Package 'via' reference manual

Title:	Virtual Arrays
Description:	The base class 'VirtualArray' is defined, which acts as a wrapper around lists allowing users to fold arbitrary sequential data into n-dimensional, R-style virtual arrays. The derived 'XArray' class is defined to be used for homogeneous lists that contain a single class of objects. The 'RasterArray' and 'SfArray' classes enable the use of stacked spatial data instead of lists.
Authors:	Adam T. Kocsis [cre, aut] , Deutsche Forschungsgemeinschaft [fnd], FAU GeoZentrum Nordbayern [fnd]
Maintainer:	Adam T. Kocsis <[email protected]>
License:	CC BY 4.0
Version:	0.2.0
Built:	2024-11-06 03:27:02 UTC
Source:	https://github.com/adamkocsis/via

Indexing to extract subsets of a 'code VirtualArray'-class object

Description

Single bracket '[' refers to indices and names within the 'VirtualArray'-class object. Use double brackets to extract layers based on their names (in the @stack).

Usage

## S4 method for signature 'VirtualArray,ANY,ANY'
x[i, j, ..., drop = TRUE]
## S4 method for signature 'VirtualArray,ANY,ANY'
x[i, j, ..., drop = TRUE]

Arguments

`x`	An object from a `VirtualArray`-derived class.
`i`	subscript of the first dimension(rows) or vector-like subsetting.
`j`	subscript of the second dimension (columns).
`...`	subscript of additional dimensions.
`drop`	`logical` in case the result of subsetting is a single element, should the `VirtualArray`-derived wrapper be dropped?

Value

An object from either the same class as x or the class of its elements.

Examples

ex <- rastex()
# numeric subsetting
firstThree <- ex[1:3]
# character subsetting
second <- ex["d"]
# logical subsetting
subscript <- rep(FALSE, length(ex))
subscript[2] <- TRUE
second2 <- ex[subscript]
data(paleocoastlines)
present<- paleocoastlines["0", ]
allMargin <- paleocoastlines[, "margin"]

ex <- rastex()
# numeric subsetting
firstThree <- ex[1:3]
# character subsetting
second <- ex["d"]
# logical subsetting
subscript <- rep(FALSE, length(ex))
subscript[2] <- TRUE
second2 <- ex[subscript]
data(paleocoastlines)
present<- paleocoastlines["0", ]
allMargin <- paleocoastlines[, "margin"]

Indexing to extract the elements of a '`VirtualArray`'-derived class object.

Description

Double bracket '[[' refers to elements'/layers' name in the @stack of the 'VirtualArray'-derived object. Use single brackets to extract elements based on their position in the 'VirtualArray'.

Usage

## S4 method for signature 'VirtualArray,ANY,ANY'
x[[i, drop = TRUE]]
## S4 method for signature 'VirtualArray,ANY,ANY'
x[[i, drop = TRUE]]

Arguments

`x`	`VirtualArray`
`i`	subscript of the first dimension(rows) or vector-like subsetting.
`drop`	`logical` should the `VirtualArray` be dropped and the element be reduced to the element class?

Value

A VirtualArray-derived class object, or an object of the class that makes up the VirtualArray

Examples

data(exemplar)
# finds a layer
exemplar[["sample1"]]
# returns a stack
exemplar[[c("sample1", "sample2")]]
# replaces a layervalues, but not the attributes of the layer
exemplar2 <- exemplar
exemplar2[["sample1"]] <- exemplar2[["sample2"]]
# compare every value in the they are all the same
exemplar2[["sample1"]]$x == exemplar2[["sample2"]]$x
data(exemplar)
# finds a layer
exemplar[["sample1"]]
# returns a stack
exemplar[[c("sample1", "sample2")]]
# replaces a layervalues, but not the attributes of the layer
exemplar2 <- exemplar
exemplar2[["sample1"]] <- exemplar2[["sample2"]]
# compare every value in the they are all the same
exemplar2[["sample1"]]$x == exemplar2[["sample2"]]$x

Replace elements of '`VirtualArray`'-class objects.

Description

Double bracket '[[' refers to layers' name in the names of the @stack member of the 'VirtualArray'. Use single brackets to replace elements based on their position in the 'VirtualArray'-class object.

Usage

## S4 replacement method for signature 'VirtualArray,ANY'
x[[i]] <- value
## S4 replacement method for signature 'VirtualArray,ANY'
x[[i]] <- value

Arguments

`x`	Object from a class derived from `VirtualArray`.
`i`	subscript of layers to replace.
`value`	`character` vector.

Value

The function has no return value.

Replace layers in an object that is of a class derived from '`VirtualArray`'.

