SpatVector.

SpatRaster cells inside the buffer distance get a value of 1.

Note that the distance unit of the buffer width parameter is meters if the CRS is (+proj=longlat), and in map units (typically also meters) if not.

Usage

## S4 method for signature 'SpatRaster'
buffer(x, width, background=0, filename="", ...)

## S4 method for signature 'SpatVector'
buffer(x, width, quadsegs=10, capstyle="round", 
		joinstyle="round", mitrelimit=NA, singlesided=FALSE)

Arguments

x

SpatRaster or SpatVector

width

numeric. Unit is meter if x has a longitude/latitude CRS, or in the units of the coordinate reference system in other cases (typically also meter). The value should be > 0 if x is a SpatRaster. If x is a SpatVector, this argument is vectorized, meaning that you can provide a different value for each geometry in x; and you can also use the name of a variable in x that has the widths

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

background

numeric. value to assign to cells outside the buffer. If this value is zero or FALSE, a boolean SpatRaster is returned

quadsegs

positive integer. Number of line segments to use to draw a quart circle

capstyle

character. One of "round", "square" or "flat". Ignored if is.lonlat(x)

joinstyle

character. One of "round", "mitre" or "bevel". Ignored if is.lonlat(x)

mitrelimit

numeric. Place an upper bound on a mitre join to avoid it from extending very far from acute angles in the input geometry. Ignored if is.lonlat(x)

singlesided

logical. If TRUE a buffer is constructed on only one side of each input line. Ignored if is.lonlat(x)

Value

Same as x

See Also

distance, elongate

Examples

r <- rast(ncols=36, nrows=18)
r[500] <- 1
b <- buffer(r, width=5000000) 
plot(b)

v <- vect(rbind(c(10,10), c(0,60)), crs="+proj=merc")
b <- buffer(v, 20)
plot(b)
points(v)

crs(v) <- "+proj=longlat" 
b <- buffer(v, 1500000)
plot(b)
points(v)

Combine SpatRaster or SpatVector objects

Description

With c you can:

– Combine SpatRaster objects. They must have the same extent and resolution. However, if x is empty (has no cell values), its geometry is ignored with a warning. Two empty SpatRasters with the same geometry can also be combined (to get a summed number of layers). Also see add<-

– Add a SpatRaster to a SpatRasterDataset or SpatRasterCollection

– Add SpatVector objects to a new or existing SpatVectorCollection

To append SpatVectors, use rbind.

Usage

## S4 method for signature 'SpatRaster'
c(x, ..., warn=TRUE)

## S4 method for signature 'SpatRasterDataset'
c(x, ...)

## S4 method for signature 'SpatRasterCollection'
c(x, ...)

## S4 method for signature 'SpatVector'
c(x, ...)

## S4 method for signature 'SpatVectorCollection'
c(x, ...)

Arguments

x

SpatRaster, SpatVector, SpatRasterDataset or SpatVectorCollection

warn

logical. If TRUE, a warning is emitted if x is an empty SpatRaster

...

as for x (you can only combine raster with raster data and vector with vector data)

Value

Same class as x

See Also

add<-

Examples

r <- rast(nrows=5, ncols=9)
values(r) <- 1:ncell(r)
x <- c(r, r*2, r*3)

Cartogram

Description

Make a cartogram, that is, a map where the area of polygons is made proportional to another variable. This can be a good way to map raw count data (e.g. votes).

Usage

## S4 method for signature 'SpatVector'
cartogram(x, var, type)

Arguments

x

SpatVector

var

character. A variable name in x

type

character. Cartogram type, only "nc" (non-contiguous) is currently supported

Value

SpatVector

See Also

plot, rescale

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
v$value <- 1:12
p <- cartogram(v, "value", "nc")
plot(v, col="light gray", border="gray")
lines(p, col="red", lwd=2)

Factors to numeric

Description

Change a categorical layer into one or more numerical layers. With as.numeric you can transfer the active category values to cell values in a non-categorical SpatRaster. catalyze creates new layers for each category.

Usage

## S4 method for signature 'SpatRaster'
as.numeric(x, index=NULL, filename="", ...)

## S4 method for signature 'SpatRaster'
catalyze(x, filename="", ...)

Arguments

x

SpatRaster

index

positive integer or category indicating the category to use. If NULL the active category is used

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

activeCat, cats

Examples

set.seed(0)
r <- rast(nrows=10, ncols=10)
values(r) <- sample(3, ncell(r), replace=TRUE) + 10
d <- data.frame(id=11:13, cover=c("forest", "water", "urban"), letters=letters[1:3], value=10:12)
levels(r) <- d
catalyze(r)

activeCat(r) <- 3
as.numeric(r)

Get cell numbers

Description

Get the cell numbers covered by a SpatVector or SpatExtent. Or that match values in a vector; or all non NA values.

Usage

## S4 method for signature 'SpatRaster,missing'
cells(x, y)

## S4 method for signature 'SpatRaster,numeric'
cells(x, y)

## S4 method for signature 'SpatRaster,SpatVector'
cells(x, y, method="simple", weights=FALSE, exact=FALSE, 
				touches=is.lines(y), small=TRUE)

## S4 method for signature 'SpatRaster,SpatExtent'
cells(x, y)

Arguments

x

SpatRaster

y

SpatVector, SpatExtent, 2-column matrix representing points, numeric representing values to match, or missing

method

character. Method for getting cell numbers for points. The default is "simple", the alternative is "bilinear". If it is "bilinear", the four nearest cells and their weights are returned

weights

logical. If TRUE and y has polygons, the approximate fraction of each cell that is covered is returned as well

exact

logical. If TRUE and y has polygons, the exact fraction of each cell that is covered is returned as well

touches

logical. If TRUE, values for all cells touched by lines or polygons are extracted, not just those on the line render path, or whose center point is within the polygon. Not relevant for points

small

logical. If TRUE, values for all cells in touched polygons are extracted if none of the cells center points is within the polygon; even if touches=FALSE

Value

numeric vector or matrix

Examples

r <- rast(ncols=10, nrows=10)
values(r) <- 1:ncell(r)
r[c(1:25, 31:100)] <- NA
r <- ifel(r > 28, r + 10, r)

# all cell numbers of cells that are not NA
cells(r)

# cell numbers that match values
x <- cells(r, c(28,38))
x$lyr.1

# cells for points
m <- cbind(x=c(0,10,-30), y=c(40,-10,20))
cellFromXY(r, m)

v <- vect(m)
cells(r, v)
cells(r, v, method="bilinear")

# cells for polygons
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
r <- rast(v)
cv <- cells(r, v)

Area covered by each raster cell

Description

Compute the area covered by individual raster cells.

Computing the surface area of raster cells is especially relevant for longitude/latitude rasters.

But note that for both angular (longitude/latitude) and for planar (projected) coordinate reference systems raster cells sizes are generally not constant, unless you are using an equal-area coordinate reference system.

For planar CRSs, the area is therefore not computed based on the linear units of the coordinate reference system, but on the *actual* area by transforming cells to longitude/latitude. If you do not want that correction, you can use transform=FALSE or init(x, prod(res(x)))

Usage

## S4 method for signature 'SpatRaster'
cellSize(x, mask=FALSE, lyrs=FALSE, unit="m", transform=TRUE, rcx=100, filename="", ...)

Arguments

x

SpatRaster

mask

logical. If TRUE, cells that are NA in x are also NA in the output

lyrs

logical. If TRUE and mask=TRUE, the output has the same number of layers as x. That is only useful if cases where the layers of x have different cells that are NA

unit

character. One of "m", "km", or "ha"

transform

logical. If TRUE, planar CRS data are transformed to lon/lat for accuracy

rcx

positive integer. The maximum number of rows and columns to be used to compute area of planar data if transform=TRUE. If x has more rows and/or columns, the raster is aggregated to match this limit, and values for the original cells are estimated by bilinear interpolation (see resample). This can save a lot of time

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

expanse

Examples

# SpatRaster 
r <- rast(nrows=18, ncols=36)
v <- 1:ncell(r)
v[200:400] <- NA
values(r) <- v

# size of each raster cell
a <- cellSize(r)

# illustration of distortion
r <- rast(ncols=90, nrows=45, ymin=-80, ymax=80)
m <- project(r, "+proj=merc")

bad <- init(m, prod(res(m)) / 1000000, names="naive")
good <- cellSize(m, unit="km", names="corrected")
plot(c(good, bad), nc=1, mar=c(2,2,1,6))

Centroids

Description

Get the centroids of polygons or lines, or centroid-like points that are guaranteed to be inside the polygons or on the lines.

Usage

## S4 method for signature 'SpatVector'
centroids(x, inside=FALSE)

Arguments

x

SpatVector

inside

logical. If TRUE the points returned are guaranteed to be inside the polygons or on the lines, but they are not the true centroids. True centroids may be outside a polygon, for example when a polygon is "bean shaped", and they are unlikely to be on their line

Value

SpatVector of points

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
x <- centroids(v)
y <- centroids(v, TRUE)

Clamp values

Description

Clamp values to a minimum and maximum value. That is, all values below a lower threshold value and above the upper threshold value become either NA, or, if values=TRUE, become the threshold value

Usage

## S4 method for signature 'SpatRaster'
clamp(x, lower=-Inf, upper=Inf, values=TRUE, filename="", ...)

## S4 method for signature 'numeric'
clamp(x, lower=-Inf, upper=Inf, values=TRUE, ...)

Arguments

x

SpatRaster

lower

numeric with the lowest acceptable value (you can specify a different value for each layer). Or a SpatRaster that has a single layer or the same number of layers as x

upper

numeric with the highest acceptable value (you can specify a different value for each layer). Or a SpatRaster that has a single layer or the same number of layers as x

values

logical. If FALSE values outside the clamping range become NA, if TRUE, they get the extreme values

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

classify

Examples

r <- rast(ncols=10, nrows=10)
values(r) <- 1:ncell(r)
rc <- clamp(r, 25, 75) 
rc

clamp time series data

Description

clamp time-series datat that are S shaped. The value in layers before the minimum value in a cell can be set to that minimum value, and the value in layers after the maximum value for a cell can be set to that maximum value.

Usage

## S4 method for signature 'SpatRaster'
clamp_ts(x, min=FALSE, max=TRUE, filename="", ...)

Arguments

x

SpatRaster

min

logical. If TRUE the time-series is clamped to the minimum value

max

logical. If TRUE the time-series is clamped to the maximum value

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

clamp, cummin, cummax

Examples

sigm <- function(x) { .8 / (1 + exp(-(x-10))) + runif(length(x))/4 }
r <- rast(ncols=10, nrows=10, nlyr=50)
s <- seq(5.2, 15,.2)
set.seed(1)
values(r) <- t(replicate(100, sigm(s)))

x <- clamp_ts(r, TRUE, TRUE) 

plot(unlist(r[4]))
lines(unlist(x[4]))

Classify (or reclassify) cell values

Description

Classify values of a SpatRaster. The function (re-)classifies groups of values to other values.

The classification is done based on the argument rcl. You can classify ranges by specifying a three-column matrix "from-to-becomes" or change specific values by using a two-column matrix "is-becomes". You can also supply a vector with "cuts" or the "number of cuts".

With "from-to-becomes" or "is-becomes" classification is done in the row order of the matrix. Thus, if there are overlapping ranges or values, the first time a number is within a range determines the reclassification value.

With "cuts" the values are sorted, so that the order in which they are provided does not matter.

Usage

## S4 method for signature 'SpatRaster'
classify(x, rcl, include.lowest=FALSE, right=TRUE, 
     others=NULL, brackets=TRUE, filename="", ...)

Arguments

x

SpatRaster

rcl

matrix for classification. This matrix must have 1, 2 or 3 columns. If there are three columns, the first two columns are "from" "to" of the input values, and the third column "becomes" has the new value for that range.

The two column matrix ("is", "becomes") can be useful for classifying integer values. In that case, the arguments right and include.lowest are ignored.

A single column matrix (or a vector) is interpreted as a set of cuts if there is more than one value. In that case the values are classified based on their location in-between the cut-values.

If a single number is provided, that is used to make that number of cuts, at equal intervals between the lowest and highest values of the SpatRaster.

include.lowest

logical, indicating if a value equal to the lowest value in rcl (or highest value in the second column, for right=FALSE) should be included.

right

logical. If TRUE, the intervals are closed on the right (and open on the left). If FALSE they are open at the right and closed at the left. "open" means that the extreme value is *not* included in the interval. Thus, right-closed and left open is (0,1] = {x | 0 < x <= 1}. You can also close both sides with right=NA, that is only meaningful if you "from-to-becomes" classification with integers. For example to classify 1-5 -> 1, 6-10 -> 2, 11-15 -> 3. That may be easier to read and write than the equivalent 1-5 -> 1, 5-10 -> 2, 10-15 -> 3 with right=TRUE and include.lowest=TRUE

others

numeric. If not NULL all values that are not matched are set to this value. Otherwise they retain their original value.

brackets

logical. If TRUE, intervals are have parenthesis or brackets around them to indicate whether they are open or closed. Only applies if rcl is a vector (or single column matrix)

filename

character. Output filename

...

Additional arguments for writing files as in writeRaster

Value

SpatRaster

Note

classify works with the "raw" values of categorical rasters, ignoring the levels (labels, categories). To change the labels of categorical rasters, use subst instead.

For model-based classification see predict

See Also

subst for simpler from-to replacement

Examples

r <- rast(ncols=10, nrows=10)
values(r) <- (0:99)/99

## from-to-becomes
# classify the values into three groups 
# all values >= 0 and <= 0.25 become 1, etc.
m <- c(0, 0.25, 1,
       0.25, 0.5, 2,
       0.5, 1, 3)
rclmat <- matrix(m, ncol=3, byrow=TRUE)
rc1 <- classify(r, rclmat, include.lowest=TRUE)

## cuts
# equivalent to the above, but now a categorical SpatRaster is returned 
rc2 <- classify(r, c(0, 0.25, 0.5, 1), include.lowest=TRUE, brackets=TRUE)
freq(rc2)

## is-becomes 
x <- round(r*3)
unique(x)
# replace 0 with NA
y <- classify(x, cbind(0, NA))
unique(y)

# multiple replacements
m <- rbind(c(2, 200), c(3, 300))
m

rcx1 <- classify(x, m)
unique(rcx1)

rcx2 <- classify(x, m, others=NA)
unique(rcx2)

Query by clicking on a map

Description

Click on a map (plot) to get the coordinates or the values of a SpatRaster or SpatVector at that location. For a SpatRaster you can also get the coordinates and cell number of the location.

This does to work well on the default RStudio plotting device. To work around that, you can first run dev.new(noRStudioGD = TRUE) which will create a separate window for plotting, then use plot() followed by click() and click on the map .

Usage

## S4 method for signature 'SpatRaster'
click(x, n=10, id=FALSE, xy=FALSE, cell=FALSE, type="p", show=TRUE, ...)

## S4 method for signature 'SpatVector'
click(x,  n=10, id=FALSE, xy=FALSE, type="p", show=TRUE, ...)

## S4 method for signature 'missing'
click(x, n=10, id=FALSE, type="p", show=TRUE, ...)

Arguments

x

SpatRaster or SpatVector, or missing

n

number of clicks on the plot (map)

id

logical. If TRUE, a numeric ID is shown on the map that corresponds to the row number of the output

xy

logical. If TRUE, xy coordinates are included in the output

cell

logical. If TRUE, cell numbers are included in the output

type

one of "n", "p", "l" or "o". If "p" or "o" the points are plotted; if "l" or "o" they are joined by lines. See ?locator

show

logical. Print the values after each click?

...

additional graphics parameters used if type != "n" for plotting the locations. See ?locator

Value

The value(s) of x at the point(s) clicked on (or touched by the box drawn). A data.frame with the value(s) of all layers of SpatRaster x for the cell(s) clicked on; or with the attributes of the geometries of SpatVector x that intersect with the box drawn).

Note

The plot only provides the coordinates for a spatial query, the values are read from the SpatRaster or SpatVector that is passed as an argument. Thus you can extract values from an object that has not been plotted, as long as it spatially overlaps with with the extent of the plot.

Unless the process is terminated prematurely values at at most n positions are determined. The identification process can be terminated, depending on how you interact with R, by hitting Esc, or by clicking the right mouse button and selecting "Stop" from the menu, or from the "Stop" menu on the graphics window.

See Also

draw

Examples

## Not run: 
r <-rast(system.file("ex/elev.tif", package="terra"))
plot(r)
click(r, n=1)
## now click on the plot (map)

## End(Not run)

Coercion to vector, matrix or array

Description

Coercion of a SpatRaster to a vector, matrix or array. Or coerce a SpatExtent to a vector or matrix

Usage

## S4 method for signature 'SpatRaster'
as.vector(x, mode='any')

## S4 method for signature 'SpatRaster'
as.matrix(x, wide=FALSE, ...)

## S4 method for signature 'SpatRaster'
as.array(x)

## S4 method for signature 'SpatExtent'
as.vector(x, mode='any')

## S4 method for signature 'SpatExtent'
as.matrix(x, ...)

Arguments

x

SpatRaster or SpatVector

wide

logical. If FALSE each layer in the SpatRaster becomes a column in the matrix and each cell in the SpatRaster becomes a row. If TRUE each row in the SpatRaster becomes a row in the matrix and each column in the SpatRaster becomes a column in the matrix

mode

this argument is ignored

...

additional arguments (none implemented)

Value

vector, matrix, or array

See Also

as.data.frame and as.polygons

Examples

r <- rast(ncols=2, nrows=2)
values(r) <- 1:ncell(r)

as.vector(r)
as.matrix(r)
as.matrix(r, wide=TRUE)
as.data.frame(r, xy=TRUE)
as.array(r)

as.vector(ext(r))
as.matrix(ext(r))

Color table

Description

Get or set color table(s) associated with a SpatRaster. Color tables are used for associating colors with values, for use in mapping (plot).

Usage

## S4 method for signature 'SpatRaster'
coltab(x)

## S4 replacement method for signature 'SpatRaster'
coltab(x, ..., layer=1)<-value

## S4 method for signature 'SpatRaster'
has.colors(x)

Arguments

x

SpatRaster

layer

positive integer, the layer number or name

value

a two-column data.frame (first column the cell value, the second column the color); a vector of colors (the first one is the color for value 0 and so on); or a four (value,red,green,blue) or five (including alpha) column data.frame also from 0 to n; or NULL to remove the color table. You can also supply a list of such data.frames to set a color table to all layers

...

additional arguments (none implemented)

Value

data.frame

Examples

r <- rast(ncols=3, nrows=2, vals=1:6)
coltb <- data.frame(value=1:6, col=rainbow(6, end=.9))
coltb

plot(r)

has.colors(r)
coltab(r) <- coltb
plot(r)
has.colors(r)

tb <- coltab(r)
class(tb)
dim(tb[[1]])

Combine geometries

Description

Combine the geometries of one SpatVector with those of another. Geometries can be combined based on overlap, shared boundaries and distance (in that order of operation).

The typical use-case of this method is when you are editing geometries and you have a number of small polygons in one SpatVector that should be part of the geometries of the another SpatVector; perhaps because they were small holes inbetween the borders of two SpatVectors.

To append SpatVectors use 'rbind' and see methods like intersect and union for "normal" polygons combinations.

Usage

## S4 method for signature 'SpatVector,SpatVector'
combineGeoms(x, y, overlap=TRUE, boundary=TRUE, distance=TRUE,
	append=TRUE, minover=0.1, maxdist=Inf, dissolve=TRUE, erase=TRUE)

Arguments

x

SpatVector of polygons

y

SpatVector of polygons geometries that are to be combined with x

overlap

logical. If TRUE, a geometry is combined with the geometry it has most overlap with, if the overlap is above minover

boundary

logical. If TRUE, a geometry is combined with the geometry it has most shared border with

distance

logical. If TRUE, a geometry is combined with the geometry it is nearest to

append

logical. Should remaining geometries be appended to the output? Not relevant if distance=TRUE

minover

numeric. The fraction of the geometry in y that overlaps with a geometry in x. Below this threshold, geometries are not considered overlapping

maxdist

numeric. Geometries further away from each other than this distance (in meters) will not be combined

dissolve

logical. Should internal boundaries be dissolved?

erase

logical. If TRUE no new overlapping areas are created

Value

SpatVector

See Also

union, erase, intersect

sharedPaths, erase, intersect

Examples

x1 <- vect("POLYGON ((0 0, 8 0, 8 9, 0 9, 0 0))")
x2 <- vect("POLYGON ((10 4, 12 4, 12 7, 11 7, 11 6, 10 6, 10 4))")

y1 <- vect("POLYGON ((5 6, 15 6, 15 15, 5 15, 5 6))")
y2 <- vect("POLYGON ((8 2, 9 2, 9 3, 8 3, 8 2))")
y3 <- vect("POLYGON ((2 6, 3 6, 3 8, 2 8, 2 6))")
y4 <- vect("POLYGON ((2 12, 3 12, 3 13, 2 13, 2 12))")

x <- rbind(x1, x2)
values(x) <- data.frame(xid=1:2)
crs(x) <- "+proj=utm +zone=1"

y <- rbind(y1, y2, y3, y4)
values(y) <- data.frame(yid=letters[1:4])
crs(y) <- "+proj=utm +zone=1"

plot(rbind(x, y), border=c(rep("red",2), rep("blue", 4)), lwd=2)
text(x, "xid")
text(y, "yid")

v <- combineGeoms(x, y)
plot(v, col=c("red", "blue"))

v <- combineGeoms(x, y, boundary=FALSE, maxdist=1, minover=.05)
plot(v, col=rainbow(4))

Compare and logical methods

Description

Standard comparison and logical operators for computations with SpatRasters. Computations are local (applied on a cell by cell basis). If multiple SpatRasters are used, these must have the same geometry (extent and resolution). These operators have been implemented:

Logical: !, &, |, isTRUE, isFALSE

Compare: ==, !=, >, <, <=, >=, is.na, is.nan, is.finite, is.infinite

See not.na for the inverse of is.na, and noNA to detect cells with missing value across layers.

The compare and logic methods implement these operators in a method that can return NA istead of FALSE and allows for setting an output filename.

The terra package does not distinguish between NA (not available) and NaN (not a number). In most cases this state is represented by NaN.

If you use a SpatRaster with a vector of multiple numbers, each element in the vector is considered a layer (with a constant value). If you use a SpatRaster with a matrix, the number of columns of the matrix must match the number of layers of the SpatRaster. The rows are used to match the cells. That is, if there are two rows, these match cells 1 and 2, and they are recycled to 3 and 4, etc.

The following method has been implemented for (SpatExtent, SpatExtent): ==

Usage

## S4 method for signature 'SpatRaster'
compare(x, y, oper, falseNA=FALSE, filename="", overwrite=FALSE, ...)

## S4 method for signature 'SpatRaster'
logic(x, oper, falseNA=FALSE, filename="", overwrite=FALSE, ...)

Arguments

x

SpatRaster

y

SpatRaster or numeric

oper

character. Operator name. For compare this can be one of "==", "!=", ">", "<", ">=", "<=" and for logic it can be one of "!", "is.na", "allNA", "noNA", "is.infinite", "is.finite", "iSTRUE", "isFALSE"

falseNA

logical. Should the result be TRUE, NA instead of TRUE, FALSE?

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

...

additional arguments for writing files as in writeRaster

Value

SpatRaster or SpatExtent

See Also

all.equal, Arith-methods. See ifel to conveniently combine operations and Math-methods or app to apply any R function to a SpatRaster.

Examples

r1 <- rast(ncols=10, nrows=10)
values(r1) <- runif(ncell(r1))
r1[10:20] <- NA
r2 <- rast(r1)
values(r2) <- 1:ncell(r2) / ncell(r2)

x <- is.na(r1)
!x
r1 == r2 
compare(r1, r2, "==")
compare(r1, r2, "==", TRUE)

Compare geometries of SpatRasters

Description

Evaluate whether two SpatRasters have the same extent, number of rows and columns, projection, resolution, and origin (or a subset of these comparisons).

Or evaluate whether two SpatVectors have the same geometries, or whether a SpatVector has duplicated geometries.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
compareGeom(x, y, ..., lyrs=FALSE, crs=TRUE, warncrs=FALSE, ext=TRUE,
	rowcol=TRUE, res=FALSE, stopOnError=TRUE, messages=FALSE)

## S4 method for signature 'SpatVector,SpatVector'
compareGeom(x, y, tolerance=0)

## S4 method for signature 'SpatVector,missing'
compareGeom(x, y, tolerance=0)

Arguments

x

SpatRaster or SpatVector

y

Same as x. If x is a SpatRaster, y can also be a list of SpatRasters. If x is a SpatVector, y can be missing

...