Description

Single bracket '[' refers to indices and names within the 'VirtualArray'-class object. Use double brackets to replace layers based on their names (in the @stack). Object types of the same kind class can be used to replace values in 'XArray'-class objects. 'SpatRaster'-class objects can be used to replace values in 'RasterArray'-class objects. Classes inheriting from 'sf' can be used with 'SfArray'-class objects.

Usage

## S4 replacement method for signature 'VirtualArray,ANY,ANY,logical'
x[i, j, ...] <- value

## S4 replacement method for signature 'RasterArray,ANY,ANY,SpatRaster'
x[i, j, ...] <- value

## S4 replacement method for signature 'SfcArray,ANY,ANY,sfc'
x[i, j, ...] <- value

## S4 replacement method for signature 'SfArray,ANY,ANY,sf'
x[i, j, ...] <- value
## S4 replacement method for signature 'VirtualArray,ANY,ANY,logical'
x[i, j, ...] <- value

## S4 replacement method for signature 'RasterArray,ANY,ANY,SpatRaster'
x[i, j, ...] <- value

## S4 replacement method for signature 'SfcArray,ANY,ANY,sfc'
x[i, j, ...] <- value

## S4 replacement method for signature 'SfArray,ANY,ANY,sf'
x[i, j, ...] <- value

Arguments

`x`	`VirtualArray`-class object.
`i`	subscript of the first dimension(rows) or vector-like subsetting.
`j`	subscript of the second dimension (columns).
`...`	subscript of additional dimensions.
`value`	A same class object as `x`.

Value

The function has no return value.

Examples

ex <- rastex() 
# replace third element with missing value
ex[3] <- NA
# duplicate first element and make it the second too
ex[2] <- ex[1]
ex

ex <- rastex() 
# replace third element with missing value
ex[3] <- NA
# duplicate first element and make it the second too
ex[2] <- ex[1]
ex

Aggregate raster cells in a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

## S4 method for signature 'RasterArray'
aggregate(x, ...)
## S4 method for signature 'RasterArray'
aggregate(x, ...)

Arguments

`x`	a `RasterArray`-class object.
`...`	arguments passed to the `aggregate` function.

Value

An aggregated RasterArray-class object.

Examples

library(terra)
ex <- rastex()
agg <- aggregate(ex, 30)
library(terra)
ex <- rastex()
agg <- aggregate(ex, 30)

Coerce into an `SfcArray` or `SfArray` object

Description

Coerce into an SfcArray or SfArray object

Coerce into an SfArray or SfcArray object

Usage

as.XArray(from)

## S4 method for signature 'SfcArray'
as.XArray(from)

## S4 method for signature 'SfArray'
as.XArray(from)

as.SfcArray(from)

## S4 method for signature 'XArray'
as.SfcArray(from)

## S4 method for signature 'SfArray'
as.SfcArray(from)

as.SfArray(from)

## S4 method for signature 'XArray'
as.SfArray(from)

## S4 method for signature 'SfcArray'
as.SfArray(from)
as.XArray(from)

## S4 method for signature 'SfcArray'
as.XArray(from)

## S4 method for signature 'SfArray'
as.XArray(from)

as.SfcArray(from)

## S4 method for signature 'XArray'
as.SfcArray(from)

## S4 method for signature 'SfArray'
as.SfcArray(from)

as.SfArray(from)

## S4 method for signature 'XArray'
as.SfArray(from)

## S4 method for signature 'SfcArray'
as.SfArray(from)

Arguments

from

Either a SfcArray, SfArray or XArray-class object

Value

Either a SfcArray, SfArray or XArray-class object

Combine a one-dimensional '`VirtualArray`'-class object with other objects

Description

NOTE: Sequences that start with an NA do not yet work.

Usage

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

Arguments

`x`	`VirtualArray` object to combine wit other objects.
`...`	additional objects to combine.

Value

A VirtualArray-class object.

Column names of two-dimensional '`VirtualArray`'-derived class object.

Description

Get or set the column names of two-dimensional 'VirtualArray'-derived class objects

Usage

## S4 method for signature 'VirtualArray'
colnames(x)

## S4 replacement method for signature 'VirtualArray'
colnames(x) <- value
## S4 method for signature 'VirtualArray'
colnames(x)

## S4 replacement method for signature 'VirtualArray'
colnames(x) <- value

Arguments

`x`	`VirtualArray`-derived class object.
`value`	`character` vector.

Value

A character vector of column names or NULL.