Additional SpatRasters

lyrs

logical. If TRUE, the number of layers is compared

crs

logical. If TRUE, coordinate reference systems are compared

warncrs

logical. If TRUE, a warning is given if the crs is different (instead of an error)

ext

logical. If TRUE, bounding boxes are compared

rowcol

logical. If TRUE, number of rows and columns of the objects are compared

res

logical. If TRUE, resolutions are compared (redundant when checking extent and rowcol)

stopOnError

logical. If TRUE, code execution stops if raster do not match

messages

logical. If TRUE, warning/error messages are printed even if stopOnError=FALSE

tolerance

numeric

Value

logical (SpatRaster) or matrix of logical (SpatVector)

Examples

r1 <- rast()
r2 <- rast()
r3 <- rast()
compareGeom(r1, r2, r3)
nrow(r3) <- 10


## Not run: 
compareGeom(r1, r3)

## End(Not run)

Concatenate categorical rasters

Description

Combine two categorical rasters by concatenating their levels.

Usage

## S4 method for signature 'SpatRaster'
concats(x, y, filename="", ...)

Arguments

x

SpatRaster (with a single, categorical, layer)

y

SpatRaster (with a single, categorical, layer)

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

cats

Examples

set.seed(0)
r <- rast(nrows=10, ncols=10)
values(r) <- sample(3, ncell(r), replace=TRUE)
levels(r) <- data.frame(id=1:3, cover=c("forest", "water", "urban"))

rr <- rast(r)
values(rr) <- sample(1:3, ncell(rr), replace=TRUE)
levels(rr) <- data.frame(id=c(1:3), color=c("red", "green", "blue"))

x <- concats(r, rr)
x
levels(x)[[1]]

Contour plot

Description

Contour lines of a SpatRaster. Use add=TRUE to add the lines to the current plot. See graphics::contour for details.

if filled=TRUE, a new filled contour plot is made. See graphics::filled.contour for details.

as.contour returns the contour lines as a SpatVector.

Usage

## S4 method for signature 'SpatRaster'
contour(x, maxcells=100000, filled=FALSE, ...)

## S4 method for signature 'SpatRaster'
as.contour(x, maxcells=100000, ...)

Arguments

x

SpatRaster. Only the first layer is used

maxcells

maximum number of pixels used to create the contours

filled

logical. If TRUE, a filled.contour plot is made

...

any argument that can be passed to contour or filled.contour (graphics package)

See Also

plot

Examples

r <- rast(system.file("ex/elev.tif", package="terra"))
plot(r)
contour(r, add=TRUE)

v <- as.contour(r)
plot(r)
lines(v)

contour(r, filled=TRUE, nlevels=5)

## if you want a SpatVector with contour lines
template <- disagg(rast(r), 10)
rr <- resample(r, template)
rr <- floor(rr/100) * 100
v <- as.polygons(rr)
plot(v, 1, col=terrain.colors(7))

Convex hull, minimal bounding rotated rectangle, and minimal bounding circle

Description

Get the convex hull, the minimal bounding rotated rectangle, or minimal bounding circle of a SpatVector

Usage

## S4 method for signature 'SpatVector'
convHull(x, by="")

## S4 method for signature 'SpatVector'
minRect(x, by="")

## S4 method for signature 'SpatVector'
minCircle(x, by="")

Arguments

x

SpatVector

by

character (variable name), to get a new geometry for groups of input geometries

Value

SpatVector

Examples

p <- vect(system.file("ex/lux.shp", package="terra"))
h <- convHull(p)

hh <- convHull(p, "NAME_1")
rr <- minRect(p, "NAME_1")

plot(rr, lwd=5, border="gray")
plot(hh, "NAME_1", col=rainbow(10, alpha=.5), lwd=3, add=TRUE, plg=list(x="topright"))
lines(aggregate(p, "NAME_1"), col="blue", lty=2, lwd=2)

Cost-distance

Description

Use a friction (cost) surface to compute the cost-distance from any cell to the border of one or more target cells.

Distances are computed by summing local distances between cells, which are connected with their neighbors in 8 directions, and assuming that the path has to go through the centers of one of the neighboring raster cells.

Distances are multiplied with the friction, thus to get the cost-distance, the friction surface must express the cost per unit distance (speed) of travel.

Usage

## S4 method for signature 'SpatRaster'
costDist(x, target=0, scale=1, maxiter=50, filename="", ...)

Arguments

x

SpatRaster

target

numeric. value of the target cells (where to compute cost-distance to)

scale

numeric. Scale factor. The cost distance is divided by this number

maxiter

numeric. The maximum number of iterations. Increase this number if you get the warning that costDistance did not converge

filename

character. output filename (optional)

...

additional arguments as for writeRaster

Value

SpatRaster

See Also

gridDist, distance

Examples

r <- rast(ncols=5, nrows=5, crs="+proj=utm +zone=1 +datum=WGS84", 
		xmin=0, xmax=5, ymin=0, ymax=5, vals=1)
r[13] <- 0
d <- costDist(r)
plot(d)
text(d, digits=1)

r <- rast(ncols=10, nrows=10,  xmin=0, xmax=10, ymin=0, ymax=10, 
		   vals=10, crs="+proj=utm +zone=1 +datum=WGS84")
r[5, 1] <- -10
r[2:3, 1] <- r[1, 2:4] <- r[2, 5] <- 0
r[3, 6] <- r[2, 7] <- r[1, 8:9] <- 0
r[6, 6:10] <- NA
r[6:9, 6] <- NA

d <- costDist(r, -10)
plot(d)
text(d, digits=1, cex=.8)

Replace values with values from another object

Description

Replace NA or other values in SpatRaster x with the values of SpatRaster y

For polygons: areas of x that overlap with y are replaced by y or, if identity=TRUE intersected with y.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
cover(x, y, values=NA, filename="", ...)

## S4 method for signature 'SpatVector,SpatVector'
cover(x, y, identity=FALSE, expand=TRUE)

Arguments

x

SpatRaster or SpatVector

y

Same as x

values

numeric. The cell values in x to be replaced by the values in y

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

identity

logical. If TRUE overlapping areas are intersected rather than replaced

expand

logical. Should parts of y that are outside of x be included?

Value

SpatRaster

Examples

r1 <- r2 <- rast(ncols=36, nrows=18)
values(r1) <- 1:ncell(r1)
values(r2) <- runif(ncell(r2))
r2 <- classify(r2, cbind(-Inf, 0.5, NA))
r3 <- cover(r2, r1)


p <- vect(system.file("ex/lux.shp", package="terra"))
e <- as.polygons(ext(6, 6.4, 49.75, 50))
values(e) <- data.frame(y=10)

cv <- cover(p, e)
plot(cv, col=rainbow(12))
ci <- cover(p, e, identity=TRUE)
lines(e, lwd=3)

plot(ci, col=rainbow(12))
lines(e, lwd=3)

Get the coordinates of SpatVector geometries or SpatRaster cells

Description

Get the coordinates of a SpatVector or SpatRaster cells. A matrix or data.frame of the x (longitude) and y (latitude) coordinates is returned.

Usage

## S4 method for signature 'SpatVector'
crds(x, df=FALSE, list=FALSE)

## S4 method for signature 'SpatRaster'
crds(x, df=FALSE, na.rm=TRUE, na.all=FALSE)

Arguments

x

SpatRaster or SpatVector

df

logical. If TRUE a data.frame is returned instead of a matrix

list

logical. If TRUE a list is returned instead of a matrix

na.rm

logical. If TRUE cells that are NA are excluded. Ignored if the SpatRaster is a template with no associated cell values

na.all

logical. If TRUE cells are only ignored if na.rm=TRUE and their value is NA for all layers instead of for any layer

Value

matrix or data.frame

See Also

geom returns the complete structure of SpatVector geometries. For SpatRaster see xyFromCell

Examples

x1 <- rbind(c(-175,-20), c(-140,55), c(10, 0), c(-140,-60))
x2 <- rbind(c(-125,0), c(0,60), c(40,5), c(15,-45))
x3 <- rbind(c(-10,0), c(140,60), c(160,0), c(140,-55))
x4 <- rbind(c(80,0), c(105,13), c(120,2), c(105,-13))
z <- rbind(cbind(object=1, part=1, x1), cbind(object=2, part=1, x2), 
           cbind(object=3, part=1, x3), cbind(object=3, part=2, x4))
colnames(z)[3:4] <- c('x', 'y')
z <- cbind(z, hole=0)
z[(z[, "object"]==3 & z[,"part"]==2), "hole"] <- 1

p <- vect(z, "polygons")
crds(p)

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
g <- crds(v)
head(g)

Cut out a geographic subset

Description

Cut out a part of a SpatRaster or SpatVector.

You can crop a SpatRaster with a SpatExtent, or with another object from which an extent can be obtained. Note that the SpatRaster returned may not have the exactly the same extent as the SpatExtent supplied because you can only select entire cells (rows and columns), and you cannot add new areas. See methods like resample and disagg to force SpatRasters to align and extend to add rows and/or columns.

You can only crop rectangular areas of a SpatRaster, but see argument mask=TRUE for setting cell values within SpatRaster to NA; or use the mask method after crop for additional masking options.

You can crop a SpatVector with another SpatVector. If these are not polygons, the minimum convex hull is used. Unlike with intersect the geometries and attributes of y are not transferred to the output. You can also crop a SpatVector with a rectangle (SpatRaster, SpatExtent).

Usage

## S4 method for signature 'SpatRaster'
crop(x, y, snap="near", mask=FALSE, touches=TRUE, extend=FALSE, filename="", ...)

## S4 method for signature 'SpatRasterDataset'
crop(x, y, snap="near", extend=FALSE)

## S4 method for signature 'SpatRasterCollection'
crop(x, y, snap="near", extend=FALSE)

## S4 method for signature 'SpatVector'
crop(x, y, ext=FALSE)

## S4 method for signature 'SpatGraticule'
crop(x, y)

Arguments

x

SpatRaster or SpatVector

y

SpatRaster, SpatVector, SpatExtent, or any other object that has a SpatExtent (ext returns a SpatExtent)

snap

character. One of "near", "in", or "out". Used to align y to the geometry of x

mask

logical. Should y be used to mask? Only used if y is a SpatVector, SpatRaster or sf

touches

logical. If TRUE and mask=TRUE, all cells touched by lines or polygons will be masked, not just those on the line render path, or whose center point is within the polygon

extend

logical. Should rows and/or columns be added if y is beyond the extent of x? Also see extend

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

ext

logical. Use the extent of y instead of y. This also changes the behavior when y is an extent in two ways: (1) points that are on the extent boundary are removed and (2) lon/lat extents that go beyond -180 or 180 degrees longitude are wrapped around the earth to include areas at the other end of the dateline

Value

SpatRaster

See Also

intersect, extend

See window for a virtual and sometimes more efficient way to crop a dataset.

Examples

r <- rast(xmin=0, xmax=10, ymin=0, ymax=10, nrows=25, ncols=25)
values(r) <- 1:ncell(r)
e <- ext(-5, 5, -5, 5)
rc <- crop(r, e)

# crop and mask
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
cm <- crop(r, v[9:12,], mask=TRUE)
plot(cm)
lines(v)

# crop vector
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
e <- ext(6.15, 6.3, 49.7, 49.8)
x <- crop(v, e)
plot(x, "NAME_1")

Cross-tabulate

Description

Cross-tabulate the layers of a SpatRaster to create a contingency table.

Usage

## S4 method for signature 'SpatRaster,missing'
crosstab(x, digits=0, long=FALSE, useNA=FALSE)

Arguments

x

SpatRaster

digits

integer. The number of digits for rounding the values before cross-tabulation

long

logical. If TRUE the results are returned in 'long' format data.frame instead of a table

useNA

logical, indicting if the table should includes counts of NA values

Value

A table or data.frame

See Also

freq, zonal

Examples

r <- s <- rast(nc=5, nr=5)
set.seed(1)
values(r) <- runif(ncell(r)) * 2
values(s) <- runif(ncell(r)) * 3
x <- c(r, s)

crosstab(x)

rs <- r/s
r[1:5] <- NA
s[20:25] <- NA
x <- c(r, s, rs)
crosstab(x, useNA=TRUE, long=TRUE)

Get or set a coordinate reference system

Description

Get or set the coordinate reference system (CRS), also referred to as a "projection", of a SpatRaster or SpatVector.

Setting a new CRS does not change the data itself, it just changes the label. So you should only set the CRS of a dataset (if it does not come with one) to what it *is*, not to what you would *like it to be*. See project to *transform* an object from one CRS to another.

Usage

## S4 method for signature 'SpatRaster'
crs(x, proj=FALSE, describe=FALSE, parse=FALSE)

## S4 method for signature 'SpatVector'
crs(x, proj=FALSE, describe=FALSE, parse=FALSE)

## S4 method for signature 'character'
crs(x, proj=FALSE, describe=FALSE, parse=FALSE)

## S4 replacement method for signature 'SpatRaster'
crs(x, warn=FALSE)<-value

## S4 replacement method for signature 'SpatVector'
crs(x, warn=FALSE)<-value

Arguments

x

SpatRaster or SpatVector

proj

logical. If TRUE the crs is returned in PROJ-string notation

describe

logical. If TRUE the name, EPSG code, and the name and extent of the area of use are returned if known

warn

logical. If TRUE, a message is printed when the object already has a non-empty crs

value

character string describing a coordinate reference system. This can be in a WKT format, as a <authority:number> code such as "EPSG:4326", or a PROJ-string format such as "+proj=utm +zone=12" (see Note)

parse

logical. If TRUE, wkt parts are parsed into a vector (each line becomes an element)

Value

character or modified SpatRaster/Vector

Note

Projections are handled by the PROJ/GDAL libraries. Recent changes in the PROJ library to improve transformations between datums have degraded the library's usability. The PROJ developers suggest to no longer use the proj-string notation to define a CRS, but use the WKT2 or <authority>:<code> notation instead. These alternative systems work for formally described CRSs that are in databases, but they do not cover the infinite number of CRSs that exist. It is not practical to define one's own custom CRS with WKT2. Moreover, unlike the proj-notation, these newer systems are hard to read and that leads to code that cannot be easily understood and, therefore, is more error-prone.

It is still possible to use the PROJ-string notation with one major caveat: the datum should be WGS84 (or the equivalent NAD83) – if you want to transform your data to a coordinate reference system with a different datum. Thus as long as you use WGS84, or an ellipsoid instead of a datum, you can safely use PROJ-strings to represent your CRS; including to define your own custom CRS.

You can also set the crs to "local" to get an informal coordinate system on an arbitrary Euclidean (Cartesian) plane with units in meter.

Examples

r <- rast()
crs(r)
crs(r, describe=TRUE, proj=TRUE)

crs(r) <- "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"
crs(r)

# You can use epsg codes
crs(r)  <- "epsg:25831"
crs(r, describe=TRUE)$area

crs("epsg:25831", describe=TRUE)

Data type of a SpatRaster or SpatVector

Description

Get the data types of the fields (attributes, variables) of a SpatVector or of the file(s) associated with a SpatRaster. A (layer of a) SpatRaster has no datatype if it has no values, or if the values are in memory.

Usage

## S4 method for signature 'SpatRaster'
datatype(x, bylyr=TRUE)

## S4 method for signature 'SpatVector'
datatype(x)

Arguments

x

SpatRaster or SpatVector

bylyr

logical. If TRUE a value is returned for each layer. Otherwise, a value is returned for each data source (such as a file)

Value

character

See Also

Raster data types to check / set the type of SpatRaster values.

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
datatype(v)

f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
datatype(r)

# no data type
datatype(rast())

Deep copy

Description

Make a deep copy of a SpatRaster or SpatVector. This is occasionally useful when wanting to use a replacement function in a shallow copy. That is a copy that was created like this: x <- y. If you use a replacement function to change an object, its shallow copies also change.

Usage

## S4 method for signature 'SpatRaster'
deepcopy(x)

## S4 method for signature 'SpatVector'
deepcopy(x)

Arguments

x

SpatRaster or SpatVector

Value

Same as x

Examples

r <- rast(ncols=10, nrows=10, nl=3)
tm <- as.Date("2001-05-03") + 1:3
time(r) <- tm
time(r)
x <- r
time(x) <- tm + 365
time(x)
time(r)

y <- deepcopy(r)
time(y) <- tm - 365
time(y)
time(r)

# or make a new object like this
z <- rast(r)
time(z) <- tm
time(z)
time(r)

Add additional nodes to lines or polygons

Description

Add additional nodes to lines or polygons. This can be useful to do prior to using project such that the path does not change too much.

Usage

## S4 method for signature 'SpatVector'
densify(x, interval, equalize=TRUE, flat=FALSE)

Arguments

x

SpatVector

interval

positive number, specifying the desired minimum distance between nodes. The unit is meter for lonlat data, and in the linear unit of the crs for planar data

equalize

logical. If TRUE, new nodes are spread at equal intervals between old nodes

flat

logical. If TRUE, the earth's curvature is ignored for lonlat data, and the distance unit is degrees, not meter

Value

SpatVector

Examples

v <- vect(rbind(c(-120,-20), c(-80,5), c(-40,-60), c(-120,-20)), 
  type="polygons", crs="+proj=longlat")
vd <- densify(v, 200000)

p <- project(v, "+proj=robin")
pd <- project(vd, "+proj=robin")

# good 
plot(pd, col="gray", border="red", lwd=10)
points(pd, col="gray")

# bad
lines(p, col="blue", lwd=3)
points(p, col="blue", cex=2)
plot(p, col="blue", alpha=.1, add=TRUE)
legend("topright", c("good", "bad"), col=c("red", "blue"), lty=1, lwd=3)

## the other way around does not work
## unless the original data was truly planar (e.g. derived from a map)
x <- densify(p, 250000)
y <- project(x, "+proj=longlat")
# bad
plot(y)
# good
lines(vd, col="red")

Density plot

Description

Create density plots of the cell values of a SpatRaster

Usage

## S4 method for signature 'SpatRaster'
density(x, maxcells=100000, plot=TRUE, main, ...)

Arguments

x

SpatRaster

maxcells

the maximum number of (randomly sampled) cells to be used for creating the plot

plot

if TRUE produce a plot, else return a density object

main

character. Caption of plot(s)

...

additional arguments passed to plot

Value

density plot (and a density object, returned invisibly if plot=TRUE)

Examples

logo <- rast(system.file("ex/logo.tif", package="terra"))
density(logo)

deprecated methods

Description

These methods are deprecated and will be removed in future versions

Usage

## S4 method for signature 'SpatRaster'
setCats(x, ...)

## S4 method for signature 'SpatRaster'
area(x, ...)

Arguments

x

object

...

additional arguments


depth of SpatRaster layers

Description

Get or set the depth of the layers of a SpatRaster. Experimental.

Usage

## S4 method for signature 'SpatRaster'
depth(x)

## S4 replacement method for signature 'SpatRaster'
depth(x)<-value

Arguments

x

SpatRaster

value

numeric vector

Value

numeric

See Also

time

Examples

s <- rast(system.file("ex/logo.tif", package="terra"))   

depth(s) <- 1:3
depth(s)

describe

Description

Describe the properties of spatial data in a file as generated with the "GDALinfo" tool.

Usage

## S4 method for signature 'character'
describe(x, sds=FALSE, meta=FALSE, parse=FALSE, options="", print=FALSE, open_opt="")

Arguments

x

character. The name of a file with spatial data. Or a fully specified subdataset within a file such as "NETCDF:\"AVHRR.nc\":NDVI"

sds

logical. If TRUE the description or metadata of the subdatasets is returned (if available)

meta

logical. Get the file level metadata instead

parse

logical. If TRUE, metadata for subdatasets is parsed into components (if meta=TRUE)

options

character. A vector of valid options (if meta=FALSE) including "json", "mm", "stats", "hist", "nogcp", "nomd", "norat", "noct", "nofl", "checksum", "proj4", "listmdd", "mdd <value>" where <value> specifies a domain or 'all', "wkt_format <value>" where value is one of 'WKT1', 'WKT2', 'WKT2_2015', or 'WKT2_2018', "sd <subdataset>" where <subdataset> is the name or identifier of a sub-dataset. See https://gdal.org/programs/gdalinfo.html. Ignored if sds=TRUE

print

logical. If TRUE, print the results

open_opt

character. Driver specific open options

Value

character (invisibly, if print=FALSE)

Examples

f <- system.file("ex/elev.tif", package="terra")
describe(f)
describe(f, meta=TRUE)
#g <- describe(f, options=c("json", "nomd", "proj4"))
#head(g)

Lagged differences

Description

Compute the difference between consecutive layers in a SpatRaster.

Usage

## S4 method for signature 'SpatRaster'
diff(x, lag=1, filename="", ...)

Arguments

x

SpatRaster

lag

positive integer indicating which lag to use

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

Examples

s <- rast(system.file("ex/logo.tif", package="terra"))   
d <- diff(s)

Dimensions of a SpatRaster or SpatVector and related objects

Description

Get the number of rows (nrow), columns (ncol), cells (ncell), layers (nlyr), sources (nsrc), the size size (nlyr(x)*ncell(x)), or spatial resolution of a SpatRaster.

length returns the number of sub-datasets in a SpatRasterDataset or SpatVectorCollection.

For a SpatVector length(x) is the same as nrow(x).

You can also set the number of rows or columns or layers. When setting dimensions, all cell values are dropped.

Usage

## S4 method for signature 'SpatRaster'
ncol(x)

## S4 method for signature 'SpatRaster'
nrow(x)

## S4 method for signature 'SpatRaster'
nlyr(x)

## S4 method for signature 'SpatRaster'
ncell(x)

## S4 method for signature 'SpatRaster'
nsrc(x)

## S4 replacement method for signature 'SpatRaster,numeric'
ncol(x)<-value

## S4 replacement method for signature 'SpatRaster,numeric'
nrow(x)<-value

## S4 replacement method for signature 'SpatRaster,numeric'
nlyr(x)<-value

## S4 method for signature 'SpatRaster'
res(x)

## S4 replacement method for signature 'SpatRaster,numeric'
res(x)<-value

## S4 method for signature 'SpatRaster'
xres(x)

## S4 method for signature 'SpatRaster'
yres(x)

## S4 method for signature 'SpatVector'
ncol(x)

## S4 method for signature 'SpatVector'
nrow(x)

## S4 method for signature 'SpatVector'
length(x)

Arguments

x

SpatRaster or SpatVector or related objects

value

For ncol and nrow: positive integer. For res: one or two positive numbers

Value

integer

See Also

ext

Examples

r <- rast()
ncol(r)
nrow(r)
nlyr(r)
dim(r)
nsrc(r)
ncell(r)

rr  <- c(r,r)
nlyr(rr)
nsrc(rr)
ncell(rr)

nrow(r) <- 18
ncol(r) <- 36
# equivalent to
dim(r) <- c(18, 36) 

dim(r)
dim(r) <- c(10, 10, 5)
dim(r)

xres(r)
yres(r)
res(r)

res(r) <- 1/120
# different xres and yres
res(r) <- c(1/120, 1/60)

Direction

Description

The direction (azimuth) to or from the nearest cell that is not NA. The direction is expressed in radians, unless you use argument degrees=TRUE.

Usage

## S4 method for signature 'SpatRaster'
direction(x, from=FALSE, degrees=FALSE, filename="", ...)

Arguments

x

SpatRaster

filename

Character. Output filename (optional)

degrees

Logical. If FALSE (the default) the unit of direction is radians.

from

Logical. Default is FALSE. If TRUE, the direction from (instead of to) the nearest cell that is not NA is returned

...

Additional arguments as for writeRaster

Value

SpatRaster

See Also

distance

Examples

r <- rast(ncol=36,nrow=18, crs="+proj=merc")
values(r) <- NA
r[306] <- 1
b <- direction(r, degrees=TRUE) 
plot(b)

crs(r) <- "+proj=longlat"
b <- direction(r) 
plot(b)

Disaggregate raster cells or vector geometries

Description

SpatRaster: Create a SpatRaster with a higher resolution (smaller cells). The values in the new SpatRaster are the same as in the larger original cells.

SpatVector: Separate multi-objects (points, lines, polygons) into single objects; or further into segments (for lines or polygons).

Usage

## S4 method for signature 'SpatRaster'
disagg(x, fact, method="near", filename="", ...)

## S4 method for signature 'SpatVector'
disagg(x, segments=FALSE)

Arguments

x

SpatRaster or SpatVector

fact

positive integer. Aggregation factor expressed as number of cells in each direction (horizontally and vertically). Or two integers (horizontal and vertical aggregation factor) or three integers (when also aggregating over layers)

method

character. Either "near" for nearest or "bilinear" for bilinear interpolation

segments

logical. Should (poly-)lines or polygons be disaggregated into their line-segments?

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

aggregate, resample

Examples

r <- rast(ncols=10, nrows=10)
rd <- disagg(r, fact=c(10, 2))
ncol(rd)
nrow(rd)
values(r) <- 1:ncell(r)
rd <- disagg(r, fact=c(4, 2))

Geographic distance

Description

If x is a SpatRaster:

If y is missing this method computes the distance, for all cells that are NA in SpatRaster x to the nearest cell that is not NA (or other values, see arguments "target" and "exclude").

If y is a numeric value, the cells with that value are ignored. That is, distance to or from these cells is not computed (only if grid=FALSE).

If y is a SpatVector, the distance to that SpatVector is computed for all cells. For lines and polygons this is done after rasterization; and only the overlapping areas of the vector and raster are considered (for now).

The distance is always expressed in meter if the coordinate reference system is longitude/latitude, and in map units otherwise. Map units are typically meter, but inspect crs(x) if in doubt.

Results are more precise, sometimes much more precise, when using longitude/latitude rather than a planar coordinate reference system, as these distort distance.

If x is a SpatVector:

If y is missing, a distance matrix between all objects in x is computed. A distance matrix object of class "dist" is returned.

If y is a SpatVector the geographic distance between all objects is computed (and a matrix is returned). If both sets have the same number of points, and pairwise=TRUE, the distance between each pair of objects is computed, and a vector is returned.

The distance is always expressed in meter, except when the coordinate reference system is longitude/latitude AND one of the SpatVector(s) consists of lines or polygons. In that case the distance is in degrees, and thus not very useful (this will be fixed soon). Otherwise, results are more precise, sometimes much more precise, when using longitude/latitude rather than a planar coordinate reference system, as these distort distance.

If x is a matrix:

x should consist of two columns, the first with "x" (or longitude) and the second with "y" coordinates (or latitude). If y is a also a matrix, the distance between each points in x and all points in y is computed, unless pairwise=TRUE

If y is missing, the distance between each points in x with all other points in x is computed, unless sequential=TRUE

Usage

## S4 method for signature 'SpatRaster,missing'
distance(x, y, target=NA, exclude=NULL, unit="m", haversine=TRUE, filename="", ...)

## S4 method for signature 'SpatRaster,SpatVector'
distance(x, y, unit="m", rasterize=FALSE, haversine=TRUE, filename="", ...)

## S4 method for signature 'SpatVector,ANY'
distance(x, y, sequential=FALSE, pairs=FALSE, symmetrical=TRUE, unit="m")

## S4 method for signature 'SpatVector,SpatVector'
distance(x, y, pairwise=FALSE, unit="m")

## S4 method for signature 'matrix,matrix'
distance(x, y, lonlat, pairwise=FALSE)

## S4 method for signature 'matrix,missing'
distance(x, y, lonlat, sequential=FALSE, pairs=FALSE, symmetrical=TRUE)

Arguments

x

SpatRaster, SpatVector, or two-column matrix with coordinates (x,y) or (lon,lat)

y

missing, numeric, SpatVector, or two-column matrix

target

numeric. The value of the cells for which distances to cells that are not NA should be computed

exclude

numeric. The value of the cells that should not be considered for computing distances

unit

character. Can be either "m" or "km"

haversine

logical. Use the haversine formula for lon/lat data use the haversine formula? If FALSE, the more precise but slower method of Karney (2003) is used

rasterize

logical. If TRUE distance is computed from the cells covered by the geometries after rasterization. This can be much faster in some cases

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

sequential

logical. If TRUE, the distance between sequential geometries is returned

pairwise

logical. If TRUE and if x and y have the same size (number of rows), the pairwise distances are returned instead of the distances between all elements

lonlat

logical. If TRUE the coordinates are interpreted as angular (longitude/latitude). If FALSE they are interpreted as planar

pairs

logical. If TRUE a "from", "to", "distance" matrix is returned

symmetrical

logical. If TRUE and pairs=TRUE, the distance between a pair is only included once. The distance between geometry 1 and 3 is included, but the (same) distance between 3 and 1 is not

Value

SpatRaster or numeric or matrix or distance matrix (object of class "dist")

Note

The distance unit is in meters.

A distance matrix can be coerced into a matrix with as.matrix

References

Karney, C.F.F., 2013. Algorithms for geodesics, J. Geodesy 87: 43-55. doi:10.1007/s00190-012-0578-z.

Examples

#lonlat
r <- rast(ncols=36, nrows=18, crs="+proj=longlat +datum=WGS84")
r[500] <- 1
d <- distance(r) 
plot(d / 100000)

#planar
rr <- rast(ncols=36, nrows=18, crs="+proj=utm +zone=1 +datum=WGS84")
rr[500] <- 1
d <- distance(rr) 

rr[3:10, 3:10] <- 99
e <- distance(rr, exclude=99) 

p1 <- vect(rbind(c(0,0), c(90,30), c(-90,-30)), crs="+proj=longlat +datum=WGS84")
dp <- distance(r, p1) 

d <- distance(p1)
d
as.matrix(d)

p2 <- vect(rbind(c(30,-30), c(25,40), c(-9,-3)), crs="+proj=longlat +datum=WGS84")
dd <- distance(p1, p2)
dd
pd <- distance(p1, p2, pairwise=TRUE)
pd
pd == diag(dd)


# polygons, lines
crs <- "+proj=utm +zone=1"
p1 <- vect("POLYGON ((0 0, 8 0, 8 9, 0 9, 0 0))", crs=crs)
p2 <- vect("POLYGON ((5 6, 15 6, 15 15, 5 15, 5 6))", crs=crs)
p3 <- vect("POLYGON ((2 12, 3 12, 3 13, 2 13, 2 12))", crs=crs)
p <- rbind(p1, p2, p3)
L1 <- vect("LINESTRING(1 11, 4 6, 10 6)", crs=crs)
L2 <- vect("LINESTRING(8 14, 12 10)", crs=crs)
L3 <- vect("LINESTRING(1 8, 12 14)", crs=crs)
lns <- rbind(L1, L2, L3)
pts <- vect(cbind(c(7,10,10), c(3,5,6)), crs=crs)

distance(p1,p3)
distance(p)
distance(p,pts)
distance(p,lns)
distance(pts,lns)

Make a dot-density map

Description

Create the dots for a dot-density map and add these to the current map. Dot-density maps are made to display count data. For example of population counts, where each dot represents n persons. The dots are returned as a SpatVector. It there is an active graphics device, the dots are added to it with points.

Usage

## S4 method for signature 'SpatVector'
dots(x, field, size,  ...)

Arguments

x

SpatVector

field

character of numeric indicating field name. Or numeric vector of the same length as x

size

positive number indicating the number of cases associated with each dot

...

graphical arguments passed to points

Value

SpatVector (invisibly)

See Also

plot, cartogram, points

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
v$population <- 1000*(1:12)^2
plot(v, lwd=3, col="light gray", border="white")
d <- dots(v, "population", 1000, col="red", cex=.75)
lines(v)
d

Draw a polygon, line, extent, or points

Description

Draw on a plot (map) to get a SpatVector or SpatExtent object for later use. After calling the function, start clicking on the map. When you are done, press ESC. You can also preset the maximum number of clicks.

This does to work well on the default RStudio plotting device. To work around that, you can first run dev.new(noRStudioGD = TRUE) which will create a separate window for plotting, then use plot() followed by click() and click on the map .

Usage

## S4 method for signature 'character'
draw(x="extent", col="red", lwd=2, id=FALSE, n=1000, xpd=TRUE, ...)

Arguments

x

character. The type of object to draw. One of "extent", "polygon", "line", or "points"

col

the color to be used

lwd

the width of the lines to be drawn

id

logical. If TRUE, a numeric ID is shown on the map

n

the maximum number of clicks (does not apply when x=="extent" in which case n is always 2

xpd

logical. If TRUE, you can draw outside the current plotting area

...

additional graphics arguments for drawing

Value

SpatVector or SpatExtent

See Also

click


elongate lines

Description

Elongate SpatVector lines

Usage

## S4 method for signature 'SpatVector'
elongate(x, length=1, flat=FALSE)

Arguments

x

SpatVector

length

positive number indicating how much the lines should be elongated at each end. The unit is meter is the crs is lonlat and it is the same as the linear unit of the crs on other cases (also meter in most cases)

flat

logical. If TRUE, the earth's curvature is ignored for lonlat data, and the distance unit is degrees, not meter

Value

SpatVector

See Also

buffer, crop and erase

Examples

v <- vect(cbind(c(0,1,2), c(0,0,2)), "lines", crs="lonlat")
e <- elongate(v, 100000)
plot(e)
points(e)
geom(e)

Erase parts of a SpatVector object

Description

Erase parts of a SpatVector with another SpatVector or with a SpatExtent. You can also erase (parts of) polygons with the other polygons of the same SpatVector.

Usage

## S4 method for signature 'SpatVector,SpatVector'
erase(x, y)

## S4 method for signature 'SpatVector,missing'
erase(x, sequential=TRUE)

## S4 method for signature 'SpatVector,SpatExtent'
erase(x, y)

Arguments

x

SpatVector

y

SpatVector or SpatExtent

sequential

logical. Should areas be erased sequentially? See Details

Details

If polygons are erased sequentially, everything that is covered by the first polygon is removed from all other polygons, then everything that is covered by (what is remaining of) the second polygon is removed, etc.

If polygons are not erased sequentially, all overlapping areas are erased and only the areas covered by a single geometry are returned.

Value

SpatVector or SpatExtent

See Also

crop and intersect for the inverse.

The equivalent for SpatRaster is mask

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)

# polygons with polygons or extent

e <- ext(5.6, 6, 49.55, 49.7)
x <- erase(v, e)

p <- vect("POLYGON ((5.8 49.8, 6 49.9, 6.15 49.8, 6 49.6, 5.8 49.8))")
y <- erase(v, p)

# lines with polygons
lns <- as.lines(rast(v, ncol=10, nrow=10))[12:22]
eln <- erase(lns, v)
plot(v)
lines(lns, col='blue', lwd=4, lty=3)
lines(eln, col='red', lwd=2)


## self-erase
h <- convHull(v[-12], "NAME_1")
he <- erase(h)
plot(h, lwd=2, border="red", lty=2)
lines(he, col="gray", lwd=3)

Get the expanse (area) of individual polygons or for all (summed) raster cells

Description

Compute the area covered by polygons or for all raster cells that are not NA.

This method computes areas for longitude/latitude rasters, as the size of the cells is constant in degrees, but not in square meters. But it can also be important if the coordinate reference system is planar, but not equal-area.

For vector data, the best way to compute area is to use the longitude/latitude CRS. This is contrary to (erroneous) popular belief that suggest that you should use a planar coordinate reference system. This is done automatically, if transform=TRUE.

Usage

## S4 method for signature 'SpatRaster'
expanse(x, unit="m", transform=TRUE, byValue=FALSE,
			zones=NULL, wide=FALSE, usenames=FALSE)

## S4 method for signature 'SpatVector'
expanse(x, unit="m", transform=TRUE)

Arguments

x

SpatRaster or SpatVector

unit

character. Output unit of area. One of "m", "km", or "ha"

transform

logical. If TRUE, planar CRS are transformed to lon/lat for accuracy

byValue

logical. If TRUE, the area for each unique cell value is returned

zones

NULL or SpatRaster with the same geometry identifying zones in x

wide

logical. Should the results be in "wide" rather than "long" format?

usenames

logical. If TRUE layers are identified by their names instead of their numbers

Value

SpatRaster: data.frame with at least two columns ("layer" and "area") and possibly also "value" (if byValue is TRUE), and "zone" (if zones is TRUE). If x has no values, the total area of all cells is returned. Otherwise, the area of all cells that are not NA is returned.

SpatVector: numeric (one value for each (multi-) polygon geometry.

See Also

cellSize for a the size of individual cells of a raster, that can be summed with global or with zonal to get the area for different zones.

Examples

### SpatRaster 
r <- rast(nrows=18, ncols=36)
v <- 1:ncell(r)
v[200:400] <- NA
values(r) <- v

# summed area in km2
expanse(r, unit="km")

# all cells 
expanse(rast(r), unit="km")

r <- rast(ncols=90, nrows=45, ymin=-80, ymax=80)
m <- project(r, "+proj=merc")

expanse(m, unit="km")
expanse(m, unit="km", transform=FALSE)

m2 <- c(m, m)
values(m2) <- cbind(c(1,2,NA,NA), c(11:14))
expanse(m2, unit="km", byValue=TRUE, wide=TRUE)


v <- vect(system.file("ex/lux.shp", package="terra"))
r <- rast(system.file("ex/elev.tif", package="terra"))
r <- round((r-50)/100)
levels(r) <- data.frame(id=1:5, name=c("forest", "water", "urban", "crops", "grass"))
expanse(r, byValue=TRUE)

g <- rasterize(v, r, "NAME_1")
expanse(r, byValue=TRUE, zones=g, wide=TRUE)


### SpatVector
v <- vect(system.file("ex/lux.shp", package="terra"))

a <- expanse(v)
a
sum(a)

Create, get or set a SpatExtent

Description

Get a SpatExtent of a SpatRaster, SpatVector, or other spatial objects. Or create a SpatExtent from a vector (length=4; order=xmin, xmax, ymin, ymax)

You can set the extent of a SpatRaster, but you cannot set the extent of a SpatVector (see rescale for that). See set.ext to set the extent in place.

Usage

## S4 method for signature 'SpatRaster'
ext(x, cells=NULL)

## S4 method for signature 'SpatVector'
ext(x)

## S4 method for signature 'numeric'
ext(x, ..., xy=FALSE)

## S4 replacement method for signature 'SpatRaster,SpatExtent'
ext(x)<-value

## S4 replacement method for signature 'SpatRaster,numeric'
ext(x)<-value

Arguments

x

SpatRaster

cells

positive integer (cell) numbers to subset the extent to area covered by these cells

value

SpatExtent, or numeric vector of length four (xmin, xmax, ymin, ymax)

...

if x is a single numeric value, additional numeric values for xmax, ymin, and ymax

xy

logical. Set this to TRUE to indicate that coordinates are in (xmin, ymin, xmax, ymax) order, instead of in the terra standard order of (xmin, xmax, ymin, ymax)

Value

A SpatExtent object.

Examples

r <- rast()
e <- ext(r)
as.vector(e)
as.character(e)

ext(r) <- c(0, 2.5, 0, 1.5)
r
er <- ext(r)

round(er)
# go "in"
floor(er)
# go "out"
ceiling(er)

ext(r) <- e

Extend

Description

Enlarge the spatial extent of a SpatRaster. See crop if you (also) want to remove rows or columns.

Note that you can only enlarge SpatRasters with entire rows and columns. Therefore, the extent of the output SpatRaster may not be exactly the same as the requested. Depending on argument snap it may be a bit smaller or larger.

You can also enlarge a SpatExtent with this method, or with an algebraic notation (see examples)

Usage

## S4 method for signature 'SpatRaster'
extend(x, y, snap="near", fill=NA, filename="", overwrite=FALSE, ...) 

## S4 method for signature 'SpatExtent'
extend(x, y)

Arguments

x

SpatRaster or SpatExtent

y

If x is a SpatRaster, y should be a SpatExtent, or an object from which it can be extracted (such as SpatRaster and SpatVector objects). Alternatively, you can provide one, two or four non-negative integers indicating the number of rows and columns that need to be added at each side (a single positive integer when the number of rows and columns to be added is equal; or 2 number (columns, rows), or four (left column, right column, bottom row, top row). If x is a SpatExtent, y should likewise be a numeric vector of 1, 2, or 4 elements

snap

character. One of "near", "in", or "out". Used to align y to the geometry of x

fill

numeric. The value used to for the new raster cells

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

...

additional arguments for writing files as in writeRaster

Value

SpatRaster or SpatExtent

See Also

crop, merge, ext, resample

Examples

r <- rast(xmin=-150, xmax=-120, ymin=30, ymax=60, ncols=36, nrows=18)
values(r) <- 1:ncell(r)
e <- ext(-180, -100, 40, 70)
re <- extend(r, e)

# extend with a number of rows and columns (at each side)
re2 <- extend(r, c(2,10))

# SpatExtent
e <- ext(r)
e
extend(e, 10)
extend(e, c(10, -10, 0, 20))


# add 10 columns / rows on all sides
e + 10
# double extent
e * 2
# increase extent by 25%
e * 1.25

Extract values from a SpatRaster

Description

Extract values from a SpatRaster for a set of locations. The locations can be a SpatVector (points, lines, polygons), a data.frame or matrix with (x, y) or (longitude, latitude – in that order!) coordinates, or a vector with cell numbers.

When argument y is a SpatVector the first column has the ID (record number) of the SpatVector used (unless you set ID=FALSE).

Alternatively, you can use zonal after using rasterize with a SpatVector (this may be more efficient in some cases).

Usage

## S4 method for signature 'SpatRaster,SpatVector'
extract(x, y, fun=NULL, method="simple", cells=FALSE, xy=FALSE,
    ID=TRUE, weights=FALSE, exact=FALSE, touches=is.lines(y), small=TRUE,
	layer=NULL, bind=FALSE, raw=FALSE, ...)

## S4 method for signature 'SpatRaster,SpatExtent'
extract(x, y, cells=FALSE, xy=FALSE)

## S4 method for signature 'SpatRaster,matrix'
extract(x, y, cells=FALSE, method="simple")

## S4 method for signature 'SpatRaster,numeric'
extract(x, y, xy=FALSE, raw=FALSE)

## S4 method for signature 'SpatVector,SpatVector'
extract(x, y)

Arguments

x

SpatRaster or SpatVector of polygons

y

SpatVector (points, lines, or polygons). Alternatively, for points, a 2-column matrix or data.frame (x, y) or (lon, lat). Or a vector with cell numbers

fun

function to summarize the extracted data by line or polygon geometry. You can use fun=table to tabulate raster values for each line or polygon geometry. If weights=TRUE or exact=TRUE only mean, sum, min, max and table are accepted). Ignored if y has point geometry

method

character. method for extracting values with points ("simple" or "bilinear"). With "simple" values for the cell a point falls in are returned. With "bilinear" the returned values are interpolated from the values of the four nearest raster cells

cells

logical. If TRUE the cell numbers are also returned, unless fun is not NULL. Also see cells

xy

logical. If TRUE the coordinates of the cells are also returned, unless fun is not NULL. See xyFromCell

ID

logical. Should an ID column be added? If so, the first column returned has the IDs (record numbers) of y

weights

logical. If TRUE and y has polygons, the approximate fraction of each cell that is covered is returned as well, for example to compute a weighted mean

exact

logical. If TRUE and y has polygons, the exact fraction of each cell that is covered is returned as well, for example to compute a weighted mean

touches

logical. If TRUE, values for all cells touched by lines or polygons are extracted, not just those on the line render path, or whose center point is within the polygon. Not relevant for points; and always considered TRUE when weights=TRUE or exact=TRUE

small

logical. If TRUE, values for all cells in touched polygons are extracted if none of the cells center points is within the polygon; even if touches=FALSE

layer

character or numeric to select the layer to extract from for each geometry. If layer is a character it can be a name in y or a vector of layer names. If it is numeric, it must be integer values between 1 and nlyr(x)

bind

logical. If TRUE, a SpatVector is returned consisting of the input SpatVector y and the cbind-ed extracted values

raw

logical. If TRUE, a matrix is returned with the "raw" numeric cell values. If FALSE, a data.frame is returned and the cell values are transformed to factor, logical, or integer values, where appropriate

...

additional arguments to fun if y is a SpatVector. For example na.rm=TRUE. Or arguments passed to the SpatRaster,SpatVector method if y is a matrix (such as the method and cells arguments)

Value

data.frame, matrix or SpatVector

See Also

values, zonal, extractAlong, extractRange, rapp

Examples

r <- rast(ncols=5, nrows=5, xmin=0, xmax=5, ymin=0, ymax=5)
values(r) <- 1:25
xy <- rbind(c(0.5,0.5), c(2.5,2.5))
p <- vect(xy, crs="+proj=longlat +datum=WGS84")

extract(r, xy)
extract(r, p)

r[1,]
r[5]
r[,5]

r[c(0:2, 99:101)]

f <- system.file("ex/meuse.tif", package="terra")
r <- rast(f)

xy <- cbind(179000, 330000)
xy <- rbind(xy-100, xy, xy+1000)
extract(r, xy)

p <- vect(xy)
g <- geom(p)
g

extract(r, p)

x <- r + 10
extract(x, p)

i <- cellFromXY(r, xy)
x[i]
r[i]

y <- c(x,x*2,x*3)
y[i]

## extract with a polygon
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
v <- v[1:2,]

rf <- system.file("ex/elev.tif", package="terra")
x <- rast(rf)
extract(x, v, mean, na.rm=TRUE)

z <- rast(v, resolution=.1, names="test")
values(z) <- 1:ncell(z)
e <- extract(z, v, ID=TRUE)
e
tapply(e[,2], e[,1], mean, na.rm=TRUE)

x <- c(z, z*2, z/3)
names(x) <- letters[1:3]

e <- extract(x, v, ID=TRUE)
de <- data.frame(e)
aggregate(de[,2:4], de[,1,drop=FALSE], mean)

extract values along lines

Description

Extract raster values along a line. That is, the returned values are ordered along the line. That is not the case with extract

Usage

extractAlong(x, y, ID=TRUE, cells=FALSE, xy=FALSE, online=FALSE, bilinear=TRUE)

Arguments

x

SpatRaster

y

SpatVector with lines geometry

ID

logical. Should an ID column be added? If so, the first column returned has the IDs (record numbers) of input SpatVector y

cells

logical. If TRUE the cell numbers are also returned

xy

logical. If TRUE the coordinates of the cells traversed by y are also returned. See xyFromCell

online

logical. If TRUE the returned coordinates are snapped to y

bilinear

logical. If TRUE the returned raster values computed with bilinear interpolation from the nearest four cells. Only relevant if online=TRUE

Value

data.frame

See Also

extract

Examples

r <- rast(ncols=36, nrows=18, vals=1:(18*36))
cds1 <- rbind(c(-50,0), c(0,60), c(40,5), c(15,-45), c(-10,-25))
cds2 <- rbind(c(80,20), c(140,60), c(160,0), c(140,-55))
lines <- vect(list(cds1, cds2), "lines")

extractAlong(r, lines)

Extract values for a range of layers from a SpatRaster

Description

Extract values from a SpatRaster for a set of locations and a range of layers. To extract values for a single or all layers, use extract

Usage

## S4 method for signature 'SpatRaster'
extractRange(x, y, first, last, lyr_fun=NULL, 
		geom_fun=NULL, ID=FALSE, na.rm=TRUE, ...)

Arguments

x

SpatRaster

y

SpatVector (points, lines, or polygons). Alternatively, for points, a 2-column matrix or data.frame (x, y) or (lon, lat). Or a vector with cell numbers

first

layer name of number, indicating the first layer in the range of layers to be considered

last

layer name or number, indicating the last layer in the range to be considered

lyr_fun

function to summarize the extracted data across layers

geom_fun

function to summarize the extracted data for each line or polygon geometry. Ignored if y has point geometry

ID

logical. Should an ID column be added? If so, the first column returned has the IDs (record numbers) of y

na.rm

logical. Should missing values be ignored?

...

additional arguments passed to extract

Value

numeric or data.frame

See Also

extract

Examples

r <- rast(system.file("ex/logo.tif", package="terra"))   
xy <- data.frame(c(50,80), c(30, 60))
extract(r, xy)
extract(r, xy, layer=c("red", "green"))
extractRange(r, xy, first=1:2, last=3:2, lyr_fun=sum)

Get or compute the minimum and maximum cell values

Description

The minimum and maximum value of a SpatRaster are returned or computed (from a file on disk if necessary) and stored in the object.

Usage

## S4 method for signature 'SpatRaster'
minmax(x, compute=FALSE)
## S4 method for signature 'SpatRaster'
hasMinMax(x)
## S4 method for signature 'SpatRaster'
setMinMax(x, force=FALSE)

Arguments

x

SpatRaster

compute

logical. If TRUE min and max values are computed if they are not available

force

logical. If TRUE min and max values are recomputed even if already available

Value

minmax: numeric matrix of minimum and maximum cell values by layer

hasMinMax: logical indicating whether the min and max values are available.

setMinMax: nothing. Used for the side-effect of computing the minimum and maximum values of a SpatRaster

Examples

r <- rast(system.file("ex/elev.tif", package="terra"))
minmax(r)

Categorical rasters

Description

A SpatRaster layer can represent a categorical variable (factor). Like factors, SpatRaster categories are stored as integers that have an associated label.