Examples

data(paleocoastlines)
colnames(paleocoastlines)
colnames(paleocoastlines) <- c("a", "b")
data(paleocoastlines)
colnames(paleocoastlines)
colnames(paleocoastlines) <- c("a", "b")

Cropping a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

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

Arguments

`x`	a `RasterArray` class object.
`y`	an `SpatExtent`-class object, or any object from which an extent object can be extracted (see Details)
`...`	arguments passed to the `crop` function.

Value

A cropped RasterArray-class object.

Examples

ex <- rastex()
# crop to a specific area
if(requireNamespace("terra", quietly=TRUE)){
 ext <- terra::ext(c(                
   xmin = 106.58,
   xmax = 157.82,
   ymin = -45.23,
   ymax = 1.14 
 )) 
 # cropping all 
 au<- crop(ex, ext)
}

ex <- rastex()
# crop to a specific area
if(requireNamespace("terra", quietly=TRUE)){
 ext <- terra::ext(c(                
   xmin = 106.58,
   xmax = 157.82,
   ymin = -45.23,
   ymax = 1.14 
 )) 
 # cropping all 
 au<- crop(ex, ext)
}

Dimensions of '`VirtualArray`'-derived class objects

Description

The function returns the dimensions of the array in which elements are organized.

Usage

## S4 method for signature 'VirtualArray'
dim(x)
## S4 method for signature 'VirtualArray'
dim(x)

Arguments

`x`	A `VirtualArray`-derived class object.

Value

A numeric vector.

Examples

data(exemplar)
dim(exemplar)
data(exemplar)
dim(exemplar)

Dimensions of layers in a '`VirtualArray`'-class object

Description

The funcion will return the dimensions 'SpatRaster'-class layers.

Usage

dimlayer(x, ...)

## S4 method for signature 'RasterArray'
dimlayer(x)
dimlayer(x, ...)

## S4 method for signature 'RasterArray'
dimlayer(x)

Arguments

`x`	A `VirtualArray` class object.
`...`	additional arguments passed to class-specific methods.

Value

A numeric vector with the number of rows and columns in the VirtualArrays.

Names of a multidimensional '`VirtualArray`'-derived class object.

Description

Get or set the dimnames of multidimensional VirtualArray-derived class object.

Usage

## S4 method for signature 'VirtualArray'
dimnames(x)

## S4 replacement method for signature 'VirtualArray'
dimnames(x) <- value
## S4 method for signature 'VirtualArray'
dimnames(x)

## S4 replacement method for signature 'VirtualArray'
dimnames(x) <- value

Arguments

`x`	`RasterArray` or `SfArray` object.
`value`	`character` vector.

Value

A list of character vectors or NULL.

Examples

ex <- rastex()
dimnames(ex)
data(paleocoastlines)
dimnames(paleocoastlines)
dimnames(paleocoastlines)[[2]] <- c("first", "second")
names(dimnames(paleocoastlines)) <- c("age", "type")
ex <- rastex()
dimnames(ex)
data(paleocoastlines)
dimnames(paleocoastlines)
dimnames(paleocoastlines)[[2]] <- c("first", "second")
names(dimnames(paleocoastlines)) <- c("age", "type")

Disaggregate raster cells in a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

## S4 method for signature 'RasterArray'
disagg(x, ...)
## S4 method for signature 'RasterArray'
disagg(x, ...)

Arguments

`x`	a `RasterArray` class object.
`...`	arguments passed to the `disagg` function.

Value

A disaggregated RasterArray class object.

Examples

ex <- rastex() 
disagg <- disagg(ex, 3)
ex <- rastex() 
disagg <- disagg(ex, 3)

Example '`XArray`'-class object

Description

A 'XArray'-class objects of data.frames, which were made from a single data.frame with random sampling. The original object had two columns, the first (x) an integer seqence 1:100, the second y a variable produced with 0.5 * x -30 + N(0,10).

Usage

data(exemplar)
data(exemplar)

Format

: XArray with 3 sample sizes (rows), and 4 different seeds (column).

Extent of a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

## S4 method for signature 'RasterArray'
ext(x, ...)
## S4 method for signature 'RasterArray'
ext(x, ...)

Arguments

`x`	a `RasterArray`-class object.
`...`	arguments passed to the `ext` function.

Value

An aggregated RasterArray-class object.

Examples

ex <- rastex()
extent <- ext(ex)
ex <- rastex()
extent <- ext(ex)

Positions of missing values in a '`RasterArray`'-class object

Description

The function behaves similar to the regular is.na() function applied to the proxy object of a 'RasterArray'.

Usage

## S3 method for class 'RasterArray'
is.na(x)
## S3 method for class 'RasterArray'
is.na(x)

Arguments

`x`	A `RasterArray` class object.

Value

A logical vector, matrix or array matching the structure of the RasterArray.

Examples

ex <- rastex() 
ex[2] <- NA
is.na(ex)

ex <- rastex() 
ex[2] <- NA
is.na(ex)

Names of layers in the `stack` of a '`VirtualArray`'-class object

Description

Names of layers in the stack of a 'VirtualArray'-class object

Usage

layers(x, ...)

## S4 method for signature 'VirtualArray'
layers(x)
layers(x, ...)

## S4 method for signature 'VirtualArray'
layers(x)

Arguments

`x`	A `VirtualArray`-derived class object.
`...`	additional arguments passed to class-specific methods.

Value

A character vector of names.

Examples

# names of layers in the stack
data(exemplar)
layers(exemplar)
# names of layers in the stack
data(exemplar)
layers(exemplar)

Names of one-dimensional '`VirtualArray`'-derived class objects.

Description

Get or set the names of one-dimensional 'VirtualArray'-derived class objects

Usage

## S4 method for signature 'VirtualArray'
names(x)

## S4 replacement method for signature 'VirtualArray'
names(x) <- value
## S4 method for signature 'VirtualArray'
names(x)

## S4 replacement method for signature 'VirtualArray'
names(x) <- value

Arguments

`x`	`VirtualArray`-derived class object.
`value`	`character` vector.

Value

A character vector of names or NULL.

Examples

ex <- rastex()
names(ex)
names(ex)[4] <- "weirdo"
# NULL
ex <- rastex()
names(ex)
names(ex)[4] <- "weirdo"
# NULL

Number of cells in a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

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

Arguments

`x`	a `RasterArray` class object.

Value

A numeric value.

Examples

ex <- rastex()
ncell(ex)
ex <- rastex()
ncell(ex)

Number of columns and rows of a '`VirtualArray`'-derived class object.

Description

Unlike the ncol and nrow functions of the 'terra' package, this function returns the number of columns and rows of the 'VirtualArray'-derived container, rather than the dimensions of the contained 'SpatRaster'-class object.

Usage

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

## S4 method for signature 'VirtualArray'
nrow(x)
## S4 method for signature 'VirtualArray'
ncol(x)

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

Arguments

`x`	A `VirtualArray`-derived class object.

Value

A numeric value of the number of columns and rows.

Examples

data(paleocoastlines)
ncol(paleocoastlines)
nrow(paleocoastlines)
data(paleocoastlines)
ncol(paleocoastlines)
nrow(paleocoastlines)

Redefine bounds of a named matrix

Description

The function restructures a matrix and extends its current limits to a range defined by a names attribute

Usage

newbounds(x, cols = NULL, rows = NULL)
newbounds(x, cols = NULL, rows = NULL)

Arguments

`x`	The matrix to be restructured.
`cols`	Column names guiding the restructuring.
`rows`	Row names guiding the restructuring.

Details

This is essentially a subsetting function that allows you to subset even when the rownames or colnames vector extends beyond the bounds of a matrix and traditional subsetting methods result in the notorious 'out of bounds' error.

Value

A matrix with extended bounds.

Examples

a<-matrix(1:9, ncol=3)
rownames(a) <- c("a", "c", "d")
newbounds(a, rows=letters[1:5])
a<-matrix(1:9, ncol=3)
rownames(a) <- c("a", "c", "d")
newbounds(a, rows=letters[1:5])

Number of elements or layers in a '`VirtualArray`'-derived class object

Description

Function to return the length of the array in which elements are organized.

Usage

nlayers(x)

## S4 method for signature 'list'
nlayers(x)

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

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

## S4 method for signature 'XArray'
nlayers(x)

## S4 method for signature 'RasterArray'
nlayers(x)
nlayers(x)

## S4 method for signature 'list'
nlayers(x)

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

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

## S4 method for signature 'XArray'
nlayers(x)

## S4 method for signature 'RasterArray'
nlayers(x)

Arguments

`x`	a `VirtualArray`-derived class object.

Details

The length() function returns the number elements that should be present based on the array structure itself, and not the total number of values stored in the object. As the object can contain missing values, the number of actual layers can be queried with nlayers.

Value

A numeric value.

Examples

ex <- rastex()
# omit third element
ex[3] <- NA
# number of elements in the RasterArray
length(ex)
# remaining number values in the stack 
length(ex@stack)
# the number of remaining layers in the RasterArray
nlayers(ex)

ex <- rastex()
# omit third element
ex[3] <- NA
# number of elements in the RasterArray
length(ex)
# remaining number values in the stack 
length(ex@stack)
# the number of remaining layers in the RasterArray
nlayers(ex)

Names as numerics

Description

The set of functions return names of objects directly cast to numeric values.