The categories can be inspected with levels and cats. They are represented by a data.frame that must have two or more columns, the first one identifying the (integer) cell values and the other column(s) providing the category labels.

If there are multiple columns with categories, you can set the "active" category to choose the one you want to use.

cats returns the entire data.frame, whereas levels only return two columns: the index and the active category.

To set categories for the first layer of a SpatRaster, you can provide levels<- with a data.frame or a list with a data.frame. To set categories for multiple layers you can provide levels<- with a list with one element (that either has a data.frame or is NULL) for each layer. Use categories to set the categories for a specific layer or specific layers.

droplevels removes categories that are not used (declared but not present as values in the raster) if levels=NULL.

addCats adds additional categories to a layer that already is categorical. It adds new variables, not new levels of an existing categorical variable.

Usage

## S4 method for signature 'SpatRaster'
levels(x)

## S4 replacement method for signature 'SpatRaster'
levels(x)<-value

## S4 method for signature 'SpatRaster'
cats(x, layer)

## S4 method for signature 'SpatRaster'
categories(x, layer=1, value, active=1, ...)

## S4 method for signature 'SpatRaster'
droplevels(x, level=NULL, layer=1)

## S4 method for signature 'SpatRaster'
addCats(x, value, merge=FALSE, layer=1)

Arguments

x

SpatRaster

layer

the layer name or number (positive integer); or 0 for all layers

value

a data.frame (ID, category) that define the categories. Or NULL to remove them

active

positive integer, indicating the column in value to be used as the active category (zero based to skip the first column with the cell values; that is 1 is the second column in value)

level

the categories to remove for the layer specified with layer

merge

logical. If TRUE, the categories are combined with merge using the first column of value as ID. If FALSE the categories are combined with cbind

...

additional arguments (none)

Value

list of data.frames (levels, cats) or logical (is.factor)

See Also

activeCat, catalyze, set.cats, as.factor, is.factor

Examples

set.seed(0)
r <- rast(nrows=10, ncols=10)
values(r) <- sample(3, ncell(r), replace=TRUE)
is.factor(r)

cls <- data.frame(id=1:3, cover=c("forest", "water", "urban"))
levels(r) <- cls
is.factor(r)
r

plot(r, col=c("green", "blue", "light gray"))
text(r, digits=3, cex=.75, halo=TRUE)

# raster starts at 3
x <- r + 2
is.factor(x)

# Multiple categories
d <- data.frame(id=3:5, cover=cls[,2], letters=letters[1:3], value=10:12)
levels(x) <- d
x

# get current index
activeCat(x)
# set index 
activeCat(x) <- 3
activeCat(x)
activeCat(x) <- "letters"
plot(x, col=c("green", "blue", "light gray"))
text(x, digits=3, cex=.75, halo=TRUE)

r <- as.numeric(x)
r

p <- as.polygons(x)
plot(p, "letters", col=c("green", "blue", "light gray"))

Remove holes from polygons

Description

Remove the holes in SpatVector polygons. If inverse=TRUE the holes are returned (as polygons).

Usage

## S4 method for signature 'SpatVector'
fillHoles(x, inverse=FALSE)

Arguments

x

SpatVector

inverse

logical. If TRUE the holes are returned as polygons

Value

SpatVector

Examples

x <- rbind(c(-10,0), c(140,60), c(160,0), c(140,-55))
hole <- rbind(c(80,0), c(105,13), c(120,2), c(105,-13))

z <- rbind(cbind(object=1, part=1, x, hole=0), 
		   cbind(object=1, part=1, hole, hole=1))
colnames(z)[3:4] <- c('x', 'y')
p <- vect(z, "polygons", atts=data.frame(id=1))
p

f <- fillHoles(p)
g <- fillHoles(p, inverse=TRUE)

plot(p, lwd=16, border="gray", col="light yellow")
polys(f, border="blue", lwd=3, density=4, col="orange")
polys(g, col="white", lwd=3)

Fill time gaps in a SpatRaster

Description

Add empty layers in between existing layers such that the time step between each layer is the same. See approximate to estimate values for these layer (and other missing values)

Usage

## S4 method for signature 'SpatRaster'
fillTime(x, filename="", ...)

Arguments

x

SpatRaster

filename

character. Output filename

...

list with named options for writing files as in writeRaster

Value

SpatRaster

See Also

approximate

Examples

r <- rast(system.file("ex/logo.tif", package="terra"))   
s <- c(r, r)
time(s) <- as.Date("2001-01-01") + c(0:2, 5:7)
time(s)
ss <- fillTime(s)
time(ss)

a <- approximate(ss)

Flip or reverse a raster

Description

Flip the values of a SpatRaster by inverting the order of the rows (vertical=TRUE) or the columns (vertical=FALSE).

rev is the same as a horizontal *and* a vertical flip.

Usage

## S4 method for signature 'SpatRaster'
flip(x, direction="vertical", filename="", ...)

## S4 method for signature 'SpatVector'
flip(x, direction="vertical")

## S4 method for signature 'SpatRaster'
rev(x)

Arguments

x

SpatRaster or SpatVector

direction

character. Should (partially) match "vertical" to flip by rows, or "horizontal" to flip by columns

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

trans, rotate

Examples

r <- rast(nrow=18, ncol=36)
m <- matrix(1:ncell(r), nrow=18)
values(r) <- as.vector(t(m))
rx <- flip(r, direction="h")

values(r) <- as.vector(m)
ry <- flip(r, direction="v")

v <- rev(r)

Focal values

Description

Calculate focal ("moving window") values for each cell.

Usage

## S4 method for signature 'SpatRaster'
focal(x, w=3, fun="sum", ..., na.policy="all", fillvalue=NA, 
		expand=FALSE, silent=TRUE, filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster

w

window. The window can be defined as one (for a square) or two numbers (row, col); or with an odd-sized weights matrix. See Details.

fun

function that takes multiple numbers, and returns a numeric vector (one or multiple numbers). For example mean, modal, min or max

...

additional arguments passed to fun such as na.rm

na.policy

character. Can be used to determine the cells of x for which focal values should be computed. Must be one of "all" (compute for all cells), "only" (only for cells that are NA) or "omit" (skip cells that are NA). Note that the value of this argument does not affect which cells around each focal cell are included in the computations (use na.rm=TRUE to ignore cells that are NA for that)

fillvalue

numeric. The value of the cells in the virtual rows and columns outside of the raster

expand

logical. If TRUE The value of the cells in the virtual rows and columns outside of the raster are set to be the same as the value on the border. Only available for "build-in" funs such as mean, sum, min and max

silent

logical. If TRUE error messages are printed that may occur when trying fun to determine the length of the returned value. This can be useful in debugging a fun that does not work

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

additional arguments for writing files as in writeRaster

Details

focal The window used must have odd dimensions. If you need even sides, you can use a matrix and add a column or row of NA's to mask out values.

Window values are typically 1 or NA to indicate whether a value is used or ignored in computations, respectively. NA values in w can be useful for creating non-rectangular (e.g. circular) windows.

A weights matrix of numeric values can also be supplied to w. In the case of a weights matrix, cells with NA weights will be ignored, and the rest of the values in the focal window will be multiplied by the corresponding weight prior to 'fun' being applied. Note, na.rm does not need to be TRUE if w contains NA values as these cells are ignored in computations.

The "mean" function is a special case, where supplying weights to w will instead calculate a weighted mean.

The "sum" function returns NA if all focal cells are NA and na.rm=TRUE. R would normally return a zero in these cases. See the difference between focal(x, fun=sum, na.rm=TRUE) and focal(x, fun=\(i) sum(i, na.rm=TRUE))

Example weight matrices

Laplacian filter: filter=matrix(c(0,1,0,1,-4,1,0,1,0), nrow=3)

Sobel filters (for edge detection):

fx=matrix(c(-1,-2,-1,0,0,0,1,2,1), nrow=3)

fy=matrix(c(1,0,-1,2,0,-2,1,0,-1), nrow=3)

Value

SpatRaster

Note

When using global lon/lat rasters, the focal window "wraps around" the date-line.

See Also

focalMat, focalValues, focal3D, focalPairs, focalReg, focalCpp

Examples

r <- rast(ncols=10, nrows=10, ext(0, 10, 0, 10))
values(r) <- 1:ncell(r)

f <- focal(r, w=3, fun=function(x, ...) quantile(x, c(.25, .5, .75), ...), na.rm=TRUE) 

f <- focal(r, w=3, fun="mean") 

# the following two statements are equivalent:
a <- focal(r, w=matrix(1/9, nc=3, nr=3))
b <- focal(r, w=3, fun=mean, na.rm=FALSE)

# but this is different
d <- focal(r, w=3, fun=mean, na.rm=TRUE)

## illustrating the effect of different 
## combinations of na.rm and na.policy
v <- vect(system.file("ex/lux.shp", package="terra"))
r <- rast(system.file("ex/elev.tif", package="terra"))
r[45:50, 45:50] <- NA

# also try "mean" or "min"
f <- "sum" 
# na.rm=FALSE
plot(focal(r, 5, f) , fun=lines(v))

# na.rm=TRUE
plot(focal(r, 5, f, na.rm=TRUE), fun=lines(v))

# only change cells that are NA
plot(focal(r, 5, f, na.policy="only", na.rm=TRUE), fun=lines(v))

# do not change cells that are NA
plot(focal(r, 5, f, na.policy="omit", na.rm=TRUE), fun=lines(v))

# does not do anything
# focal(r, 5, f, na.policy="only", na.rm=FALSE)

Three-dimensional focal values

Description

Calculate focal ("moving window") values for the three-dimensional neighborhood (window) of focal cells. See focal for two-dimensional focal computation.

Usage

## S4 method for signature 'SpatRaster'
focal3D(x, w=3, fun=mean, ..., na.policy="all", fillvalue=NA, pad=FALSE, 
	padvalue=fillvalue, expand=FALSE, silent=TRUE, 
	filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster

w

window. A rectangular prism (cuboid) defined by three numbers or by a three-dimensional array. The values are used as weights, and are usually zero, one, NA, or fractions. The window used must have odd dimensions. If you desire to use even sides, you can use an array, and pad the values with rows and/or columns that contain only NAs.

fun

function that takes multiple numbers, and returns one or multiple numbers for each focal area. For example mean, modal, min or max

...

additional arguments passed to fun such as na.rm

na.policy

character. Can be used to determine the cells of x, in the central layer, for which focal values should be computed. Must be one of "all" (compute for all cells), "only" (only for cells that are NA) or "omit" (skip cells that are NA). Note that the value of this argument does not affect which cells around each focal cell are included in the computations (use na.rm=TRUE to ignore cells that are NA in the computation of the focal value)

fillvalue

numeric. The value of the cells in the virtual rows and columns outside of the raster

pad

logical. Add virtual layers before the first and after the last layer

padvalue

numeric. The value of the cells in the virtual layers

expand

logical. Add virtual layers before the first or after the last layer that are the same as the first or last layers. If TRUE, arguments pad and padvalue are ignored

silent

logical. If TRUE error messages are printed that may occur when trying fun to determine the length of the returned value. This can be useful in debugging a function passed to fun that does not work

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

focal

Examples

r <- rast(system.file("ex/logo.tif", package="terra"))   
x <- focal3D(r, c(5,5,3), na.rm=TRUE)

a <- array(c(0,1,0,1,1,1,0,1,0, rep(1,9), 0,1,0,1,1,1,0,1,0), c(3,3,3))
a[a==0] <- NA
z <- focal3D(r, a, na.rm=TRUE)

Compute focal values with an iterating C++ function

Description

Calculate focal values with a C++ function that iterates over cells to speed up computations by avoiding an R loop (with apply).

See focal for an easier to use method.

Usage

## S4 method for signature 'SpatRaster'
focalCpp(x, w=3, fun, ..., fillvalue=NA, 
		silent=TRUE, filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster

w

window. The window can be defined as one (for a square) or two numbers (row, col); or with an odd-sized weights matrix. See the Details section in focal

fun

cppFunction that iterates over cells. For C++ functions that operate on a single focal window, or for R functions use focal instead. The function must have at least three arguments. The first argument can have any name, but it must be a Rcpp::NumericVector, Rcpp::IntegerVector or a std::vector<double>. This is the container that receives the focal values. The other two arguments ni and wi must be of type size_t. ni represents the number of cells and nw represents the size of (number of elements in) the window

...

additional arguments to fun

fillvalue

numeric. The value of the cells in the virtual rows and columns outside of the raster

silent

logical. If TRUE error messages are printed that may occur when trying fun to determine the length of the returned value. This can be useful in debugging a fun that does not work

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

focal, focalValues

Examples

## Not run: 
library(Rcpp)
cppFunction( 
	'NumericVector sum_and_multiply(NumericVector x, double m, size_t ni, size_t nw) {
		NumericVector out(ni);
		// loop over cells
		size_t start = 0;
		for (size_t i=0; i<ni; i++) {
			size_t end = start + nw;
			// compute something for a window
			double v = 0;
			// loop over the values of a window
			for (size_t j=start; j<end; j++) {
				v += x[j];
			}
			out[i] = v * m;
			start = end;
		}
		return out;
	}'
)

nr <- nc <- 10
r <- rast(ncols=nc, nrows=nr, ext= c(0, nc, 0, nr))
values(r) <- 1:ncell(r)

raw <- focalCpp(r, w=3, fun=sum_and_multiply, fillvalue=0, m=10)

# same as
f1 <- focal(r, w=3, fun=sum, fillvalue=0) *10
all(values(f1) == values(raw))

# and as
ffun <- function(x, m) { sum(x) * m }
f2 <- focal(r, w=3, fun=ffun, fillvalue=0, m=10)


# You can also use an R function with focalCpp but this
# is not recommended 

R_sm_iter <- function(x, m, ni, nw) {
	out <- NULL
	for (i in 1:ni) {
		start <- (i-1) * nw + 1
		out[i] <- sum(x[start:(start+nw-1)]) * m
	}
	out
}

fr <- focalCpp(r, w=3, fun=R_sm_iter, fillvalue=0, m=10)


## End(Not run)

Focal weights matrix

Description

Make a focal ("moving window") weight matrix for use in the focal function. The sum of the values adds up to one.

Usage

focalMat(x, d, type=c('circle', 'Gauss', 'rectangle'), fillNA=FALSE)

Arguments

x

SpatRaster

d

numeric. If type=circle, the radius of the circle (in units of the crs). If type=rectangle the dimension of the rectangle (one or two numbers). If type=Gauss the size of sigma, and optionally another number to determine the size of the matrix returned (default is 3*sigma)

type

character indicating the type of filter to be returned

fillNA

logical. If TRUE, zeros are set to NA such that they are ignored in the computations. Only applies to type="circle"

Value

matrix that can be used with focal

Examples

r <- rast(ncols=180, nrows=180, xmin=0)
focalMat(r, 2, "circle")

focalMat(r, c(2,3), "rect")

# Gaussian filter for square cells
gf <- focalMat(r, 1, "Gauss")

Focal function across two layers

Description

Calculate values such as a correlation coefficient for focal regions in two neighboring layers. A function is applied to the first and second layer, then to the second and third layer, etc.

Usage

## S4 method for signature 'SpatRaster'
focalPairs(x, w=3, fun, ..., fillvalue=NA, 
		filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster with at least two layers

w

numeric or matrix to define the focal window. The window an be defined as one (for a square) or two numbers (row, col); or with an odd-sized weights matrix. See the Details section in focal. Note that if a matrix with numbers other than zero or one are used, the values are used as weights. For this to work, fun must have an argument weights

fun

a function with at least two arguments (one for each layer). There is a built-in function "pearson" (for both the weighted and the unweighted Pearson correlation coefficient. This function has an additional argument na.rm=FALSE

...

additional arguments for fun

fillvalue

numeric. The value of the cells in the virtual rows and columns outside of the raster

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

layerCor, focalReg, focal, focal3D

Examples

r <- rast(system.file("ex/logo.tif", package="terra"))
set.seed(0)
r[[1]] <- flip(r[[1]], "horizontal")
r[[2]] <- flip(r[[2]], "vertical") + init(rast(r,1), runif)
r[[3]] <- init(rast(r,1), runif)

x <- focalPairs(r, w=5, "pearson", na.rm=TRUE)
plot(x)


# suppress warning "the standard deviation is zero"
suppressWarnings(x <- focalPairs(r, w=5, "pearson", use="complete.obs"))

z <- focalPairs(r, w=9, function(x, y) mean(x) + mean(y))

Focal regression

Description

Calculate values for a moving-window by comparing the value in one layers with the values in one to many other layers. A typical case is the computation of the coefficients for a focal linear regression model.

Usage

## S4 method for signature 'SpatRaster'
focalReg(x, w=3, fun="ols", ..., fillvalue=NA, filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster with at least two layers. The first is the "Y" (dependent) variable and the remainder are the "X" (independent) variables

w

numeric or matrix to define the focal window. The window an be defined as one (for a square) or two numbers (row, col); or with an odd-sized weights matrix. See the Details section in focal. Note that if a matrix with numbers other than zero or one are used, the values are used as weights. For this to work, fun must have an argument weights

fun

a function with at least two arguments (one for each layer). There is a built-in function "ols" for both the weighted and unweighted Ordinary Least Square regression. This function has an additional argument na.rm=FALSE and intercept=TRUE

...

additional arguments for fun

fillvalue

numeric. The value of the cells in the virtual rows and columns outside of the raster

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

focal, focal3D, focalValues

Examples

r <- rast(ncols=10, nrows=10, ext(0, 10, 0, 10))
values(r) <- 1:ncell(r)
x <- c(r, init(r, runif) * r)
f <- focalReg(x, 3)

Get focal values

Description

Get a matrix in which each row had the focal values of a cell. These are the values of a cell and a rectangular window around it.

Usage

## S4 method for signature 'SpatRaster'
focalValues(x, w=3, row=1, nrows=nrow(x), fill=NA)

Arguments

x

SpatRaster or SpatVector

w

window. The window can be defined as one (for a square) or two odd numbers (row, col); or with an odd sized matrix

row

positive integer. Row number to start from, should be between 1 and nrow(x)

nrows

positive integer. How many rows?

fill

numeric used as values for imaginary cells outside the raster

Value

matrix

Examples

r <- rast(ncol=4, nrow=4, crs="+proj=utm +zone=1 +datum=WGS84")
values(r) <- 1:ncell(r)
focalValues(r)

force counter-clockwise polygons

Description

Assure that the nodes of outer rings of polygons are in counter-clockwise order.

Usage

## S4 method for signature 'SpatVector'
forceCCW(x)

Arguments

x

SpatVector of polygons

Value

SpatVector

Examples

p <- vect("POLYGON ((2 45, 2 55, 18 55, 18 45, 2 45))")
pcc <- forceCCW(p)
geom(pcc, wkt=TRUE)

Frequency table

Description

Frequency table of the values of a SpatRaster. NAs are not counted unless value=NA.

You can provide a SpatVector or additional SpatRaster to define zones for which to do tabulations.

Usage

## S4 method for signature 'SpatRaster'
freq(x, digits=0, value=NULL, bylayer=TRUE, usenames=FALSE, zones=NULL, wide=FALSE)

Arguments

x

SpatRaster

digits

integer. Used for rounding the values before tabulation. Ignored if NA

value

numeric. An optional single value to only count the number of cells with that value. This value can be NA

bylayer

logical. If TRUE tabulation is done by layer

usenames

logical. If TRUE layers are identified by their names instead of their numbers Only relevant if bylayer is TRUE

zones

SpatRaster or SpatVector to define zones for which the tabulation should be done

wide

logical. Should the results by "wide" instead of "long"?

Value

A data.frame with 3 columns (layer, value, count) unless bylayer=FALSE in which case adata.frame with two columns is returned (value, count).

Examples

r <- rast(nrows=10, ncols=10)
set.seed(2)
values(r) <- sample(5, ncell(r), replace=TRUE)

freq(r)

x <- c(r, r/3)
freq(x, bylayer=FALSE)
freq(x)

freq(x, digits=1)
freq(x, digits=-1)

freq(x, value=5)

Find gaps between polygons

Description

Get the gaps between polygons of a SpatVector

Usage

## S4 method for signature 'SpatVector'
gaps(x)

Arguments

x

SpatVector

Value

SpatVector

See Also

sharedPaths, topology, and fillHoles to get or remove polygon holes

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
h <- convHull(v[-12], "NAME_1")
g <- gaps(h)

GDAL version, supported file formats, and cache size

Description

Set the GDAL warning level or get a data.frame with the available GDAL drivers (file formats), or, if warn=NA and drivers=FALSE, you get the version numbers of one or all of the GDAL, PROJ and GEOS libraries.

GDAL is the software library that terra builds on to read and write spatial data and for some raster data processing. PROJ is used for transformation of coordinates ("projection") and GEOS is used for geometric operations with vector data.

Usage

gdal(warn=NA, drivers=FALSE, lib="gdal")
gdalCache(size=NA)
setGDALconfig(option, value="")
getGDALconfig(option)

Arguments

warn

If NA and drivers=FALSE, the version of the library specified by lib is returned. Otherwise, the value should be an integer between 1 and 4 representing the level of GDAL warnings and errors that are passed to R. 1 = warnings and errors; 2 = errors only (recoverable errors as a warning); 3 = irrecoverable errors only; 4 = ignore all errors and warnings. The default setting is 3

drivers

logical. If TRUE a data.frame with the raster and vector data formats that are available.

lib

character. "gdal", "proj", or "geos", or any other value to get the versions numbers of all three

size

numeric. The new cache size in MB

option

character. GDAL configuration option name, or a "name=value" string (in which case the value argument is ignored

value

character. value for GDAL configuration option. Use "" to reset it to its default value

Value

character

See Also

describe for file-level metadata "GDALinfo"

Examples

gdal()
gdal(2)
head(gdal(drivers=TRUE))

Get the geometry (coordinates) of a SpatVector

Description

Get the geometry of a SpatVector. If wkt=FALSE, this is a five-column matrix or data.frame: the vector object ID, the IDs for the parts of each object (e.g. five polygons that together are one spatial object), the x (longitude) and y (latitude) coordinates, and a flag indicating whether the part is a "hole" (only relevant for polygons).

If wkt=TRUE, the "well-known text" representation is returned as a character vector.

Usage

## S4 method for signature 'SpatVector'
geom(x, wkt=FALSE, hex=FALSE, df=FALSE, list=FALSE, xnm="x", ynm="y")

Arguments

x

SpatVector

wkt

logical. If TRUE the WKT geometry is returned (unless hex is also TRUE)

hex

logical. If TRUE the hexadecimal geometry is returned

df

logical. If TRUE a data.frame is returned instead of a matrix (only if wkt=FALSE, hex=FALSE, and list=FALSE)

list

logical. If TRUE a nested list is returned with data.frames of coordinates

xnm

character. If list=TRUE the "x" column name for the coordinates data.frame

ynm

character. If list=TRUE the "y" column name for the coordinates data.frame

Value

matrix, vector, data.frame, or list

See Also

crds, xyFromCell

Examples

x1 <- rbind(c(-175,-20), c(-140,55), c(10, 0), c(-140,-60))
x2 <- rbind(c(-125,0), c(0,60), c(40,5), c(15,-45))
x3 <- rbind(c(-10,0), c(140,60), c(160,0), c(140,-55))
x4 <- rbind(c(80,0), c(105,13), c(120,2), c(105,-13))
z <- rbind(cbind(object=1, part=1, x1), cbind(object=2, part=1, x2), 
           cbind(object=3, part=1, x3), cbind(object=3, part=2,  x4))
colnames(z)[3:4] <- c('x', 'y')
z <- cbind(z, hole=0)
z[(z[, "object"]==3 & z[,"part"]==2), "hole"] <- 1

p <- vect(z, "polygons")
geom(p)

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
g <- geom(v)
head(g)

w <- geom(v, wkt=TRUE)
substr(w, 1, 60)

Geometry type of a SpatVector

Description

Get the geometry type (points, lines, or polygons) of a SpatVector. See datatype for the data types of the fields (attributes, variables) of a SpatVector.

Usage

## S4 method for signature 'SpatVector'
geomtype(x)

## S4 method for signature 'SpatVector'
is.points(x)

## S4 method for signature 'SpatVector'
is.lines(x)

## S4 method for signature 'SpatVector'
is.polygons(x)

Arguments

x

SpatVector

Value

character

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)

geomtype(v)
is.polygons(v)
is.lines(v)
is.points(v)

names(v)
datatype(v)

global statistics

Description

Compute global statistics, that is summarized values of an entire SpatRaster.

If x is very large global can fail, except when fun is one of these built-in functions "mean", "min", "max", "sum", "prod", "range" (min and max), "rms" (root mean square), "sd" (sample standard deviation), "std" (population standard deviation), "isNA" (number of cells that are NA), "notNA" (number of cells that are not NA).