Usage

nums(x)

colnums(x)

rownums(x)
nums(x)

colnums(x)

rownums(x)

Arguments

`x`	Object with names, colnames or rownames attributes.

Value

Numeric vector.

Examples


# base R object
a <- 1:10
names(a) <- seq(10, 100, 10)
nums(a)

# XArray
data(exemplar)
colnums(exemplar)
rownums(exemplar)
# base R object
a <- 1:10
names(a) <- seq(10, 100, 10)
nums(a)

# XArray
data(exemplar)
colnums(exemplar)
rownums(exemplar)

The total number of values in a '`RasterArray`'-class object

Description

The total number of values in a 'RasterArray'-class object

Usage

nvalues(x, ...)

## S4 method for signature 'RasterArray'
nvalues(x)
nvalues(x, ...)

## S4 method for signature 'RasterArray'
nvalues(x)

Arguments

`x`	A `RasterArray`-class object.
`...`	additional arguments passed to class-specific methods.

Value

A numeric value.

Examples

ex <- rastex()
nvalues(ex)
ex <- rastex()
nvalues(ex)

PaleoMAP PaleoCoastlines (excerpt)

Description

A dataset containing the coastline reconstructions based on the PaleoMAP PaleoDEMS https://www.earthbyte.org/paleodem-resource-scotese-and-wright-2018/ and the Paleobiology Database https://paleobiodb.org for 0, 10 and 20Ma.

Usage

data(paleocoastlines)
data(paleocoastlines)

Format

A SfcArray with 3 continental margin and 3 paleocoastline layers (3 rows and 2 columns).

Details

This is version v7. The article describing the entire set is under review. Once that is published, the entire dataset will be available.

Source

Kocsis, A. T., & Scotese, C. R. (2020). PaleoMAP PaleoCoastlines data [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3903164

Project a '`RasterArray`'-class object

Description

The method implemets the project function for 'RasterArray'-class objects.

The method is inherited from the 'SpatRaster' class. See project for details.

Usage

project

## S4 method for signature 'RasterArray'
project(x, y, ...)
project

## S4 method for signature 'RasterArray'
project(x, y, ...)

Arguments

`x`	A `RasterArray` object to project.
`y`	A `RasterArray` the same options as in `project`.
`...`	additional arguments as for `project`.

Format

An object of class standardGeneric of length 1.

Value

A projected RasterArray-class object.

Examples

# project first three to mollweide
ex <- rastex() 
mollEx <- project(ex[1:3], y="ESRI:54009")
# project first three to mollweide
ex <- rastex() 
mollEx <- project(ex[1:3], y="ESRI:54009")

The proxy of an from a class derived from '`VirtualArray`'

Description

This function returns an object that symbolizes the structure of layers in the 'XArray', 'RasterArray' or 'SfArray'.

Usage

proxy(x, ...)

## S4 method for signature 'VirtualArray'
proxy(x)
proxy(x, ...)

## S4 method for signature 'VirtualArray'
proxy(x)

Arguments

`x`	`XArray`, `RasterArray` or `SfArray` object.
`...`	additional arguments passed to class-specific methods.

Details

The proxy method wraps the names of layers in the @stack using the @index slot of the 'VirtualArray'.

Value

A vector, matrix or array of characters representing the VirtualArray structure.

Examples

data(exemplar)
proxy(exemplar)

data(paleocoastlines)
proxy(paleocoastlines)
data(exemplar)
proxy(exemplar)

data(paleocoastlines)
proxy(paleocoastlines)

Array of '`SpatRaster`'-class objects

Description

Array class for easier navigation of multilayer rasters

Arguments

`stack`	A `SpatRaster` object.
`index`	A `vector`, `matrix` or `array` type object. Includes either the indices of layers in the stack, or their names.
`dim`	A `numeric` vector. Same as for `array`, creates `proxy` procedurally.

Details

The class implements structures to organize single-layer 'SpatRaster'-class objects that have the same dimensions and coordinate reference system. Subsetting rules were defined using the proxy object in the @index slot. See examples for implementations.

The class has two slots: @stack: A 'SpatRaster'-class object with multiple layers, the actual data. index: A proxy object that represents the organization of the layer in the array.

Value

A 'RasterArray'-class object.

Examples

# example data
  ex <- rastex()
  st <-ex@stack
  ind <- 1:6
  names(ind) <- letters[1:length(ind)]
  ra<- RasterArray(stack=st, index=ind)
  
# example data
  ex <- rastex()
  st <-ex@stack
  ind <- 1:6
  names(ind) <- letters[1:length(ind)]
  ra<- RasterArray(stack=st, index=ind)

Procedural example structure to demonstrate the capabilities of the '`RasterArray`' class

Description

Binary versions of SpatRaster-class objects are problematic, this function is used to instantiate a RasterArray example.