The reason that this can fail with large raster and a custom function is that all values need to be loaded into memory. To circumvent this problem you can run global with a sample of the cells.

You can compute a weighted mean or sum by providing a SpatRaster with weights.

Usage

## S4 method for signature 'SpatRaster'
global(x, fun="mean", weights=NULL, maxcell=Inf, ...)

Arguments

x

SpatRaster

fun

function to be applied to summarize the values by zone. Either as one or more of these built-in character values: "max", "min", "mean", "sum", "range", "rms" (root mean square), "sd", "std" (population sd, using n rather than n-1), "isNA", "notNA"; or a proper R function (but these may fail for very large SpatRasters unless you specify maxcell)

...

additional arguments passed on to fun

weights

NULL or SpatRaster

maxcell

positive integer used to take a regular sample of x. Ignored by the built-in functions.

Value

A data.frame with a row for each layer

See Also

zonal for "zonal" statistics, and app or Summary-methods for "local" statistics, and extract for summarizing values for polygons. Also see focal for "focal" or "moving window" operations.

Examples

r <- rast(ncols=10, nrows=10)
values(r) <- 1:ncell(r)
global(r, "sum")
global(r, "mean", na.rm=TRUE)
x <- c(r, r/10)
global(x, c("sum", "mean", "sd"), na.rm=TRUE)

global(x, function(i) min(i) / max(i))

Create a graticule

Description

Create a graticule. That is, a grid of lon/lat lines that can be used to on a projected map.

The object returned, a SpatGraticule, can be plotted with plot and lines. There is also a crop method.

Usage

graticule(lon=30, lat=30, crs="")

Arguments

lon

numeric. Either a single number (the interval between longitudes), or a vector with longitudes

lat

numeric. Either a single number (the interval between latitudes), or a vector with latitudes

crs

character. The coordinate reference system to use

Value

SpatGraticule

See Also

plot<SpatGraticule>.

Examples

g <- graticule(60, 30, crs="+proj=robin")
g

graticule(90, c(-90, -60, -23.5, 0, 23.5, 60, 90), crs="+proj=robin")

Distance on a grid

Description

The function calculates the distance to cells of a SpatRaster when the path has to go through the centers of the eight neighboring raster cells.

The default distance (when scale=1, is meters if the coordinate reference system (CRS) of the SpatRaster is longitude/latitude (+proj=longlat) and in the linear units of the CRS (typically meters) in other cases.

Distances are computed by summing local distances between cells, which are connected with their neighbors in 8 directions.

The shortest distance to the cells with the target value is computed for all cells that are not NA. Cells that are NA cannot be traversed and are ignored, unless the target itself is NA, in which case the distance to the nearest cell that is not NA is computed for all cells that are NA.

Usage

## S4 method for signature 'SpatRaster'
gridDist(x, target=0, scale=1, maxiter=50, filename="", ...)

Arguments

x

SpatRaster

target

numeric. value of the target cells (where to compute distance to)

scale

numeric. Scale factor. For longitude/latitude data 1 = "m" and 1000 = "km". For planar data that is also the case of the distance unit of the crs is "m"

maxiter

numeric. The maximum number of iterations. Increase this number if you get the warning that costDistance did not converge. Only relevant when target is not NA

filename

character. output filename (optional)

...

additional arguments as for writeRaster

Value

SpatRaster

See Also

See distance for "as the crow flies" distance, and costDist for distance across a landscape with variable friction

Examples

# global lon/lat raster
r <- rast(ncol=10,nrow=10, vals=1)
r[48] <- 0
r[66:68] <- NA
d <- gridDist(r) 
plot(d)


# planar
crs(r) <- "+proj=utm +zone=15 +ellps=GRS80 +datum=NAD83 +units=m +no_defs"
d <- gridDist(r) 
plot(d)

# distance to cells that are not NA 
rr <- classify(r, cbind(1, NA))
dd <- gridDist(rr, NA)

Add halo-ed text to a plot

Description

Add text to a plot that has a "halo". That is, a buffer around it to enhance visibility.

Usage

halo(x, y=NULL, labels, col="black", hc="white", hw=0.1, ...)

Arguments

x, y

numeric. coordinates where the text labels should be written

labels

character. The text to be written

col

character. The main color to be used

hc

character. The halo color

hw

numeric. The halo width

...

additional arguments to pass to text

See Also

text, plot

Examples

r <- rast(nrows=4, ncols=4)
values(r) <- 1:ncell(r)
plot(r, col="blue", legend=FALSE)

text(-100, 20, "hello", cex=2)
halo(50, 20, "hello", cex=2)

halo(0, -20, "world", font=3, hc="light blue", cex=2, hw=.2)
halo(0, 90, "world", font=2, cex=2, hw=.2, xpd=TRUE, pos=2)
halo(0, 90, "world", col="white", font=2, hc="blue", cex=2, hw=.2, xpd=TRUE, pos=4)

head and tail of a SpatRaster or SpatVector

Description

Show the head (first values) or tail (last values) of a SpatRaster or of the attributes of a SpatVector.

Usage

head(x, ...) 
tail(x, ...)

Arguments

x

SpatRaster or SpatVector

...

additional arguments passed on to other methods

Value

matrix (SpatRaster) or data.frame (SpatVector)

See Also

show, geom

Examples

r <- rast(nrows=25, ncols=25)
values(r) <- 1:ncell(r)
head(r)
tail(r)

Histogram

Description

Create a histogram of the values of a SpatRaster. For large datasets a sample of maxcell is used.

Usage

## S4 method for signature 'SpatRaster'
hist(x, layer, maxcell=1000000, plot=TRUE, maxnl=16, main, ...)

Arguments

x

SpatRaster

layer

positive integer or character to indicate layer numbers (or names). If missing, all layers up to maxnl are used

maxcell

integer. To regularly sample very large objects

plot

logical. Plot the histogram or only return the histogram values

maxnl

positive integer. The maximum number of layers to use. Ignored if layer is not missing

main

character. Main title(s) for the plot. Default is the value of names

...

additional arguments. See hist

Value

This function is principally used for plotting a histogram, but it also returns an object of class "histogram" (invisibly if plot=TRUE).

See Also

pairs, boxplot

Examples

r1 <- r2 <- rast(nrows=50, ncols=50)
values(r1) <- runif(ncell(r1))
values(r2) <- runif(ncell(r1))
rs <- r1 + r2
rp <- r1 * r2

opar <- par(no.readonly =TRUE)
par(mfrow=c(2,2))
plot(rs, main='sum')
plot(rp, main='product')
hist(rs)
a <- hist(rp)
a
x <- c(rs, rp, sqrt(rs))
hist(x)
par(opar)

Compare two SpatRasters for equality

Description

Compare two SpatRasters for equality.

First the attributes of the objects are compared. If these are the same, a the raster cells are compared as well. This can be time consuming, and you may prefer to use a sample instead with all.equal

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
identical(x, y)

Arguments

x

SpatRaster

y

SpatRaster

Value

single logical value

See Also

all.equal, compareGeom

Examples

x <- sqrt(1:100)
mat <- matrix(x, 10, 10)
r1 <- rast(nrows=10, ncols=10, xmin=0, vals = x)
r2 <- rast(nrows=10, ncols=10, xmin=0, vals = t(mat))

identical(r1, r2)
identical(r1, r1*1)
identical(rast(r1), rast(r2))

ifelse for SpatRasters

Description

Implementation of ifelse for SpatRasters. This method allows for a concise expression of what can otherwise be achieved with a combination of classify, mask, and cover.

ifel is an R equivalent to the Con method in ArcGIS (arcpy).

Usage

## S4 method for signature 'SpatRaster'
ifel(test, yes, no, filename="", ...)

Arguments

test

SpatRaster with logical (TRUE/FALSE) values

yes

SpatRaster or numeric

no

SpatRaster or numeric

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

Examples

r <- rast(nrows=5, ncols=5, xmin=0, xmax=1, ymin=0, ymax=1)
values(r) <- c(-10:0, NA, NA, NA, 0:10)

x <- ifel(r > 1, 1, r)
# same as 
a <- classify(r, cbind(1, Inf, 1))
# or
b <- app(r, fun=function(i) {i[i > 1] <- 1; i})
# or 
d <- clamp(r, -Inf, 1)
# or (not recommended for large datasets)
e <- r
e[e>1] <- 1

## other examples
f <- ifel(is.na(r), 100, r)

z <- ifel(r > -2 & r < 2, 100, 0)

# nested expressions
y <- ifel(r > 1, 1, ifel(r < -1, -1, r))

k <- ifel(r > 0, r+10, ifel(r < 0, r-10, 3))

SpatRaster image method

Description

Plot (make a map of) the values of a SpatRaster via image. See plot if you need more fancy options such as a legend.

Usage

## S4 method for signature 'SpatRaster'
image(x, y=1, maxcell=500000, ...)

Arguments

x

SpatRaster

y

positive integer indicating the layer to be plotted, or a character indicating the name of the layer

maxcell

positive integer. Maximum number of cells to use for the plot

...

additional arguments as for graphics::image

See Also

plot

Examples

f <- system.file("ex/elev.tif", package="terra") 
r <- rast(f)
image(r)
image(r, col=rainbow(24))

Impose the geometry of a SpatRaster to those in a SpatRasterCollection.

Description

Warp the members of a SpatRasterCollection to match the geometry of a SpatRaster.

Usage

## S4 method for signature 'SpatRasterCollection'
impose(x, y, filename="", ...)

Arguments

x

SpatRasterCollection

y

SpatRaster

filename

character. Output filename

...

list with named options for writing files as in writeRaster

Value

SpatRaster

See Also

resample


Initialize a SpatRaster with values

Description

Create a SpatRaster with values reflecting a cell property: 'x', 'y', 'col', 'row', 'cell' or 'chess'. Alternatively, a function can be used. In that case, cell values are initialized without reference to pre-existing values. E.g., initialize with a random number (fun=runif). While there are more direct ways of achieving this for small objects (see examples) for which a vector with all values can be created in memory, the init function will also work for SpatRasters with many cells.

Usage

## S4 method for signature 'SpatRaster'
init(x, fun, filename="", ...)

Arguments

x

SpatRaster

fun

function to be applied. This must be a either single number, multiple numbers, a function, or one of a set of known character values. A function must take the number of cells as a single argument to return a vector of values with a length equal to the number of cells, such as fun=runif. Allowed character values are 'x', 'y', 'row', 'col', 'cell', and 'chess' to get the x or y coordinate, row, col or cell number or a chessboard pattern (alternating 0 and 1 values)

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

Examples

r <- rast(ncols=10, nrows=5, xmin=0, xmax=10, ymin=0, ymax=5)
x <- init(r, fun="cell")
y <- init(r, fun=runif)

# initialize with a single value 
z <- init(r, fun=8)

Change values in-place

Description

These "in-place" replacement methods assign new value to an object without making a copy. That is efficient, but if there is a copy of the object that you made by standard assignment (e.g. with y <- x), that copy is also changed.

set.names is the in-place replacement version of names<-.

set.ext is the in-place replacement version of ext<-

set.values is the in-place replacement version of [<-.

set.cats is the in-place replacement version of categories

set.crs is the in-place replacement version of crs<-

Usage

## S4 method for signature 'SpatRaster'
set.names(x, value, index=1:nlyr(x), validate=FALSE)
## S4 method for signature 'SpatRasterDataset'
set.names(x, value, index=1:length(x), validate=FALSE)
## S4 method for signature 'SpatVector'
set.names(x, value, index=1:ncol(x), validate=FALSE)

## S4 method for signature 'SpatRaster'
set.ext(x, value)
## S4 method for signature 'SpatVector'
set.ext(x, value)

## S4 method for signature 'SpatRaster'
set.crs(x, value)
## S4 method for signature 'SpatVector'
set.crs(x, value)

## S4 method for signature 'SpatRaster'
set.values(x, cells, values, layer=0)

## S4 method for signature 'SpatRaster'
set.cats(x, layer=1, value, active=1)

## S4 method for signature 'SpatRaster'
set.RGB(x, value, type="rgb")

Arguments

x

SpatRaster

value

character for set.names. For set.cats: a data.frame with columns (value, category) or vector with category names. For set.RGB 3 or 4 numbers indicating the RGB(A) layers

index

positive integer indicating layer(s) to assign a name to

validate

logical. Make names valid and/or unique?

cells

cell numbers or missing

values

replacement values or missing to load all values into memory

layer

positive integer(s) indicating to which layer(s) to you want to assign these categories or to which you want to set these values. A number < 1 indicates "all layers"

active

positive integer indicating the active category (column number in value, but not counting the first column

type

character. The color space. One of "rgb" "hsv", "hsi" and "hsl"

Value

logical (invisibly)

Examples

s <- rast(ncols=5, nrows=5, nlyrs=3)
x <- s
names(s)
names(s) <- c("a", "b", "c")
names(s)
names(x)

x <- s
set.names(s, c("e", "f", "g"))
names(s)
names(x)

set.ext(x, c(0,180,0,90))

f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)

#values from file to memory
set.values(r)

# change values
set.values(r, 1:1000, 900)

Make an inset map

Description

Make an inset map or scale the extent of a SpatVector

Usage

## S4 method for signature 'SpatVector'
inset(x, e, loc="", scale=0.2, background="white", 
	perimeter=TRUE, box=NULL, pper, pbox, offset=0.1, add=TRUE, ...)

## S4 method for signature 'SpatRaster'
inset(x, e, loc="", scale=0.2, background="white", 
	perimeter=TRUE, box=NULL, pper, pbox, offset=0.1, add=TRUE, ...)

## S4 method for signature 'SpatVector'
inext(x, e, y=NULL, gap=0)

Arguments

x

SpatVector, SpatRaster

e

SpatExtent to set the size and location of the inset. Or missing

loc

character. One of "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"

scale

numeric. The relative size of the inset, used when x is missing

background

color for the background of the inset. Use NA for no background color

perimeter

logical. If TRUE a perimeter (border) is drawn around the inset

box

SpatExtent or missing, to draw a box on the inset, e.g. to show where the map is located in a larger area

pper

list with graphical parameters (arguments) such as col and lwd for the perimeter line

pbox

list with graphical parameters (arguments) such as col and lwd for the box (line)

offset

numeric. Value between 0.1 and 1 to indicate the relative distance between what is mapped and the bounding box

add

logical. Add the inset to the map?

...

additional arguments passed to plot for the drawing of x

y

SpatVector. If not NULL, y is scaled based with the parameters for x. This is useful, for example, when x represent boundaries, and y points within these boundaries

gap

numeric to add space between the SpatVector and the SpatExtent

Value

scaled and shifted SpatVector or SpatRaster (returned invisibly)

See Also

sbar, rescale, shift

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
x <- v[v$NAME_2 == "Diekirch", ]

plot(x, density=10, col="blue")
inset(v)

# more elaborate
plot(x, density=10, col="blue")
inset(v, col = "brown", border="lightgrey", perimeter=TRUE, 
		pper=list(col="orange", lwd=3, lty=2), 
		box=ext(x), pbox=list(col="blue", lwd=2))

cols <- rep("light grey", 12)
cols[2] <- "red"
e <- ext(c(6.2, 6.3, 49.9, 50))
b <- ext(x)+0.02
inset(v, e=e, col=cols, box=b)

# with a SpatRaster
ff <- system.file("ex/elev.tif", package="terra")
r <- rast(ff)
r <- crop(r, ext(x) + .01)
plot(r, type="int", mar=c(2,2,2,2), plg=list(x="topright"))
lines(v, lwd=1.5)
lines(x, lwd=2.5)
inset(v, col=cols, loc="topleft", scale=0.15)

# a more complex one
plot(r, plg=list(title="meter\n", shrink=.2, cex=.8))
lines(v, lwd=4, col="white")
lines(v, lwd=1.5)
lines(x, lwd=2.5)
text(x, "NAME_2", cex=1.5, halo=TRUE)
sbar(6, c(6.04, 49.785), type="bar", below="km", label=c(0,3,6), cex=.8)
s <- inset(v, col=cols, box=b, scale=.2, loc="topright", background="light yellow",
	pbox=list(lwd=2, lty=5, col="blue"))

# note the returned inset SpatVector
s
lines(s, col="orange")

Interpolate points using a moving window

Description

Interpolate points within a moving window using inverse distance weighting. The maximum number of points used can be restricted, optionally by selecting the nearest points.

Usage

## S4 method for signature 'SpatRaster,SpatVector'
interpIDW(x, y, field, radius, power=2, smooth=0,
       maxPoints=Inf, minPoints=1, near=TRUE, fill=NA, filename="", ...)

## S4 method for signature 'SpatRaster,matrix'
interpIDW(x, y, radius, power=2, smooth=0, 
       maxPoints=Inf, minPoints=1, near=TRUE, fill=NA, filename="", ...)

Arguments

x

SpatRaster

y

SpatVector or matrix with three columns (x,y,z)

field

character. field name in SpatVector y

radius

numeric. The radius of the circle (single number). If near=FALSE, it is also possible to use two or three numbers. Two numbers are interpreted as the radii of an ellipse (x and y-axis). A third number should indicated the desired, counter clockwise, rotation of the ellipse (in degrees)

power

numeric. Weighting power

smooth

numeric. Smoothing parameter

minPoints

numeric. The minimum number of points to use. If fewer points are found in a search ellipse it is considered empty and the fill value is returned

maxPoints

numeric. The maximum number of points to consider in a search area. Additional points are ignored. If fewer points are found, the fill value is returned

near

logical. Should the nearest points within the neighborhood be used if maxPoints is reached?

fill

numeric. value to use to fill empty cells

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

rasterizeWin, rasterize, interpNear, interpolate

Examples

r <- rast(ncol=100, nrow=100, crs="local", xmin=0, xmax=50, ymin=0, ymax=50)
set.seed(100)
x <- runif(25, 5, 45)
y <- runif(25, 5, 45)
z <- sample(25)
xyz <- cbind(x,y,z)

x <- interpIDW(r, xyz, radius=5, power=1, smooth=1, maxPoints=5)

Nearest neighbor interpolation

Description

Nearest neighbor interpolation of points, using a moving window

Usage

## S4 method for signature 'SpatRaster,SpatVector'
interpNear(x, y, field, radius, interpolate=FALSE, fill=NA, filename="", ...)

## S4 method for signature 'SpatRaster,matrix'
interpNear(x, y, radius, interpolate=FALSE, fill=NA, filename="", ...)

Arguments

x

SpatRaster

y

SpatVector or matrix with three columns (x,y,z)

field

character. field name in SpatVector y

radius

numeric. The radius of the circle (single number). If interpolate=FALSE it is also possible to use two or three numbers. Two numbers are interpreted as the radii of an ellipse (x and y-axis). A third number should indicated the desired, counter clockwise, rotation of the ellipse (in degrees)

interpolate

logical. Should the nearest neighbor values be linearly interpolated between points?

fill

numeric. value to use to fill empty cells

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

rasterizeWin, rasterize, interpIDW, interpolate

Examples

r <- rast(ncol=100, nrow=100, crs="local", xmin=0, xmax=50, ymin=0, ymax=50)
set.seed(100)
x <- runif(25, 5, 45)
y <- runif(25, 5, 45)
z <- sample(25)
xyz <- cbind(x,y,z)

x <- interpNear(r, xyz, radius=5)

p <- vect(data.frame(xyz), geom=c("x", "y")) 
v <- voronoi(p)

plot(x, col=rainbow(25))
lines(v)

# plot(v, col=rainbow(25)); points(p)

Spatial interpolation

Description

Make a SpatRaster with interpolated values using a fitted model object of classes such as "gstat" (gstat package) or "Krige" (fields package), or any other model that has location (e.g., "x" and "y", or "longitude" and "latitude") as predictors (independent variables). If x and y are the only predictors, it is most efficient if you provide an empty (no associated data in memory or on file) SpatRaster for which you want predictions. If there are more spatial predictor variables, provide these as a SpatRaster in the first argument of the function. If you do not have x and y locations as implicit predictors in your model you should use predict instead.

Usage

## S4 method for signature 'SpatRaster'
interpolate(object, model, fun=predict, ..., xyNames=c("x", "y"), 
       factors=NULL, const=NULL, index = NULL, cores=1, cpkgs=NULL, 
	   na.rm=FALSE, filename="", overwrite=FALSE, wopt=list())

Arguments

object

SpatRaster

model

model object

fun

function. Default value is "predict", but can be replaced with e.g. "predict.se" (depending on the class of model), or a custom function (see examples)

...

additional arguments passed to fun

xyNames

character. variable names that the model uses for the spatial coordinates. E.g., c("longitude", "latitude")

factors

list with levels for factor variables. The list elements should be named with names that correspond to names in object such that they can be matched. This argument may be omitted for some models from which the levels can be extracted from the model object

const

data.frame. Can be used to add a constant for which there is no SpatRaster for model predictions. This is particularly useful if the constant is a character-like factor value

index

positive integer or NULL. Allows for selecting of the variable returned if the model returns multiple variables

cores

positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used

cpkgs

character. The package(s) that need to be loaded on the nodes to be able to run the model.predict function (see examples in predict)

na.rm

logical. If TRUE, cells with NA values in the predictors are removed from the computation. This option prevents errors with models that cannot handle NA values. In most other cases this will not affect the output. An exception is when predicting with a model that returns predicted values even if some (or all!) variables are NA

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

Value

SpatRaster

See Also

predict, interpIDW, interpNear

Examples

r <- rast(system.file("ex/elev.tif", package="terra"))
ra <- aggregate(r, 10)
xy <- data.frame(xyFromCell(ra, 1:ncell(ra)))
v <- values(ra)
i <- !is.na(v)
xy <- xy[i,]
v <- v[i]

## Not run: 
library(fields) 
tps <- Tps(xy, v)
p <- rast(r)

# use model to predict values at all locations
p <- interpolate(p, tps)
p <- mask(p, r)
plot(p)

### change "fun" from predict to fields::predictSE to get the TPS standard error
## need to use "rast(p)" to remove the values
se <- interpolate(rast(p), tps, fun=predictSE)
se <- mask(se, r)
plot(se)

### another predictor variable, "e"
e <- (init(r, "x") * init(r, "y")) / 100000000
names(e) <- "e"

z <- as.matrix(extract(e, xy)[,-1])

## add as another independent variable
xyz <- cbind(xy, z)
tps2 <- Tps(xyz, v)
p2 <- interpolate(e, tps2, xyOnly=FALSE)

## as a linear covariate
tps3 <- Tps(xy, v, Z=z)

## Z is a separate argument in Krig.predict, so we need a new function
## Internally (in interpolate) a matrix is formed of x, y, and elev (Z)

pfun <- function(model, x, ...) {
   predict(model, x[,1:2], Z=x[,3], ...)
}
p3 <- interpolate(e, tps3, fun=pfun)


#### gstat examples
library(gstat)
library(sp)
data(meuse)

### inverse distance weighted (IDW)
r <- rast(system.file("ex/meuse.tif", package="terra"))
mg <- gstat(id = "zinc", formula = zinc~1, locations = ~x+y, data=meuse, 
            nmax=7, set=list(idp = .5))
z <- interpolate(r, mg, debug.level=0, index=1)
z <- mask(z, r)

## with a model built with an `sf` object you need to provide custom function

library(sf)
sfmeuse <- st_as_sf(meuse, coords = c("x", "y"), crs=crs(r))
mgsf <- gstat(id = "zinc", formula = zinc~1, data=sfmeuse,  nmax=7, set=list(idp = .5))

interpolate_gstat <- function(model, x, crs, ...) {
	v <- st_as_sf(x, coords=c("x", "y"), crs=crs)
	p <- predict(model, v, ...)
	as.data.frame(p)[,1:2]
}

zsf <- interpolate(r, mgsf, debug.level=0, fun=interpolate_gstat, crs=crs(r), index=1)
zsf <- mask(zsf, r)

### kriging

### ordinary kriging
v <- variogram(log(zinc)~1, ~x+y, data=meuse)
mv <- fit.variogram(v, vgm(1, "Sph", 300, 1))
gOK <- gstat(NULL, "log.zinc", log(zinc)~1, meuse, locations=~x+y, model=mv)
OK <- interpolate(r, gOK, debug.level=0)

## universal kriging
vu <- variogram(log(zinc)~elev, ~x+y, data=meuse)
mu <- fit.variogram(vu, vgm(1, "Sph", 300, 1))
gUK <- gstat(NULL, "log.zinc", log(zinc)~elev, meuse, locations=~x+y, model=mu)
names(r) <- "elev"
UK <- interpolate(r, gUK, debug.level=0)

## co-kriging
gCoK <- gstat(NULL, 'log.zinc', log(zinc)~1, meuse, locations=~x+y)
gCoK <- gstat(gCoK, 'elev', elev~1, meuse, locations=~x+y)
gCoK <- gstat(gCoK, 'cadmium', cadmium~1, meuse, locations=~x+y)
gCoK <- gstat(gCoK, 'copper', copper~1, meuse, locations=~x+y)
coV <- variogram(gCoK)
plot(coV, type='b', main='Co-variogram')
coV.fit <- fit.lmc(coV, gCoK, vgm(model='Sph', range=1000))
coV.fit
plot(coV, coV.fit, main='Fitted Co-variogram')
coK <- interpolate(r, coV.fit, debug.level=0)
plot(coK)

## End(Not run)

Intersection

Description

You can intersect SpatVectors with each other or with a SpatExtent. Intersecting points with points uses the extent of y to get the intersection. Intersecting of points and lines is not supported because of numerical inaccuracies with that. You can use buffer, to create polygons from lines and use these with intersect.