Usage

rastex()
rastex()

Value

A two-dimensional RasterArray-class object, with three rows and four columns.

Examples

# create example
example <- rastex()

# subset - single bracket
example['b']

# subset - single bracket
example[c(4, 6)]

# subset - double bracket
example[["layer_2"]]
# create example
example <- rastex()

# subset - single bracket
example['b']

# subset - single bracket
example[c(4, 6)]

# subset - double bracket
example[["layer_2"]]

Resampling a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

## S4 method for signature 'RasterArray,ANY'
resample(x, y, ...)
## S4 method for signature 'RasterArray,ANY'
resample(x, y, ...)

Arguments

`x`	a `RasterArray`-class object.
`y`	The y argument of the `resample` function.
`...`	arguments passed to the `resample` function.

Value

A resampled RasterArray-class object.

Examples

ex <- rastex()
if(requireNamespace("terra", quietly=TRUE)){
  template <- terra::rast(res=5)
  resampled <- resample(ex, template)
}
ex <- rastex()
if(requireNamespace("terra", quietly=TRUE)){
  template <- terra::rast(res=5)
  resampled <- resample(ex, template)
}

Rotate a '`RasterArray`'-class object

Description

The method is inherited from the 'SpatRaster' class.

Usage

## S4 method for signature 'RasterArray'
rotate(x, ...)
## S4 method for signature 'RasterArray'
rotate(x, ...)

Arguments

`x`	(`RasterArray`) Object.
`...`	Additional arguments passed to the `rotate` function.

Value

A RasterArray-class object.

Row names of two-dimensional '`VirtualArray`'-derived class objects.

Description

Get or set the row names of two-dimensional 'VirtualArray'-derived class object

Usage

## S4 method for signature 'VirtualArray'
rownames(x)

## S4 replacement method for signature 'VirtualArray'
rownames(x) <- value
## S4 method for signature 'VirtualArray'
rownames(x)

## S4 replacement method for signature 'VirtualArray'
rownames(x) <- value

Arguments

`x`	`VirtualArray`-class object.
`value`	`character` vector.

Value

A character vector of row names or NULL.

Examples

data(paleocoastlines)
rownames(paleocoastlines)
rownames(paleocoastlines) <- paste(rownames(paleocoastlines), "Ma")
data(paleocoastlines)
rownames(paleocoastlines)
rownames(paleocoastlines) <- paste(rownames(paleocoastlines), "Ma")

Array of '`sf`'-derived class data

Description

Array class for easier navigation of vector spatial datasets

Arguments

`stack`	A `list` of `sf`-class objects or `sfc`-class objects.
`index`	A `vector`, `matrix` or `array` type object. Includes either the indices of layers in the stack, or their names.
`dim`	A `numeric` vector. Same as for `array`, creates `proxy` procedurally.

Details

The class implements structures to organize entire 'sfc' and 'sf' objects that share coordinate reference systems. The 'SfcArray' class is derived from 'XArray' and represents arrays of geometry sets. The 'SfArray' class is derived from 'SfArray', that allows the wrapping of 'sf' objects with attributes. Subsetting rules were defined using the proxy object in the @index slot. See examples for implementations.

The classes have two slots: @stack: A list object with multiple 'sf' class layers, the actual data. @index: A proxy object that represents the organization of the layers.

Value

An 'SfcArray' or 'SfArray'-class object.

Examples

# example data
  library(sf) 
  data(paleocoastlines) 
  st <-paleocoastlines@stack
  ind <- 1:nlayers(st)
  dim(ind) <- c(3,2)
  dimnames(ind) <- list(age=c(0, 10, 20), c("margin", "coastlines"))
  sa<- SfcArray(stack=st, index=ind)
  
# example data
  library(sf) 
  data(paleocoastlines) 
  st <-paleocoastlines@stack
  ind <- 1:nlayers(st)
  dim(ind) <- c(3,2)
  dimnames(ind) <- list(age=c(0, 10, 20), c("margin", "coastlines"))
  sa<- SfcArray(stack=st, index=ind)

Bounding box of an '`SfArray`'-class object

Description

The method is inherited from the 'sf' class.

Usage

## S3 method for class 'SfcArray'
st_bbox(obj, ...)
## S3 method for class 'SfcArray'
st_bbox(obj, ...)

Arguments

`obj`	a `sf`-class object.
`...`	arguments passed to the `st_bbox` function.