You can also intersect two SpatExtents.

When intersecting two SpatRasters these need to be aligned (have the same origin and spatial resolution). The values of the returned SpatRaster are TRUE where both input rasters have values, FALSE where one has values, and NA in all other cells.

When intersecting a SpatExtent and a SpatRaster, the SpatExtent is first aligned to the raster cell boundaries.

See crop for the intersection of a SpatRaster with a SpatExtent (or the extent of a SpatRaster or SpatVector) if you want a SpatRaster (not a SpatExtent) as output.

See is.related(x, y, "intersects") to find out which geometries of a SpatVector intersect. You can spatially subset a SpatVector with another one with x[y].

Usage

## S4 method for signature 'SpatVector,SpatVector'
intersect(x, y)

## S4 method for signature 'SpatVector,SpatExtent'
intersect(x, y)

## S4 method for signature 'SpatExtent,SpatVector'
intersect(x, y)

## S4 method for signature 'SpatExtent,SpatExtent'
intersect(x, y)

## S4 method for signature 'SpatRaster,SpatRaster'
intersect(x, y)

## S4 method for signature 'SpatRaster,SpatExtent'
intersect(x, y)

## S4 method for signature 'SpatExtent,SpatRaster'
intersect(x, y)

Arguments

x

SpatVector, SpatExtent, or SpatRaster

y

SpatVector, SpatExtent, or SpatRaster

Value

Same as x

See Also

union, crop, relate, [

Examples

e1 <- ext(-10, 10, -20, 20)
e2 <- ext(0, 20, -40, 5)
intersect(e1, e2)

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
e <- ext(5.6, 6, 49.55, 49.7)
x <- intersect(v, e)

p <- vect(c("POLYGON ((5.8 49.8, 6 49.9, 6.15 49.8, 6 49.6, 5.8 49.8))", 
"POLYGON ((6.3 49.9, 6.2 49.7, 6.3 49.6, 6.5 49.8, 6.3 49.9))"), crs=crs(v))
values(p) <- data.frame(pid=1:2, area=expanse(p))

y <- intersect(v, p)

r <- s <- rast(ncol=5, nrow=5, xmin=1, xmax=5, ymin=1, ymax=5)
r[5:20] <- 5:20
s[11:20] <- 11:20
rs <- intersect(r, s)

u <- shift(r, .8)
us <- intersect(u, s)

Raster value types

Description

The values in a SpatRaster layer are by default numeric, but they can also be set to be logical (Boolean), integer, or categorical (factor).

For a SpatRaster, as.logical and isTRUE is equivalent to as.bool. isFALSE is equivalent to !as.bool, and as.integer is the same as as.int.

as.bool and as.int force the values into the correct range (e.g. whole integers) but in-memory cell values are still stored as numeric. They will behave like the assigned types, though, and will be written to files with that data type (if the file type supports it).

See levels and cats to create categorical layers by setting labels.

Usage

## S4 method for signature 'SpatRaster'
is.bool(x)

## S4 method for signature 'SpatRaster'
as.bool(x, filename, ...)

## S4 method for signature 'SpatRaster'
is.int(x)

## S4 method for signature 'SpatRaster'
as.int(x, filename, ...)

## S4 method for signature 'SpatRaster'
is.factor(x)

## S4 method for signature 'SpatRaster'
as.factor(x)

Arguments

x

SpatRaster

filename

character. Output filename

...

list with named options for writing files as in writeRaster

Value

The as.* methods return a new SpatRaster, whereas the is.* methods return a logical value for each layer in x.

See Also

levels and cats to create categorical layers (and set labels).

Examples

r <- rast(nrows=10, ncols=10, vals=1:100)
is.bool(r)
z <- as.bool(r)
is.bool(z)

x <- r > 25
is.bool(x)

rr <- r/2
is.int(rr)
is.int(round(rr))

Check if a SpatExtent or SpatVector is empty

Description

An empty SpatExtent has no area

An empty SpatVector has no geometries.

Usage

## S4 method for signature 'SpatExtent'
is.empty(x)

## S4 method for signature 'SpatVector'
is.empty(x)

Arguments

x

SpatVector or SpatExtent

Value

logical

Examples

e <- ext(0,0,0,0)
is.valid(e)
is.empty(e)

v <- vect()
is.valid(v)
is.empty(v)

Check for longitude/latitude crs

Description

Test whether a SpatRaster or SpatVector has a longitude/latitude coordinate reference system (CRS), or perhaps has one. That is, when the CRS is unknown ("") but the x coordinates are within -181 and 181 and the y coordinates are within -90.1 and 90.1. For a SpatRaster you can also test if it has a longitude/latitude CRS and it is "global" (covers all longitudes).

A warning is given if the CRS is missing or if it is specified as longitude/latitude but the coordinates do not match that.

Usage

## S4 method for signature 'SpatRaster'
is.lonlat(x, perhaps=FALSE, warn=TRUE, global=FALSE)

## S4 method for signature 'SpatVector'
is.lonlat(x, perhaps=FALSE, warn=TRUE)

## S4 method for signature 'character'
is.lonlat(x, perhaps=FALSE, warn=TRUE)

Arguments

x

SpatRaster or SpatVector

perhaps

logical. If TRUE and the CRS is unknown, the method returns TRUE if the coordinates are plausible for longitude/latitude

warn

logical. If TRUE, a warning is given if the CRS is unknown but assumed to be lon/lat and perhaps=TRUE

global

logical. If TRUE, the method tests if the raster covers all longitudes (from -180 to 180 degrees) such that the extreme columns are in fact adjacent

Value

logical or NA

Examples

r <- rast()
is.lonlat(r)
is.lonlat(r, global=TRUE)

crs(r) <- ""
is.lonlat(r)
is.lonlat(r, perhaps=TRUE, warn=FALSE)

crs(r) <- "+proj=lcc +lat_1=48 +lat_2=33 +lon_0=-100 +ellps=WGS84"
is.lonlat(r)

Check for rotation

Description

Check if a SpatRaster is "rotated" and needs to be rectified before it can be used

See rectify

Usage

## S4 method for signature 'SpatRaster'
is.rotated(x)

Arguments

x

SpatRaster

Value

logical. One value for each raster data *source*

See Also

rectify

Examples

r <- rast(nrows=10, ncols=10, vals=1:100)
is.rotated(r)

Check or fix polygon or extent validity

Description

Check the validity of polygons or attempt to fix it. Or check the validity of a SpatExtent.

Usage

## S4 method for signature 'SpatVector'
is.valid(x, messages=FALSE, as.points=FALSE)

## S4 method for signature 'SpatVector'
makeValid(x)

## S4 method for signature 'SpatExtent'
is.valid(x)

Arguments

x

SpatVector or SpatExtent

messages

logical. If TRUE the error messages are returned

as.points

logical. If TRUE, it is attempted to return locations where polygons are invalid as a SpatVector or points

Value

logical

See Also

topology

Examples

w <- vect("POLYGON ((0 -5, 10 0, 10 -10, 0 -5))")
is.valid(w)

w <- vect("POLYGON ((0 -5, 10 0, 10 -10, 4 -2, 0 -5))")
is.valid(w)
is.valid(w, TRUE)

plot(w)
points(cbind(4.54, -2.72), cex=2, col="red")


e <- ext(0, 1, 0, 1)
is.valid(e)

ee <- ext(0, 0, 0, 0)
is.valid(ee)

k_means

Description

Compute k-means clusters for a SpatRaster. For large SpatRasters (with ncell(x) > maxcell) this is done in two steps. First a sample of the cells is used to compute the cluster centers. Then each cell is assigned to a cluster by computing the distance to these centers.

Usage

## S4 method for signature 'SpatRaster'
k_means(x, centers=3, ..., maxcell=1000000, filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster

centers

either the number of clusters, or a set of initial (distinct) cluster centres. If a number, a random set of (distinct) cells in x is chosen as the initial centres

...

additional arguments passed to kmeans

maxcell

positive integer. The size of the regular sample used if it is smaller than ncell(x)

filename

character. Output filename (ignored if as.raster=FALSE)

overwrite

logical. If TRUE, filename is overwritten

wopt

list with additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

kmeans

Examples

f <- system.file("ex/logo.tif", package = "terra")
r <- rast(f)
km <- k_means(r, centers=5)
km

Apply a function to layers of a SpatRaster, or sub-datasets of a SpatRasterDataset

Description

Apply a function to a SpatRaster, using layers as arguments.

The number of arguments in function fun must match the number of layers in the SpatRaster (or the number of sub-datasets in the SpatRasterDataset). For example, if you want to multiply two layers, you could use this function: fun=function(x,y){return(x*y)} percentage: fun=function(x,y){return(100 * x / y)}. If you combine three layers you could use fun=function(x,y,z){return((x + y) * z)}

Before you use the function, test it to make sure that it is vectorized. That is, it should work for vectors longer than one, not only for single numbers. Or if the input SpatRaster(s) have multiple layers, it should work for a matrix (multiple cells) of input data (or matrices in the case of a SpatRasterDataSet). The function must return the same number of elements as its input vectors, or multiples of that. Also make sure that the function is NA-proof: it should returns the same number of values when some or all input values are NA. And the function must return a vector or a matrix, not a data.frame. To test it, run it with do.call(fun, data) (see examples).

Use app for summarize functions such as sum, that take any number of arguments; and tapp to do so for groups of layers.

Usage

## S4 method for signature 'SpatRaster'
lapp(x, fun, ..., usenames=FALSE, cores=1, filename="", overwrite=FALSE, wopt=list())

## S4 method for signature 'SpatRasterDataset'
lapp(x, fun, ..., usenames=FALSE, recycle=FALSE, 
    filename="", overwrite=FALSE, wopt=list())

Arguments

x

SpatRaster or SpatRasterDataset

fun

a function that takes a vector and can be applied to each cell of x

...

additional arguments to be passed to fun

usenames

logical. Use the layer names (or dataset names if x is a SpatRasterDataset) to match the function arguments? If FALSE, argument matching is by position

cores

positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used. You can also supply a cluster object

recycle

logical. Recycle layers to match the subdataset with the largest number of layers

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

Value

SpatRaster

Note

Use sapp or lapply to apply a function that takes a SpatRaster as argument to each layer of a SpatRaster (that is rarely necessary).

See Also

app, tapp, math

Examples

s <- rast(system.file("ex/logo.tif", package="terra")) + 1  
ss <- s[[2:1]]

fvi <- function(x, y){ (x - y ) / (x + y) } 
# test the function
data <- list(c(1:5,NA), 6:1)
do.call(fvi, data)

x <- lapp(ss, fun=fvi )

# which is the same as supplying the layers to "fun"
# in some cases this will be much faster 
y <- fvi(s[[2]], s[[1]])

f2 <- function(x, y, z){ (z - y + 1) / (x + y + 1) } 
p1 <- lapp(s, fun=f2 )

p2 <- lapp(s[[1:2]], f2, z=200)

# the usenames argument

fvi2 <- function(red, green){ (red - green ) / (red + green) } 
names(s)
x1 <- lapp(s[[1:2]], fvi2, usenames=TRUE)
x2 <- lapp(s[[2:1]], fvi2, usenames=TRUE)
# x1 and x2 are the same, despite the change in the order of the layers
# x4 is also the same, but x3 is not
x3 <- lapp(s[[2:1]], fvi2, usenames=FALSE)
x4 <- lapp(s, fvi2, usenames=TRUE)

# while this would fail because 
# there are too many layers in s
# x5 <- lapp(s, fvi2, usenames=FALSE)

pairs(c(x1, x2, x3, x4))

## SpatRasterDataset
x <- sds(s, s[[1]]+50)
fun <- function(x, y) { x/y }

# test "fun"
data <- list(matrix(1:9, ncol=3), matrix(9:1, ncol=3))
do.call(fun, data)

lapp(x, fun, recycle=TRUE)

# the same, more concisely
z <- s / (s[[1]]+50)

Correlation and (weighted) covariance

Description

Compute correlation, (weighted) covariance, or similar summary statistics that compare the values of all pairs of the layers of a SpatRaster.

Usage

## S4 method for signature 'SpatRaster'
layerCor(x, fun, w, asSample=TRUE, use="everything", maxcell=Inf, ...)

Arguments

x

SpatRaster

fun

character. The statistic to compute: either "cov" (covariance), "weighted.cov" (weighted covariance), or "cor" (pearson correlation coefficient) or your own function that takes two vectors as argument to compute a single number

w

SpatRaster with the weights to compute the weighted covariance. It should have a single layer and the same geometry as x

asSample

logical. If TRUE, the statistic for a sample (denominator is n-1) is computed, rather than for the population (denominator is n). Only for the standard functions

use

character. To decide how to handle missing values. This must be (an abbreviation of) one of "everything", "complete.obs", "pairwise.complete.obs", "masked.complete". With "pairwise.complete.obs", the value for a pair of layers is computed for all cells that are not NA in that pair. Therefore, it may be that the (number of) cells used varies between pairs. The benefit of this approach is that all available data is used. Use "complete.obs", if you want to only use the values from cells that are not NA in any of the layers. By using "masked.complete" you indicate that all layers have NA values in the same cells

maxcell

positive integer. The maximum number of cells to be used. If this is smaller than ncell(x), a regular sample of x is used

...

additional arguments for fun (if it is a proper function)

Value

If fun is one of the three standard statistics, you get a list with three items: the correlation or (weighted) covariance matrix, the (weighted) means, and the number of data cells in each comparison. The means are also a matrix because they may depend on the combination of layers if different cells have missing values and these are excluded from the computation. The rows of the mean matrix represent the layer whose (weighted) mean is being calculated and the columns represent the layer it is being paired with. Only cells with non-missing observations for both layers are used in the calculation of the (weighted) mean. The diagonals of the mean and n matrices are set to missing.

If fun is a function, you get a single matrix.

References

For the weighted covariance:

See Also

global, cov.wt, weighted.mean

Examples

b <- rast(system.file("ex/logo.tif", package="terra"))   
layerCor(b, "pearson")

layerCor(b, "cov")

# weigh by column number
w <- init(b, fun="col")
layerCor(b, "weighted.cov", w=w)

Linear units of the coordinate reference system

Description

Get the linear units of the coordinate reference system (crs) of a SpatRaster or SpatVector expressed in m. The value returned is used internally to transform area and perimeter measures to meters. The value returned for longitude/latitude crs is zero.

Usage

## S4 method for signature 'SpatRaster'
linearUnits(x)

## S4 method for signature 'SpatVector'
linearUnits(x)

Arguments

x

SpatRaster or SpatVector

Value

numeric (meter)

See Also

crs

Examples

x <- rast()
crs(x) <- ""
linearUnits(x)

crs(x) <- "+proj=longlat +datum=WGS84"
linearUnits(x)

crs(x) <- "+proj=utm +zone=1 +units=cm"
linearUnits(x)

crs(x) <- "+proj=utm +zone=1 +units=km"
linearUnits(x)

crs(x) <- "+proj=utm +zone=1 +units=us-ft"
linearUnits(x)

Add points, lines, or polygons to a map

Description

Add a vector geometries to a plot (map) with points, lines, or polys.

These are simpler alternatives for plot(x, add=TRUE)

These methods also work for a small(!) SpatRaster. Only cells that are not NA in the first layer are used.

Usage

## S4 method for signature 'SpatVector'
points(x, col, cex=0.7, pch=16, alpha=1, ...)

## S4 method for signature 'SpatVector'
lines(x, y=NULL, col, lwd=1, lty=1, arrows=FALSE, alpha=1, ...)

## S4 method for signature 'SpatVector'
polys(x, col, border="black", lwd=1, lty=1, alpha=1, ...)

## S4 method for signature 'SpatRaster'
points(x, ...)

## S4 method for signature 'SpatRaster'
lines(x, mx=10000, ...)

## S4 method for signature 'SpatRaster'
polys(x, mx=10000, dissolve=TRUE, ...)

## S4 method for signature 'SpatExtent'
points(x, col="black", alpha=1, ...)

## S4 method for signature 'SpatExtent'
lines(x, col="black", alpha=1, ...)

## S4 method for signature 'SpatExtent'
polys(x, col, alpha=1, ...)

Arguments

x

SpatVector or SpatExtent

y

missing or SpatVector. If both x and y have point geometry and the same number of rows, lines are drawn between pairs of points

col

character. Colors

border

character. color(s) of the polygon borders. Use NULL or NA to not draw a border

cex

numeric. point size magnifier. See par

pch

positive integer, point type. See points. On some (linux) devices, the default symbol "16" is a not a very smooth circle. You can use "20" instead (it takes a bit longer to draw) or "1" for an open circle

alpha

number between 0 and 1 to set transparency

lwd

numeric, line-width. See par

lty

positive integer, line type. See par

arrows

logical. If TRUE and y is a SpatVector, arrows are drawn intead of lines. See ?arrows for additional arguments

mx

positive number. If the number of cells of SpatRaster x is higher, the method will fail with an error message

dissolve

logical. Should boundaries between cells with the same value be removed?

...

additional graphical arguments such as lwd, cex and pch

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)

r <- rast(v)
values(r) <- 1:ncell(r)
plot(r)
lines(v)
points(v)

Make tiles or get their extents

Description

Divide a SpatRaster into "tiles". The cells of another SpatRaster (normally with a much lower resolution) or a SpatVector with polygon geometry can be used to define the tiles. You can also provide one or two numbers to indicate the number of rows and columns per tile.

getTileExtents returns the extents of the (virtual) tiles, while makeTiles creates files for the tiles and returns their filenames.

Usage

## S4 method for signature 'SpatRaster'
makeTiles(x, y, filename="tile_.tif", extend=FALSE,
		na.rm=FALSE, buffer=0, overwrite=FALSE, ...)

## S4 method for signature 'SpatRaster'
getTileExtents(x, y, extend=FALSE, buffer=0)

Arguments

x

SpatRaster

y

SpatRaster or SpatVector defining the zones; or numeric specifying the number of rows and columns for each zone (1 or 2 numbers if the number of rows and columns is not the same)

filename

character. Output filename template. Filenames will be altered by adding the tile number for each tile

extend

logical. If TRUE, the extent of y is expanded to assure that it covers all of x

na.rm

logical. If TRUE, tiles with only missing values are ignored

buffer

integer. The number of additional rows and columns added to each tile. Can be a single number, or two numbers to specify a separate number of rows and columns. This allows for creating overlapping tiles that can be used for computing spatial context dependent values with e.g. focal. The expansion is only inside x, no rows or columns outside of x are added

overwrite

logical. If TRUE, existing tiles are overwritten; otherwise they are skipped (without error or warning)

...

additional arguments for writing files as in writeRaster

Value

character (filenames) or matrix (extents)

See Also

vrt to create a virtual raster from tiles and crop for sub-setting arbitrary parts of a SpatRaster.

Examples

r <- rast(ncols=100, nrows=100)
values(r) <- 1:ncell(r)
x <- rast(ncols=2, nrows=2)

getTileExtents(r, x)
getTileExtents(r, x, buffer=3)


filename <- paste0(tempfile(), "_.tif")
ff <- makeTiles(r, x, filename)
ff

vrt(ff)

Make a VRT header file

Description

Create a VRT header file for a "flat binary" raster file that needs a header file to be able to read it, but does not have it.

Usage

makeVRT(filename, nrow, ncol, nlyr=1, extent, xmin, ymin, xres, yres=xres, xycenter=TRUE,
   crs="+proj=longlat", lyrnms="", datatype, NAflag=NA, bandorder="BIL", byteorder="LSB",
   toptobottom=TRUE, offset=0, scale=1)

Arguments

filename

character. raster filename (without the ".vrt" extension)

nrow

positive integer, the number of rows

ncol

positive integer, the number of columns

nlyr

positive integer, the number of layers

extent

SpatExtent or missing

xmin

numeric. minimum x coordinate (only used if extent is missing)

ymin

numeric. minimum y coordinate (only used if extent is missing)

xres

positive number. x resolution

yres

positive number. y resolution)

xycenter

logical. If TRUE, xmin and xmax represent the coordinates of the center of the extreme cell, in stead of the coordinates of the outside corner. Only used of extent is missing

crs

character. Coordinate reference system description

lyrnms

character. Layer names

datatype

character. One of "INT2S", "INT4S", "INT1U", "INT2U", "INT4U", "FLT4S", "FLT8S". If missing, this is guessed from the file size (INT1U for 1 byte per value, INT2S for 2 bytes and FLT4S for 4 bytes per value). This may be wrong because, for example, 2 bytes per value may in fact be INT2U (with the U for unsigned) values

NAflag

numeric. The value used as the "NA flag"

bandorder

character. One of "BIL", "BIP", or "BSQ". That is Band Interleaved by Line, or by Pixel, or Band SeQuential

byteorder

character. One of "LSB", "MSB". "MSB" is common for files generated on Linux systems, whereas "LSB" is common for files generated on windows

toptobottom

logical. If FALSE, the values are read bottom to top

offset

numeric. offset to be applied

scale

numeric. scale to be applied

Value

character (.VRT filename)

See Also

vrt to create a vrt for a collection of raster tiles


map.pal arrow

Description

Get a color palette for mapping. These palettes were copied from GRASS.

Usage

map.pal(name, n=50, ...)

Arguments

name

character (name of a palette, see Details), or missing (to get the available names)

n

numeric. The number of colors

...

additional arguments that are passed to colorRamp

Details

Name Description
aspect aspect oriented grey colors
bcyr blue through cyan through yellow to red
bgyr blue through green through yellow to red
blues white to blue
byg blue through yellow to green
byr blue through yellow to red
curvature for terrain curvatures
differences differences oriented colors
elevation maps relative ranges of raster values to elevation color ramp
grass GRASS GIS green (perceptually uniform)
greens white to green
grey grey scale
grey.eq histogram-equalized grey scale
grey.log histogram logarithmic transformed grey scale
gyr green through yellow to red
haxby relative colors for bathymetry or topography
inferno perceptually uniform sequential color table inferno
magma perceptually uniform sequential color table magma
oranges white to orange
plasma perceptually uniform sequential color table plasma
rainbow rainbow color table
ramp color ramp
random random color table
reds white to red
roygbiv
rstcurv terrain curvature
ryb red through yellow to blue
ryg red through yellow to green
sepia yellowish-brown through to white
viridis perceptually uniform sequential color table viridis
water water depth
wave color wave

Value

none

See Also

terrain.colors

Examples

map.pal("elevation", 10)

r <- rast(system.file("ex/elev.tif", package="terra"))
plot(r, col=map.pal("elevation"))

map.pal()

Mask values in a SpatRaster or SpatVector

Description

If x is a SpatRaster: Create a new SpatRaster that has the same values as SpatRaster x, except for the cells that are NA (or other maskvalue) in another SpatRaster (the 'mask'), or the cells that are not covered by a SpatVector or SpatExtent. These cells become NA (or another updatevalue).

If x is a SpatVector or SpatExtent: Select geometries of x that intersect, or not intersect, with the geometries of y.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
mask(x, mask, inverse=FALSE, maskvalues=NA, 
   updatevalue=NA, filename="", ...)
   
## S4 method for signature 'SpatRaster,SpatVector'
mask(x, mask, inverse=FALSE, updatevalue=NA,
	touches=TRUE, filename="", ...)

## S4 method for signature 'SpatRaster,SpatExtent'
mask(x, mask, inverse=FALSE, updatevalue=NA,
	touches=TRUE, filename="", ...)