Value

An RasterArray class object.

Examples

data(paleocoastlines)
bb<- st_bbox(paleocoastlines)
data(paleocoastlines)
bb<- st_bbox(paleocoastlines)

Coordinate reference system of an '`SfArray`'-class object

Description

The method is inherited from the 'sf' class.

Usage

## S3 method for class 'SfcArray'
st_crs(x, ...)
## S3 method for class 'SfcArray'
st_crs(x, ...)

Arguments

`x`	a `sf`-class object.
`...`	arguments passed to the `st_crs` function.

Value

An aggregated RasterArray class object.

Examples

data(paleocoastlines)
crs <- st_crs(paleocoastlines)
data(paleocoastlines)
crs <- st_crs(paleocoastlines)

Projection change of an '`SfArray`'-class object

Description

The method is inherited from the 'sf' class.

Usage

## S3 method for class 'SfcArray'
st_transform(x, ...)
## S3 method for class 'SfcArray'
st_transform(x, ...)

Arguments

`x`	a `sf`-class object.
`...`	arguments passed to the `st_transform` function.

Value

An RasterArray-class object.

Examples

data(paleocoastlines)
moll<- st_transform(paleocoastlines, "ESRI:54009")
plot(moll["20", "margin"], col="cyan")
plot(moll["20", "coast"], add=TRUE, col="brown")
data(paleocoastlines)
moll<- st_transform(paleocoastlines, "ESRI:54009")
plot(moll["20", "margin"], col="cyan")
plot(moll["20", "coast"], add=TRUE, col="brown")

Subset a '`VirtualArray`'-class object

Description

Extract subsets of an object from a class derived from 'VirtualArray' similarly to a regular array.

Usage

## S4 method for signature 'VirtualArray'
subset(x, i, j, ..., oneDim = FALSE, drop = TRUE)
## S4 method for signature 'VirtualArray'
subset(x, i, j, ..., oneDim = FALSE, drop = TRUE)

Arguments

`x`	`VirtualArray`-class object.
`i`	subscript of the first dimension(rows) or vector-like subsetting.
`j`	subscript of the second dimension (columns).
`...`	subscript of additional dimensions.
`oneDim`	`logical` In case of multidimensional `VirtualArray`s, setting `oneDim` to `TRUE` allows the application of one dimensional subscripts.
`drop`	`logical` in case the result of subsetting is a single element, should the \codeVirtualArray wrapper be dropped?

Value

Either the same class as x, or the class that forms the element of the VirtualArray.

Examples

ex <- rastex()
# first 4
subset(ex, i=1:4)
# missing at the end
subset(ex, i=1:12)
# character subscript
subset(ex, i=c("a", "b"))
# logical subscript
subs <- rep(TRUE, length(ex))
subs[1] <- FALSE # remove first
subset(ex, i= subs)
# no drop
subset(ex, i=1, drop=FALSE)
ex <- rastex()
# first 4
subset(ex, i=1:4)
# missing at the end
subset(ex, i=1:12)
# character subscript
subset(ex, i=c("a", "b"))
# logical subscript
subs <- rep(TRUE, length(ex))
subs[1] <- FALSE # remove first
subset(ex, i= subs)
# no drop
subset(ex, i=1, drop=FALSE)

Transpose a '`VirtualArray`'-class object

Description

Transpose a 'VirtualArray'-class object

Usage

## S4 method for signature 'VirtualArray'
t(x)
## S4 method for signature 'VirtualArray'
t(x)

Arguments

`x`	A `VirtualArray`-class object.

Value

A VirtualArray-class object.

Examples

data(exemplar)
t(exemplar)
data(paleocoastlines)
t(paleocoastlines)
data(exemplar)
t(exemplar)
data(paleocoastlines)
t(paleocoastlines)

Virtual Arrays

Description

The base class 'VirtualArray' is defined, which acts as a wrapper around lists allowing users to fold arbitrary sequential data into n-dimensional, R-style virtual arrays. The derived 'XArray' class is defined to be used for homogeneous lists that contain a single class of objects. The 'RasterArray' and 'SfArray' classes enable the use of stacked spatial data instead of lists. #' This is still the pre-alpha version. As is R, this is free software and comes with ABSOLUTELY NO WARRANTY. Nevertheless, notes about found bugs and suggestions are more than welcome.

Author(s)

Adam T. Kocsis ([email protected])

Virtual array of general R objects

Description

Template for construction of virtual arrays ('VirtualArray') and a derived class ('XArray') to instantiate it with general objects.

Arguments

`stack`	A `list`-class object.
`index`	A `vector`, `matrix` or `array` type object. Includes the indices of layers in the stack.
`dim`	A `numeric` vector. Same as for `array`, creates `proxy` procedurally.

Details

The 'VirtualArray' class implements structures to organize objects of the same class in multidimensional arrays. Subsetting rules were defined using the proxy object in the index slot. The 'VirtualArray' is the base class for 'XArray' and 'RasterArray' classes. The 'XArray' class derived from VirtualArray allows the instantiation of basic virtual arrays with genearl R objects, which form a single list in the @stack slot. The 'SfArray' class is derived from the 'XArray' class.

The class has two slots: @stack: A list containing objects of the same class (i.e. layers). @index: A proxy object that represents the structure of the entities.

Value

An XArray-class object.

Examples

# 2d XArray of vectors
  data(exemplar)
  st <-exemplar@stack
  ind <- 1:nlayers(st)
  dim(ind) <- c(3,4)
  dimnames(ind) <- list(n = c(10, 20, 30), seed = 1:4)
  xa<- XArray(stack=st, index=ind)
  
# 2d XArray of vectors
  data(exemplar)
  st <-exemplar@stack
  ind <- 1:nlayers(st)
  dim(ind) <- c(3,4)
  dimnames(ind) <- list(n = c(10, 20, 30), seed = 1:4)
  xa<- XArray(stack=st, index=ind)

Resolution of a '`RasterArray`'-class object

Description

The methods are inherited from the 'SpatRaster' class, see res. Replacement is not allowed.

Usage

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

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

## S4 method for signature 'RasterArray'
res(x)
## S4 method for signature 'RasterArray'
xres(x)

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

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

Arguments

`x`	a `RasterArray`-class object.

Value

A numeric vector.

Examples

ex <- rastex() 
res(ex)
yres(ex)
xres(ex)
ex <- rastex() 
res(ex)
yres(ex)
xres(ex)

Package 'via'

Help Index

Indexing to extract subsets of a 'codeVirtualArray'-class object

Description

Usage

Arguments

Value

Examples

Indexing to extract the elements of a 'VirtualArray'-derived class object.

Description

Usage

Arguments

Value

Examples

Replace elements of 'VirtualArray'-class objects.

Description

Usage

Arguments

Value

Replace layers in an object that is of a class derived from 'VirtualArray'.

Description

Usage

Arguments

Value

Examples

Aggregate raster cells in a 'RasterArray'-class object

Description

Usage

Arguments

Value

Examples

Coerce into an SfcArray or SfArray object

Description

Usage

Arguments

Value

Combine a one-dimensional 'VirtualArray'-class object with other objects

Description

Usage

Arguments

Value

Column names of two-dimensional 'VirtualArray'-derived class object.

Description

Usage

Arguments

Value

Examples

Cropping a 'RasterArray'-class object

Description

Usage

Arguments

Value

Examples

Dimensions of 'VirtualArray'-derived class objects

Description

Usage

Arguments

Value

Examples

Dimensions of layers in a 'VirtualArray'-class object

Description

Usage

Arguments

Value

Names of a multidimensional 'VirtualArray'-derived class object.

Description

Usage

Arguments

Value

Examples

Disaggregate raster cells in a 'RasterArray'-class object

Description

Usage

Arguments

Value

Examples

Example 'XArray'-class object

Description

Usage

Format

Indexing to extract subsets of a 'code VirtualArray'-class object

Indexing to extract the elements of a '`VirtualArray`'-derived class object.

Replace elements of '`VirtualArray`'-class objects.

Replace layers in an object that is of a class derived from '`VirtualArray`'.

Aggregate raster cells in a '`RasterArray`'-class object

Coerce into an `SfcArray` or `SfArray` object

Combine a one-dimensional '`VirtualArray`'-class object with other objects

Column names of two-dimensional '`VirtualArray`'-derived class object.

Cropping a '`RasterArray`'-class object

Dimensions of '`VirtualArray`'-derived class objects

Dimensions of layers in a '`VirtualArray`'-class object

Names of a multidimensional '`VirtualArray`'-derived class object.

Disaggregate raster cells in a '`RasterArray`'-class object

Example '`XArray`'-class object

Extent of a '`RasterArray`'-class object

Positions of missing values in a '`RasterArray`'-class object

Names of layers in the `stack` of a '`VirtualArray`'-class object

Names of one-dimensional '`VirtualArray`'-derived class objects.

Number of cells in a '`RasterArray`'-class object

Number of columns and rows of a '`VirtualArray`'-derived class object.

Number of elements or layers in a '`VirtualArray`'-derived class object

The total number of values in a '`RasterArray`'-class object

Project a '`RasterArray`'-class object