## S4 method for signature 'SpatVector,SpatVector'
mask(x, mask, inverse=FALSE)

## S4 method for signature 'SpatVector,SpatExtent'
mask(x, mask, inverse=FALSE)

Arguments

x

SpatRaster or SpatVector

mask

SpatRaster or SpatVector

inverse

logical. If TRUE, areas on mask that are _not_ the maskvalue are masked

maskvalues

numeric. The value(s) in mask that indicate which cells of x should be masked (change their value to updatevalue (default = NA))

updatevalue

numeric. The value that masked cells should become (if they are not NA)

touches

logical. If TRUE, all cells touched by lines or polygons will be masked, not just those on the line render path, or whose center point is within the polygon

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

crop

Examples

f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
msk <- ifel(r < 400, NA, 1)

m <- mask(r, msk)

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)[1,]

mv1 <- mask(r, v)
mv2 <- crop(r, v, mask=TRUE)

Value matching for SpatRasters

Description

match returns a SpatRaster with the position of the matched values. The cell values are the index of the table argument.

%in% returns a 0/1 (FALSE/TRUE) SpatRaster indicating if the cells values were matched or not.

Usage

match(x, table, nomatch = NA_integer_, incomparables = NULL)

x %in% table

Arguments

x

SpatRaster

table

vector of the values to be matched against

nomatch

the value to be returned in the case when no match is found. Note that it is coerced to integer

incomparables

a vector of values that cannot be matched. Any value in x matching a value in this vector is assigned the nomatch value. For historical reasons, FALSE is equivalent to NULL

Value

SpatRaster

See Also

app, match

Examples

r <- rast(nrows=10, ncols=10)
values(r) <- 1:100
m <- match(r, c(5:10, 50:55))
n <- r %in% c(5:10, 50:55)

General mathematical methods

Description

Standard mathematical methods for computations with SpatRasters. Computations are local (applied on a cell by cell basis). If multiple SpatRasters are used, these must have the same extent and resolution. These have been implemented:

abs, sign, sqrt, ceiling, floor, trunc, cummax, cummin, cumprod, cumsum, log, log10, log2, log1p, acos, acosh, asin, asinh, atan, atanh, exp, expm1, cos, cosh, sin, sinh, tan, tanh, round, signif

Instead of directly calling these methods, you can also provide their name to the math method. This is useful if you want to provide an output filename.

The following methods have been implemented for SpatExtent: round, floor, ceiling

round has also been implemented for SpatVector, to round the coordinates of the geometries.

Usage

## S4 method for signature 'SpatRaster'
sqrt(x)

## S4 method for signature 'SpatRaster'
log(x, base=exp(1))

## S4 method for signature 'SpatRaster'
round(x, digits=0)

## S4 method for signature 'SpatRaster'
math(x, fun, digits=0, filename="", overwrite=FALSE, ...)

## S4 method for signature 'SpatVector'
round(x, digits=4)

## S4 method for signature 'SpatRaster'
cumsum(x)

Arguments

x

SpatRaster

base

a positive or complex number: the base with respect to which logarithms are computed

digits

Number of digits for rounding

fun

character. Math function name

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

...

additional arguments for writing files as in writeRaster

Value

SpatRaster or SpatExtent

See Also

See app to use mathematical functions not implemented by the package, and Arith-methods for arithmetical operations. Use roll for rolling functions.

Examples

r1 <- rast(ncols=10, nrows=10)
v <- runif(ncell(r1))
v[10:20] <- NA
values(r1) <- v
r2 <- rast(r1)
values(r2) <- 1:ncell(r2) / ncell(r2)
r <- c(r1, r2)

s <- sqrt(r)
# same as 
math(r, "sqrt")

round(s, 1)

cumsum(r)

Memory available and needed

Description

mem_info prints the amount of RAM that is required and available to process a SpatRaster.

free_RAM returns the amount of RAM that is available

Usage

mem_info(x, n=1)

free_RAM()

Arguments

x

SpatRaster

n

positive integer. The number of copies of x that are needed

Value

free_RAM returns the amount of available RAM in kilobytes

Examples

mem_info(rast())

free_RAM()

Merge SpatRasters, or merge a SpatVector with a data.frame

Description

Merge multiple SpatRasters to create a new SpatRaster with a larger spatial extent. The SpatRasters must have the same origin and spatial resolution. In areas where the SpatRasters overlap, the values of the SpatRaster that is first in the sequence of arguments (or in the SpatRasterCollection) will be retained (unless first=FALSE). Cells that are NA are ignored unless na.rm=FALSE

There is also a method for merging SpatVector with a data.frame; that is, to join the data.frame to the attribute table of the SpatVector.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
merge(x, y, ..., first=TRUE, na.rm=TRUE, filename="", overwrite=FALSE, wopt=list())

## S4 method for signature 'SpatRasterCollection,missing'
merge(x, first=TRUE, na.rm=TRUE, filename="", ...)

## S4 method for signature 'SpatVector,data.frame'
merge(x, y, ...)

Arguments

x

SpatRaster, SpatRasterCollection, or SpatVector

y

missing if x is a SpatRasterCollection. SpatRaster if x is a SpatRaster. data.frame if x is a SpatVector

...

if x is a SpatRaster: additional objects of the same class as x. If x is a SpatRasterCollection: options for writing files as in writeRaster. If x is a SpatVector, the same arguments as in merge

first

logical. If TRUE, in areas where rasters overlap, the first value is used. Otherwise the last value is used

na.rm

logical. If TRUE values that are NA are ignored

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

Value

SpatRaster or SpatVector

See Also

Combining tiles with vrt may be more efficient than using merge. See mosaic for averaging overlapping regions.

See classify to merge a SpatRaster and a data.frame and union to combine SpatExtent objects.

Examples

x <- rast(xmin=-110, xmax=-80, ymin=40, ymax=70, res=1, vals=1)
y <- rast(xmin=-85, xmax=-55, ymax=60, ymin=30, res=1, vals=2)
z <- rast(xmin=-60, xmax=-30, ymax=50, ymin=20, res=1, vals=3)

m1 <- merge(x, y, z)
m2 <- merge(z, y, x)
m3 <- merge(y, x, z)

# if you have many SpatRasters, it may be convenient
# to make a SpatRasterCollection
rlist <- list(x, y, z)
rsrc <- sprc(rlist)

m <- merge(rsrc)


## SpatVector with data.frame
f <- system.file("ex/lux.shp", package="terra")
p <- vect(f)
dfr <- data.frame(District=p$NAME_1, Canton=p$NAME_2, Value=round(runif(length(p), 100, 1000)))
dfr <- dfr[1:5, ]
pm <- merge(p, dfr, all.x=TRUE, by.x=c('NAME_1', 'NAME_2'), by.y=c('District', 'Canton'))
pm
values(pm)

merge SpatRasters by timelines to create a single timeseries

Description

Combine SpatRasters with partly overlapping time-stamps to create a single time series. If there is no overlap between the SpatRasters there is no point in using this function (use c instead).

Also note that time gaps are not filled. You can use fillTime to do that.

Usage

## S4 method for signature 'SpatRasterDataset'
mergeTime(x, fun=mean, filename="", ...)

Arguments

x

SpatRasterDataset

fun

A function that reduces a vector to a single number, such as mean or min

filename

character. Output filename

...

list with named options for writing files as in writeRaster

Value

SpatRaster

Examples

r <- rast(system.file("ex/logo.tif", package="terra"))   
s1 <- c(r, r)
time(s1) <- as.Date("2001-01-01") + 0:5
s1 <- s1/10
time(s1) <- as.Date("2001-01-07") + 0:5
s2 <- s1*10
time(s2) <- as.Date("2001-01-05") + 0:5
x <- sds(s1, s1, s2)

m <- mergeTime(x, mean)

meta

Description

Get metadata associated with the sources or layers of a SpatRaster

Usage

## S4 method for signature 'SpatRaster'
meta(x, layers=FALSE)

Arguments

x

SpatRaster

layers

logical. Should the layer level metadata be returned?

Value

list


Set or get metadata

Description

You can set arbitrary metadata to a SpatRaster using "name=value" tags.

Usage

## S4 replacement method for signature 'SpatRaster'
metags(x, layer=NULL)<-value

## S4 method for signature 'SpatRaster'
metags(x, layer=NULL, name=NULL)

Arguments

x

SpatRaster

layer

NULL or positive integer. If the value is NULL, the tags assigned or returned are for the SpatRaster. Otherwise for the layer number(s)

name

character

value

character of "name=value" or two-column matrix

Value

SpatRaster (metags<-), or named character (metags)

Examples

r <- rast(ncol=5, nrow=5)
m <- cbind(c("one", "two", "three"), c("ABC", "123", "hello"))
metags(r) <- m
metags(r)

metags(r) <- c("another_tag=another_value", "one more=this value")
metags(r)

metags(r) <- c(another_tag="44", `one more`="that value")
metags(r)


metags(r, name="two")

# remove a tag
metags(r) <- cbind("one", "")
metags(r) <- "two="
metags(r)

# remove all metags
metags(r) <- NULL
metags(r)

mosaic SpatRasters

Description

Combine adjacent and (partly) overlapping SpatRasters to form a single new SpatRaster. Values in overlapping cells are averaged (by default) or can be computed with another function.

The SpatRasters must have the same origin and spatial resolution.

This method is similar to the simpler, but much faster, merge method.

Usage

## S4 method for signature 'SpatRaster,SpatRaster'
mosaic(x, y, ..., fun="mean", filename="", overwrite=FALSE, wopt=list())

## S4 method for signature 'SpatRasterCollection,missing'
mosaic(x, fun="mean", filename="", ...)

Arguments

x

SpatRaster

y

object of same class as x

...

additional SpatRasters

fun

character. One of "mean", "median", "min", "max", "modal", "sum", "first", "last"

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

Value

SpatRaster

See Also

merge

Examples

x <- rast(xmin=-110, xmax=-60, ymin=40, ymax=70, res=1, vals=1)
y <- rast(xmin=-95, xmax=-45, ymax=60, ymin=30, res=1, vals=2)
z <- rast(xmin=-80, xmax=-30, ymax=50, ymin=20, res=1, vals=3)

m1 <- mosaic(x, y, z)

m2 <- mosaic(z, y, x)

# with many SpatRasters, make a SpatRasterCollection from a list
rlist <- list(x, y, z)
rsrc <- sprc(rlist)

m <- mosaic(rsrc)

Find and remove geometries that are NA

Description

Find geometries that are NA; or remove geometries and/or records that are NA.

Usage

## S4 method for signature 'SpatVector'
is.na(x)

## S4 method for signature 'SpatVector'
na.omit(object, field=NA, geom=FALSE)

Arguments

x

SpatVector

object

SpatVector

field

character or NA. If NA, missing values in the attributes are ignored. Other values are either one or more field (variable) names, or "" to consider all fields

geom

logical. If TRUE empty geometries are removed

Value

SpatVector

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
v$test <- c(1,2,NA)
nrow(v)
x <- na.omit(v, "test")
nrow(x)

Set the NA flag

Description

The main purpose of this method is to allow correct reading of a SpatRaster that is based on a file that has an incorrect NA flag. The file is not changed, but flagged value is set to NA when values are read from the file ("lazy evaluation"). In contrast, if the values are in memory the change is made immediately.

To change values, it is generally better to use classify

Usage

## S4 method for signature 'SpatRaster'
NAflag(x)

## S4 replacement method for signature 'SpatRaster'
NAflag(x)<-value

Arguments

x

SpatRaster

value

numeric. The value to be interpreted as NA; set this before reading the values from the file. This can be a single value, or multiple values, one for each data source (file / subdataset)

Value

none or numeric

See Also

classify

Examples

s <- rast(system.file("ex/logo.tif", package="terra"))[[1]]   
NAflag(s) <- 255
plot(s)
NAflag(s)

Names of Spat* objects

Description

Get or set the names of the layers of a SpatRaster or the attributes of a SpatVector.

See set.names for in-place setting of names.

Usage

## S4 method for signature 'SpatRaster'
names(x)

## S4 replacement method for signature 'SpatRaster'
names(x)<-value

## S4 method for signature 'SpatRasterDataset'
names(x)

## S4 replacement method for signature 'SpatRasterDataset'
names(x)<-value

## S4 method for signature 'SpatVector'
names(x)

## S4 replacement method for signature 'SpatVector'
names(x)<-value

Arguments

x

SpatRaster, SpatRasterDataset, or SpatVector

value

character (vector)

Value

character

Note

terra enforces neither unique nor valid names. See make.unique to create unique names and make.names to make syntactically valid names.

Examples

s <- rast(ncols=5, nrows=5, nlyrs=3)
nlyr(s)
names(s)
names(s) <- c("a", "b", "c")
names(s)

# SpatVector names
f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
names(v)
names(v) <- paste0(substr(names(v), 1, 2), "_", 1:ncol(v))
names(v)

nearby geometries

Description

Identify geometries that are near to each other. Either get the index of all geometries within a certain distance, or the k nearest neighbors, or (with nearest) get the nearest points between two geometries.

Usage

## S4 method for signature 'SpatVector'
nearby(x, y=NULL, distance=0, k=1, centroids=TRUE, symmetrical=TRUE)

## S4 method for signature 'SpatVector'
nearest(x, y, pairs=FALSE, centroids=TRUE, lines=FALSE)

Arguments

x

SpatVector

y

SpatVector or NULL

distance

numeric. maximum distance

k

positive integer. number of neighbors. Ignored if distance > 0

centroids

logical. Should the centroids of polygons be used?

symmetrical

logical. If TRUE, a near pair is only included once. That is, if geometry 1 is near to geometry 3, the implied nearness between 3 and 1 is not reported. Ignored if k neighbors are returned

pairs

logical. If TRUE pairwise nearest points are returned (only relevant when using at least one SpatVector of lines or polygons

lines

logical. If TRUE lines between the nearest points instead of (the nearest) points

Value

matrix

See Also

relate, adjacent

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
nearby(v, distance=12000)

normalize vector data that crosses the dateline

Description

Normalize the longitude of geometries, move them if they are outside of the -180 to 180 degrees range.

Usage

## S4 method for signature 'SpatVector'
normalize.longitude(x)

Arguments

x

SpatVector

Value

SpatVector

See Also

rotate for SpatRaster

Examples

p <- vect("POLYGON ((120 10, 230 75, 230 -75, 120 10))")
normalize.longitude(p)

North arrow

Description

Add a (North) arrow to a map

Usage

north(xy=NULL, type=1, label="N", angle=0, d, head=0.1, xpd=TRUE, ...)

Arguments

xy

numeric. x and y coordinate to place the arrow. It can also be one of following character values: "bottomleft", "bottom", "bottomright", topleft", "top", "topright", "left", "right", or NULL

type

integer between 1 and 12, or a character (unicode) representation of a right pointing arrow such as "\u27A9"

label

character, to be printed near the arrow

angle

numeric. The angle of the arrow in degrees

d

numeric. Distance covered by the arrow in plot coordinates. Only applies to type=1

head

numeric. The size of the arrow "head", for type=1

xpd

logical. If TRUE, the scale bar or arrow can be outside the plot area

...

graphical arguments to be passed to other methods

Value

none

See Also

sbar, plot, inset

Examples

f <- system.file("ex/meuse.tif", package="terra")
r <- rast(f)
plot(r)
north()
north(c(178550, 332500), d=250)

## Not run: 
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
plot(r, type="interval")
sbar(15, c(6.3, 50), type="bar", below="km", label=c(0,7.5,15), cex=.8)
north(type=3, cex=.8)
north(xy=c(6.7, 49.9), type=2, angle=45, label="NE")
north(xy=c(6.6, 49.7), type=5, cex=1.25)
north(xy=c(5.5, 49.6), type=9)
north(d=.05, xy=c(5.5, 50), angle=180, label="S", lwd=2, col="blue")


## all arrows
r <- rast(res=10)
values(r) <- 1
plot(r, col="white", axes=FALSE, legend=FALSE, mar=c(0,0,0,0), reset=TRUE)
for (i in 1:12) {
	x = -200+i*30
	north(xy=cbind(x,30), type=i)
	text(x, -20, i, xpd=TRUE)
}


## End(Not run)

is not NA

Description

Shortcut method to avoid the two-step !is.na(x)

Usage

## S4 method for signature 'SpatRaster'
not.na(x, falseNA, filename="", ...)

Arguments

x

SpatRaster

falseNA

logical. Should the result be TRUE, NA instead of TRUE, FALSE?

filename

character. Output filename

...

additional arguments for writing files as in writeRaster

Value

SpatRaster

See Also

Compare-methods

Examples

r <- rast(ncols=10, nrows=10, vals=1)
r[10:20] <- NA
x <- not.na(r)

Options

Description

Get or set general options.

Usage

terraOptions(..., print=TRUE)

Arguments

...

option names and values (see Details). Or missing, to get or show the current options

print

logical. If TRUE the option names and values are printed

Details

The following options are available.

memfrac - value between 0 and 0.9 (larger values give a warning). The fraction of RAM that may be used by the program.

memmin - if memory required is below this threshold (in GB), the memory is assumed to be available. Otherwise, terra checks if it is available.

memmax - the maximum amount of RAM (in GB) that terra is allowed to use when processing a raster dataset. Should be less than what is detected (see mem_info), and higher values are ignored. Set it to a negative number or NA to not set this option. terraOptions only shows the value of memmax if it is set.

tempdir - directory where temporary files are written. The default what is returned by tempdir().

datatype - default data type. See writeRaster

todisk - logical. If TRUE write all raster data to disk (temp file if no file name is specified). For debugging.

progress - non-negative integer. A progress bar is shown if the number of chunks in which the data is processed is larger than this number. No progress bar is shown if the value is zero

verbose - logical. If TRUE debugging info is printed for some functions

Value

list. Invisibly if print=TRUE

Note

It is possible to set your own default options in "etc/.Rprofile.site" of your R installation like this

options(terra_default=list(tempdir="d:/temp", memfrac=.4))

But that may not be a good practice. It is clearer to set your favorite options at the beginning of each script.

Examples

terraOptions()
terraOptions(memfrac=0.5, tempdir = "c:/temp")
terraOptions(progress=10)
terraOptions()

Origin

Description

Get or set the coordinates of the point of origin of a SpatRaster. This is the point closest to (0, 0) that you could get if you moved towards that point in steps of the x and y resolution.

Usage

## S4 method for signature 'SpatRaster'
origin(x)

## S4 replacement method for signature 'SpatRaster'
origin(x)<-value

Arguments

x

SpatRaster

value

numeric vector of length 1 or 2

Value

A vector of two numbers (x and y coordinates)

Examples

r <- rast(xmin=-0.5, xmax = 9.5, ncols=10)
origin(r)
origin(r) <- c(0,0)
r

Pairs plot (matrix of scatterplots)

Description

Pair plots of layers in a SpatRaster. This is a wrapper around graphics function pairs.

Usage

## S4 method for signature 'SpatRaster'
pairs(x, hist=TRUE, cor=TRUE, use="pairwise.complete.obs", maxcells=100000, ...)

Arguments

x

SpatRaster

hist

logical. If TRUE a histogram of the values is shown on the diagonal

cor

logical. If TRUE the correlation coefficient is shown in the upper panels

use

argument passed to the cor function

maxcells

integer. Number of pixels to sample from each layer of a large SpatRaster

...

additional arguments (graphical parameters)

See Also

boxplot, hist

Examples

r <-rast(system.file("ex/elev.tif", package="terra"))
s <- c(r, 1/r, sqrt(r))
names(s) <- c("elevation", "inverse", "sqrt") 
pairs(s)

# to make indvidual histograms:
hist(r)
# or scatter plots:
plot(s[[1]], s[[2]])

Map panel

Description

Show multiple maps that share a single legend.

Usage

## S4 method for signature 'SpatRaster'
panel(x, main, loc.main="topleft", nc, nr, maxnl=16, 
	maxcell=500000, box=FALSE, pax=list(), plg=list(), range=NULL, ...)

Arguments

x

SpatRaster

main

character. Main plot titles (one for each layer to be plotted). You can use arguments cex.main, font.main, col.main to change the appearance

loc.main

numeric of character to set the location of the main title. Either two coordinates, or a character value such as "topleft")

nc

positive integer. Optional. The number of columns to divide the plotting device in (when plotting multiple layers)

nr

positive integer. Optional. The number of rows to divide the plotting device in (when plotting multiple layers)

maxnl

positive integer. Maximum number of layers to plot (for a multi-layer object)

maxcell

positive integer. Maximum number of cells to use for the plot

box

logical. Should a box be drawn around the map?

plg

see plot

pax

see plot

range

numeric. minimum and maximum values to be used for the continuous legend

...

arguments passed to plot("SpatRaster", "numeric") and additional graphical arguments

See Also

plot and see rasterVis::levelplot and tidyterra::autoplot for more sophisticated panel plots.

Examples

r <- rast(system.file("ex/elev.tif", package="terra"))
v <- vect(system.file("ex/lux.shp", package="terra"))
x <- c(r, r/2, r*2, r)
names(x) <- paste0("(", LETTERS[1:4], ")")
panel(x)
panel(x, fun=\()lines(v), loc.main="topright")

Detect patches (clumps) of cells

Description

Detect patches (clumps). Patches are groups of cells that are surrounded by cells that are NA. Set zeroAsNA to TRUE to also identify patches separated by cells with values of zero.

Usage

## S4 method for signature 'SpatRaster'
patches(x, directions=4, zeroAsNA=FALSE, allowGaps=TRUE, filename="", ...)

Arguments

x

SpatRaster

directions

integer indicating which cells are considered adjacent. Should be 8 (Queen's case) or 4 (Rook's case)

zeroAsNA

logical. If TRUE treat cells that are zero as if they were NA

allowGaps

logical. If TRUE there may be gaps in the patch IDs (e.g. you may have patch IDs 1, 2, 3 and 5, but not 4). If it is FALSE, these numbers will be recoded from 1 to the number of patches (4 in this example)

filename

character. Output filename

...

options for writing files as in writeRaster

Value

SpatRaster. Cell values are patch numbers

See Also

focal, boundaries

Examples

r <- rast(nrows=18, ncols=36, xmin=0)
r[1:2, 5:8] <- 1
r[5:8, 2:6] <- 1
r[7:12, 22:36] <- 1
r[15:16, 18:29] <- 1
p <- patches(r)

# zero as background instead of NA
r <- rast(nrows=10, ncols=10, xmin=0, vals=0)
r[3, 3] <- 10
r[4, 4] <- 10
r[5, 5:8] <- 12
r[6, 6:9] <- 12

# treat zeros as NA

p4 <- patches(r, zeroAsNA=TRUE)
p8 <- patches(r, 8, zeroAsNA=TRUE)

### patches for different values
# remove zeros manually
rr <- classify(r, cbind(0, NA))

# make layers for each value
s <- segregate(rr, keep=TRUE, other=NA)
p <- patches(s)


### patch ID values are not guaranteed to be consecutive
r <- rast(nrows=5, ncols=10, xmin=0)
set.seed(0)
values(r)<- round(runif(ncell(r))*0.7)
rp <- patches(r, directions=8, zeroAsNA=TRUE) 
plot(rp, type="classes"); text(rp)

## unless you set allowGaps=FALSE
rp <- patches(r, directions=8, zeroAsNA=TRUE, allowGaps=FALSE) 
plot(rp, type="classes"); text(rp)

### use zonal to remove small patches 
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
x <- classify(r, cbind(-Inf, 400, NA))
y <- patches(x)
# remove patches smaller than 100 ha
rz <- zonal(cellSize(y, unit="ha"), y, sum, as.raster=TRUE)
s <- ifel(rz < 250, NA, y)

Perimeter or length

Description

This method returns the length of lines or the perimeter of polygons.

When the crs is not longitude/latitude, you may get more accurate results by first unprojecting the SpatVector (you can use project to transform the crs to longitude/latitude)

Usage

## S4 method for signature 'SpatVector'
perim(x)

Arguments

x

SpatVector

Value

numeric (m)

Examples

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)
perim(v)

Perspective plot

Description

Perspective plot of a SpatRaster. This is an implementation of a generic function in the graphics package.

Usage

## S4 method for signature 'SpatRaster'
persp(x, maxcells=100000, ...)

Arguments

x

SpatRaster. Only the first layer is used

maxcells

integer > 0. Maximum number of cells to use for the plot. If maxpixels < ncell(x), spatSample(method="regular") is used before plotting

...

Any argument that can be passed to persp (graphics package)

See Also

persp, contour, plot

Examples

r <- rast(system.file("ex/elev.tif", package="terra"))
persp(r)

Plot with leaflet

Description

Plot the values of a SpatRaster or SpatVector to make an interactive leaflet map that is displayed in a browser.

Usage

## S4 method for signature 'SpatRaster'
plet(x, y=1, col, alpha=0.8, main=names(x), tiles=NULL, 
   wrap=TRUE, maxcell=500000, legend="bottomright", 
   shared=FALSE, panel=FALSE, collapse=TRUE, map=NULL) 


## S4 method for signature 'SpatVector'
plet(x, y="", col,fill=0.2, main=y, cex=1, lwd=2, 
	border="black", alpha=1, popup=TRUE, label=FALSE, split=FALSE,
	tiles=c("Streets", "Esri.WorldImagery", "OpenTopoMap"), 
	wrap=TRUE, legend="bottomright", collapse=FALSE, type=NULL, breaks=NULL,
	breakby="eqint", sort=TRUE, decreasing=FALSE, map=NULL, ...)


## S4 method for signature 'SpatVectorCollection'
plet(x, col, fill=0, cex=1, lwd=2, border="black", alpha=1, popup=TRUE, 
   label=FALSE, tiles=c("Streets", "Esri.WorldImagery", "OpenTopoMap"), wrap=TRUE,
   legend="bottomright", collapse=FALSE, map=NULL)


## S4 method for signature 'leaflet'
lines(x, y, col, lwd=2, alpha=1, ...)

## S4 method for signature 'leaflet'
points(x, y, col, cex=1, alpha=1, popup=FALSE, ...)

Arguments

x

SpatRaster, SpatVector, or leaflet object

y

missing, or positive integer, or character (variable or layer name) indicating the layer(s) to be plotted. If x is a SpatRater, you can select multiple layers

col

character. Vector of colors or color generating function

alpha

Number between 0 and 1 to set the transparency for lines (0 is transparent, 1 is opaque)

fill

Number between 0 and 1 to set the transparency for polygon areas (0 is transparent, 1 is opaque)

tiles

character or NULL. Names of background tile providers

wrap

logical. if TRUE, tiles wrap around

maxcell

positive integer. Maximum number of cells to use for the plot

legend

character to indicate the legend position ("bottomleft", "bottomright", "topleft" or "topright") or NULL to suppress the legend

main

character. Title for the legend. The length should be 1 if x is a SpatVector and length nlyr(x) if x is a SpatVector

shared

logical. Should the legend be the same for all rasters (if multiple layers of SpatRaster x are mapped)

map

leaflet object

...

additional arguments for drawing points, lines, or polygons passed on the the relevant leaflet function

border

character. Color for the polygon borders

collapse

logical. Should the layers "control" panel be collapsed?

split

logical. If TRUE a check-box is created to toggle each value in y (If x is a SpatVector)

cex

numeric. point size magnifier. See par

lwd

numeric, line-width. See par

popup

logical. Should pop-ups be created?

label

logical. Should mouse-over labels be added?

panel

logical. Should SpatRaster layers be shown as a panel"

type

character. Type of map/legend. One of "classes", or "interval". If not specified, the type is chosen based on the data. Use "" to suppress the legend

breaks

numeric. Either a single number to indicate the number of breaks desired, or the actual breaks. When providing this argument, the default legend becomes "interval"

breakby

character or function. Either "eqint" for equal interval breaks, "cases" for equal quantile breaks. If a function is supplied it should take a single argument (a vector of values) and create groups

sort

logical. If TRUE legends with character values are sorted. You can also supply a vector of the unique values, in the order in which you want them to appear in the legend

decreasing

logical. If TRUE, legends are sorted in decreasing order

See Also

plot

Examples

## Not run: 
if (require(leaflet) && (packageVersion("leaflet") > "2.1.1")) {

v <- vect(system.file("ex/lux.shp", package="terra"))
p <- spatSample(as.polygons(v, ext=T), 30)
values(p) = data.frame(id=11:40, name=letters[1:30])

m <- plet(v, "NAME_1", tiles="", border="blue")
m <- points(m, p, col="red", cex=2, popup=T)
lines(m, v, lwd=1, col="white")

plet(v, "NAME_1", split=TRUE, alpha=.2) |> 
  points(p, col="gray", cex=2, popup=TRUE,
  	clusterOptions = markerClusterOptions())

s <- svc(v, p)
names(s) <- c("the polys", "set of points")
plet(s, col=c("red", "blue"), lwd=1)


r <- rast(system.file("ex/elev.tif", package="terra"))
plet(r, main="Hi\nthere") |> lines(v, lwd=1)

plet(r, tiles="Streets") |> lines(v, lwd=2, col="blue")

x <- c(r, 50*classify(r, 5))
names(x) <- c("first", "second")

# each their own legend
plet(x, 1:2, tiles="Streets", collapse=FALSE) |> lines(v, lwd=2, col="blue")

# shared legend
plet(x, 1:2, tiles="Streets", shared=TRUE, collapse=FALSE) |> lines(v, lwd=2, col="blue")

}
## End(Not run)

Make a map

Description

Plot the values of a SpatRaster or SpatVector to make a map.

See points, lines or polys to add a SpatVector to an existing map (or use argument add=TRUE).

There is a separate help file for plotting a SpatGraticule or SpatExtent.

Usage

## S4 method for signature 'SpatRaster,numeric'
plot(x, y=1, col, type=NULL, mar=NULL, legend=TRUE, axes=!add, plg=list(), pax=list(), 
    maxcell=500000, smooth=FALSE, range=NULL, levels=NULL, all_levels=FALSE,
	breaks=NULL, breakby="eqint", fun=NULL, colNA=NULL, alpha=NULL, sort=FALSE, 
	decreasing=FALSE, grid=FALSE, ext=NULL, reset=FALSE, add=FALSE, buffer=FALSE, 
	background=NULL, box=axes, clip=TRUE, ...)

## S4 method for signature 'SpatRaster,missing'
plot(x, y, main, mar=NULL, nc, nr, maxnl=16, maxcell=500000, add=FALSE, ...)

## S4 method for signature 'SpatRaster,character'
plot(x, y, ...)

## S4 method for signature 'SpatVector,character'
plot(x, y, col=NULL, type=NULL, mar=NULL, add=FALSE, legend=TRUE, axes=!add, 
    main="", buffer=TRUE, background=NULL, grid=FALSE, ext=NULL, sort=TRUE, 
	decreasing=FALSE, plg=list(), pax=list(), nr, nc, colNA=NA, alpha=NULL, 
	box=axes, clip=TRUE, ...)

## S4 method for signature 'SpatVector,numeric'
plot(x, y, ...)

## S4 method for signature 'SpatVector,missing'
plot(x, y, values=NULL, ...)

Arguments

x

SpatRaster or SpatVector

y

missing or positive integer or name indicating the layer(s) to be plotted

col

character. Colors. The default is rev(grDevices::terrain.colors(50)). If x is a SpatRaster, it can also be a data.frame with two columns (value, color) to get a "classes" type legend or with three columns (from, to, color) to get an "interval" type legend

type

character. Type of map/legend. One of "continuous", "classes", or "interval". If not specified, the type is chosen based on the data

mar

numeric vector of length 4 to set the margins of the plot (to make space for the legend). The default is (3.1, 3.1, 2.1, 7.1) for a single plot with a legend and (3.1, 3.1, 2.1, 2.1) otherwise. The default for a RGB raster is 0. Use mar=NA to not set the margins

legend

logical or character. If not FALSE a legend is drawn. The character value can be used to indicate where the legend is to be drawn. For example "topright" or "bottomleft". Use plg for more refined placement. Not supported for continuous legends (the default for raster data)

axes

logical. Draw axes?

buffer

logical. If TRUE the plotting area is made slightly larger than the extent of x

background

background color. Default is no color (white)

box

logical. Should a box be drawn around the map?

clip

logical. Should the axes be clipped to the extent of x?

plg

list with parameters for drawing the legend. For the classes and interval type legend see the arguments for legend. For example x and y can be used to place the legend. You can also use keywords such as "topleft" and "bottomright" to place the legend at these locations inside the map rectangle.

Some of these do not apply to a continuous legend, or they behave a little differently. For example, only the placement keywords "left", "right", "top", and "bottom" are recognized; and when using these keywords, the legend is placed outside of the map rectangle. Additional parameters for continuous legends include:

  • digits to set the number of digits to print after the decimal point. size to change the height and/or width; the defaults are c(1,1), negative values for size flip the order of the legend.

  • at to set the location of the tic-marks

  • tic One of these partially matched values: "through", "in", "out", or "none", to choose a tic-mark placement/length that is different from the default "through and out".

pax

list with parameters for drawing axes. See the arguments for axis. Arguments side, tick and lab can be used to indicate for which of the four axes to draw a line (side), tick-mark, and/or the tick-mark labels. The default is c(1:4) for side and 1:2 for the other two. If side is changed the other two default to that value. Logical argument retro can be used to use a sexagesimal notation for the labels (degrees/minutes/hemisphere) instead of the standard decimal notation

maxcell

positive integer. Maximum number of cells to use for the plot

smooth

logical. If TRUE the cell values are smoothed (only if a continuous legend is used)

range

numeric. minimum and maximum values to be used for the continuous legend

levels

character. labels for the legend when type="classes"

all_levels

logical. If TRUE, the legend shows all levels of a categorical raster, even if they are not present in the data

breaks

numeric. Either a single number to indicate the number of breaks desired, or the actual breaks. When providing this argument, the default legend becomes "interval"

breakby

character or function. Either "eqint" for equal interval breaks, "cases" for equal quantile breaks. If a function is supplied, it should take a single argument (a vector of values) and create groups

fun

function to be called after plotting each SpatRaster layer to add something to each map (such as text, legend, lines). For example, with SpatVector v, you could do fun=function() lines(v). The function may have one argument, representing the layer that is plotted (1 to the number of layers)

colNA

character. color for the NA values

alpha

Either a single numeric between 0 and 1 to set the transparency for all colors (0 is transparent, 1 is opaque) or a SpatRaster with values between 0 and 1 to set the transparency by cell. To set the transparency for a given color, set it to the colors directly

sort

logical. If TRUE legends with categorical values are sorted. If x is a SpatVector you can also supply a vector of the unique values, in the order in which you want them to appear in the legend

decreasing

logical. If TRUE, legends are sorted in decreasing order

grid

logical. If TRUE grid lines are drawn. Their properties such as type and color can be set with the pax argument

nc

positive integer. Optional. The number of columns to divide the plotting device in (when plotting multiple layers)

nr

positive integer. Optional. The number of rows to divide the plotting device in (when plotting multiple layers)

main

character. Main plot titles (one for each layer to be plotted). You can use arguments cex.main, font.main, col.main to change the appearance; and loc.main to change the location of the main title (either two coordinates, or a character value such as "topleft")

maxnl

positive integer. Maximum number of layers to plot (for a multi-layer object)

add

logical. If TRUE add the object to the current plot

ext

SpatExtent. Can be use instead of xlim and ylim to set the extent of the plot

reset

logical. If TRUE add the margins (see argument mar) are reset to what they were before calling plot; doing so may affect the display of additional objects that are added to the map (e.g. with lines)

values

Either a vector with values to be used for plotting or a two-column data.frame, where the first column matches a variable in x and the second column has the values to be plotted

...

arguments passed to plot("SpatRaster", "numeric") and additional graphical arguments

See Also

points, lines, polys, image

Add map elements: text, sbar, north, add_legend, add_box

plot a SpatGraticule or SpatExtent,

multiple layers: plotRGB, panel

other plot types: scatterplot, hist, pairs, density, persp, contour, boxplot, barplot

Examples

## SpatRaster
f <- system.file("ex/elev.tif", package="terra") 
r <- rast(f)
plot(r)

plot(r, type="interval")

e <- c(6.37, 6.41, 49.9, 50.1)
plot(r, plg=list(ext=e, title="Legend\nTitle", title.cex=0.9), 
		pax=list(side=1:4, retro=TRUE))
north(cbind(5.8, 50.1))	

d <- classify(r, c(100,200,300,400,500,600))
plot(d, type="classes")

plot(d, type="interval", breaks=1:5) 
plot(d, type="interval", breaks=c(1,4,5), plg=list(legend=c("1-4", "4-5"))) 
plot(d, type="classes", xlim=c(5.6, 6.6), 
	plg=list(legend=c("Mr", "Xx", "As", "Zx", "Bb"), x="bottomleft"))


x <- trunc(r/200)
levels(x) <- data.frame(id=0:2, element=c("earth", "wind", "fire"))
plot(x, plg=list(x="topright"),mar=c(2,2,2,2))

oldpar <- par(no.readonly=TRUE)

# two plots with the same legend
dev.new(width=6, height=4, noRStudioGD = TRUE)
par(mfrow=c(1,2))
plot(r, range=c(50,600), mar=c(1,1,1,4))
plot(r/2, range=c(50,600), mar=c(1,1,1,4))

# as we only need one legend:
par(mfrow=c(1,2))
plot(r, range=c(50,600), mar=c(2, 2, 2, 2), plg=list(size=0.9, cex=.8), 
	pax=list(side=1:2, cex.axis=.6), box=FALSE)
#text(182500, 335000, "Two maps, one plot", xpd=NA)
plot(r/2, range=c(50,600), mar=c(2, 2, 2, 2), legend=FALSE, 
	pax=list(side=c(1,4), cex.axis=.6), box=FALSE)

par(oldpar)

# multi-layer with RGB
s <- rast(system.file("ex/logo.tif", package="terra"))   
s
plot(s)
# remove RGB
plot(s*1)
# or use layers
plot(s, 1)
plot(s, 1:3)

# fix legend by linking values and colors

x = rast(nrows = 2, ncols = 2, vals=1)
y = rast(nrows = 2, ncols = 2, vals=c(1,2,2,1))
cols = data.frame(id=1:2, col=c("red", "blue"))
plot(c(x,y), col=cols)

r  = rast(nrows=10, ncols=10, vals=1:100)
dr = data.frame(from=c(5,33,66,150), to=c(33, 66, 95,200), col=rainbow(4))
plot(r, col=dr)

### SpatVector 

f <- system.file("ex/lux.shp", package="terra")
v <- vect(f)

plot(v)

plot(v, "NAME_2", col=rainbow(12), border=c("gray", "blue"), lwd=3)

plot(v, 2, pax=list(side=1:2), plg=list(x=6.16, y=50.17, cex=.8), xlim=c(5.7, 6.7))

plot(v, 4, pax=list(side=1:2), plg=list(x=6.2, y=50.2, ncol=2), main="", box=FALSE)
 
plot(v, 1, plg=list(x=5.8, y=49.37, horiz=TRUE, cex=1.1), main="", mar=c(5,2,0.5,0.5))

plot(v, density=1:12, angle=seq(18, 360, 20), col=rainbow(12))


plot(v, "AREA", type="interval", breaks=3, mar=c(3.1, 3.1, 2.1, 3.1),
  plg=list(x="topright"), main="")

plot(v, "AREA", type="interval", breaks=c(0,200,250,350), 
	mar=c(2,2,2,2), xlim=c(5.7, 6.75),
	plg=list(legend=c("<200", "200-250", ">250"), cex=1, bty="o", 
	x=6.3, y=50.15, box.lwd=2, bg="light yellow", title="My legend"))

Plot a SpatExtent

Description

Plot a SpatExtent. Use lines to add a SpatExtent to an existing map.

See plot for plotting other object types.

Usage

## S4 method for signature 'SpatExtent,missing'
plot(x, y, ...)

Arguments

x

SpatExtent

y

missing

...

additional graphical arguments for lines

See Also

plot

Examples

r <- rast()
plot(ext(r))

Plot a graticule

Description

Plot a SpatGraticule. You can create a SpatGraticule with graticule.

Usage

## S4 method for signature 'SpatGraticule,missing'
plot(x, y, background=NULL, col="black", mar=NULL, labels=TRUE,
	retro=FALSE, lab.loc=c(1,1), lab.lon=NULL, lab.lat=NULL, lab.cex=0.65, 
	lab.col="black", off.lat=0.25, off.lon=0.25, box=FALSE, box.col="black",
	add=FALSE, ...)

Arguments

x

SpatRaster or SpatVector

y

missing or positive integer or name indicating the layer(s) to be plotted

background

background color. If NULL, no background is drawn

mar

numeric vector of length 4 to set the margins of the plot. To make space for the legend you may use something like c(3.1, 3.1, 2.1, 7.1). To fill the plotting canvas, you can use c(0,0,0,0. Use NA to not set the margins

col

character. Color for the graticule lines

labels

logical. If TRUE, show graticule labels

retro

logical. If TRUE, show "retro" instead of decimal labels with the graticule

lab.loc

numeric. The first number indicates where the longitude graticule labels should be drawn (1=bottom, 2=top, NA=not drawn, any other number=top and bottom). The second number indicates where the latitude graticule labels should be drawn (1=left, 2=right, NA=not drawn, any other number=left and right)

lab.lon

positive integers between 1 and the number of labels, indicating which longitude graticule labels should be included

lab.lat

positive integers between 1 and the number of labels, indicating which latitude graticule labels should be included

lab.cex

double. size of the label font

lab.col

character. color of the labels

off.lon

numeric. longitude labels offset

off.lat

numeric. latitude labels offset

box

logical. If TRUE, the outer lines of the graticule are drawn on top with a sold line lty=1

box.col

character. color of the outer lines of the graticule if box=TRUE

add

logical. Add the graticule to the current plot?

...

additional graphical arguments passed to lines

See Also

graticule, plot, points, lines, polys, image, scatterplot, scale bar: sbar, north arrow: north

Examples

g <- graticule(60, 30, crs="+proj=robin")

plot(g, background="azure", col="red", lty=2, box=TRUE)
plot(g, background="azure", col="light gray", lab.loc=c(1,2), 
		lab.lon=c(2,4,6), lab.lat=3:5, lty=3, retro=TRUE)

Red-Green-Blue plot of a multi-layered SpatRaster

Description

Make a Red-Green-Blue plot based on three layers in a SpatRaster. The layers (sometimes referred to as "bands" because they may represent different bandwidths in the electromagnetic spectrum) are combined such that they represent the red, green and blue channel. This function can be used to make "true" (or "false") color images from Landsat and other multi-spectral satellite images.

Note that the margins of the plot are set to zero (no axes or titles are visible) but can be set with the mar argument.

An alternative way to plot RGB images is to first use colorize to create a single layer SpatRaster with a color-table and then use plot.

Usage

## S4 method for signature 'SpatRaster'
plotRGB(x, r=1, g=2, b=3, a=NULL, scale=NULL, mar=0, 
		stretch=NULL, smooth=TRUE, colNA="white", alpha=NULL, bgalpha=NULL, 
		zlim=NULL, zcol=FALSE, axes=FALSE ,...)

Arguments

x

SpatRaster

r

integer between 1 and nlyr(x). Layer to use as the Red channel

g

integer between 1 and nlyr(x). Layer to use as the Green channel

b

integer between 1 and nlyr(x). Layer to use as the Blue channel

a

NULL or integer between 1 and nlyr(x). Layer to use as the alpha (transparency) channel. If not NULL, argument alpha is ignored

scale

integer. Maximum (possible) value in the three channels. Defaults to 255 or to the maximum value of x if that is known and larger than 255

mar

numeric vector recycled to length 4 to set the margins of the plot. Use mar=NULL or mar=NA to not set the margins

stretch

character. Option to stretch the values to increase contrast: "lin" (linear) or "hist" (histogram). The linear stretch uses stretch with arguments minq=0.02 and maxq=0.98

smooth

logical. If TRUE, smooth the image when drawing to get the appearance of a higher spatial resolution

colNA

color. The color used for cells that have NA values

alpha

transparency. Integer between 0 (transparent) and 255 (opaque)

bgalpha

Background transparency. Integer between 0 (transparent) and 255 (opaque)

zlim

numeric vector of length 2. Range of values to plot (optional). If this is set, and stretch="lin" is used, then the values are stretched within the range of zlim. This allows creating consistent coloring between SpatRasters with different cell-value ranges, even when stretching the colors for improved contrast

zcol

logical. If TRUE the values outside the range of zlim get the color of the extremes of the range. Otherwise, the values outside the zlim range get the color of NA values (see argument "colNA")

axes

logical. If TRUE axes are drawn (and arguments such as main="title" will be honored)

...

graphical parameters as in plot<SpatRaster-method>

See Also

plot, colorize, RGB

Examples

b <- rast(system.file("ex/logo.tif", package="terra"))   
plotRGB(b)
plotRGB(b, mar=2)
plotRGB(b, 3, 2, 1)

b[1000:2000] <- NA
plotRGB(b, 3, 2, 1, stretch="hist")

SpatRaster PCA with prcomp

Description

Compute principal components for SpatRaster layers. This method may be preferred to princomp for its greater numerical accuracy. However, it is slower and for very large rasters it can only be done with a sample. This may be good enough but see princomp if you want to use all values. Unlike princomp, in this method the sample variances are used with n-1 as the denominator.

Usage

## S4 method for signature 'SpatRaster'
prcomp(x, retx=TRUE, center=TRUE, scale.=FALSE, 
		tol=NULL, rank.=NULL, maxcell=Inf)

Arguments

x

SpatRaster

retx

a logical value indicating whether the rotated variables should be returned

center

a logical value indicating whether the variables should be shifted to be zero centered. Alternately, a vector of length equal the number of columns of x can be supplied. The value is passed to scale

scale.

a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. The default is FALSE for consistency with S, but in general scaling is advisable. Alternatively, a vector of length equal the number of columns of x can be supplied. The value is passed to scale

tol

a value indicating the magnitude below which components should be omitted. (Components are omitted if their standard deviations are less than or equal to tol times the standard deviation of the first component.) With the default null setting, no components are omitted (unless rank. is specified less than min(dim(x))). Other settings for tol could be tol = 0 or tol = sqrt(.Machine$double.eps), which would omit essentially constant components

rank.

optionally, a number specifying the maximal rank, i.e., maximal number of principal components to be used. Can be set as alternative or in addition to tol, useful notably when the desired rank is considerably smaller than the dimensions of the matrix

maxcell

positive integer. The maximum number of cells to be used. If this is smaller than ncell(x), a regular sample of x is used

Value

prcomp object

See Also

princomp, prcomp

Examples

f <- system.file("ex/logo.tif", package = "terra")
r <- rast(f)
pca <- prcomp(r)
x <- predict(r, pca)

# use "index" to get a subset of the components
p <- predict(r, pca, index=1:2)

Spatial model predictions

Description

Make a SpatRaster with predictions from a fitted model object (for example, obtained with glm or randomForest). The first argument is a SpatRaster object with the predictor variables. The names in the SpatRaster should exactly match those expected by the model. Any regression like model for which a predict method has been implemented (or can be implemented) can be used.

The method should work if the model's predict function returns a vector, matrix or data.frame (or a list that can be coerced to a data.frame). In other cases it may be necessary to provide a custom "predict" function that wraps the model's predict function to return the values in the required form. See the examples.

This approach of using model predictions is commonly used in remote sensing (for the classification of satellite images) and in ecology, for species distribution modeling.

Usage

## S4 method for signature 'SpatRaster'
predict(object, model, fun=predict, ..., const=NULL, na.rm=FALSE,
          index=NULL, cores=1, cpkgs=NULL, filename="", overwrite=FALSE, wopt=list())

Arguments

object

SpatRaster

model

fitted model of any class that has a "predict" method (or for which you can supply a similar method as fun argument. E.g. glm, gam, or randomForest

fun

function. The predict function that takes model as first argument. The default value is predict, but can be replaced with e.g. predict.se (depending on the type of model), or your own custom function

...

additional arguments for fun

const

data.frame. Can be used to add a constant value as a predictor variable so that you do not need to make a SpatRaster layer for it

na.rm

logical. If TRUE, cells with NA values in the any of the layers of x are removed from the computation (even if the NA cell is in a layer that is not used as a variable in the model). This option prevents errors with models that cannot handle NA values when makeing predictions. In most other cases this will not affect the output. However, there are some models that return predicted values even if some (or all) variables are NA

index

integer or character. Can be used to to select a subset of the model output variables

cores

positive integer. If cores > 1, a 'parallel' package cluster with that many cores is created and used

cpkgs

character. The package(s) that need to be loaded on the nodes to be able to run the model.predict function (see examples)

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

wopt

list with named options for writing files as in writeRaster

Value

SpatRaster

See Also

interpolate for spatial model prediction

Examples

logo <- rast(system.file("ex/logo.tif", package="terra"))   
names(logo) <- c("red", "green", "blue")
p <- matrix(c(48, 48, 48, 53, 50, 46, 54, 70, 84, 85, 74, 84, 95, 85, 
   66, 42, 26, 4, 19, 17, 7, 14, 26, 29, 39, 45, 51, 56, 46, 38, 31, 
   22, 34, 60, 70, 73, 63, 46, 43, 28), ncol=2)

a <- matrix(c(22, 33, 64, 85, 92, 94, 59, 27, 30, 64, 60, 33, 31, 9,
   99, 67, 15, 5, 4, 30, 8, 37, 42, 27, 19, 69, 60, 73, 3, 5, 21,
   37, 52, 70, 74, 9, 13, 4, 17, 47), ncol=2)

xy <- rbind