Merge pull request #5 from ropensci/allow-geographic-coordinate-systems

Allow geographic coordinate systems

DESCRIPTION

@@ -29,7 +29,7 @@ Suggests:
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "srr::srr_stats_roclet"))
 Depends: 
     R (>= 3.5.0)

NAMESPACE

@@ -23,10 +23,13 @@ importFrom(assertthat,assert_that)
 importFrom(grDevices,colorRampPalette)
 importFrom(graphics,abline)
 importFrom(methods,formalArgs)
+importFrom(parallel,clusterEvalQ)
 importFrom(parallel,clusterExport)
 importFrom(parallel,parLapply)
 importFrom(parallel,parLapplyLB)
 importFrom(pbapply,pblapply)
+importFrom(pbapply,pboptions)
+importFrom(pbapply,pbvapply)
 importFrom(stats,approx)
 importFrom(stats,getCall)
 importFrom(stats,quantile)
@@ -40,14 +43,17 @@ importFrom(terra,"crs<-")
 importFrom(terra,"nlyr<-")
 importFrom(terra,"res<-")
 importFrom(terra,"values<-")
+importFrom(terra,adjacent)
 importFrom(terra,app)
 importFrom(terra,as.matrix)
 importFrom(terra,classify)
 importFrom(terra,compareGeom)
 importFrom(terra,crs)
 importFrom(terra,distance)
 importFrom(terra,ext)
+importFrom(terra,extend)
 importFrom(terra,extract)
+importFrom(terra,is.lonlat)
 importFrom(terra,ncell)
 importFrom(terra,nlyr)
 importFrom(terra,plot)

NEWS.md

@@ -1,3 +1,17 @@
+# rangr 1.0.4 (2024-05-30)
+
+### Major improvements
+
+-   Added support for lon/lat rasters as input maps
+
+### Minor improvements
+
+-   Default value of `max_dist` in `initialise()` is now equal to 0.99 quantile of `kernel_fun` instead of 0.9
+
+-   Added examples of lon/lat rasters to package data
+
+-   Input maps (`K_map` and `n1_map`) are now wrapped in `sim_data` object
+
 # rangr 1.0.3 (2024-01-23)
 
 ### Minor improvements

R/K_get_interpolation.R

@@ -8,12 +8,12 @@
 #' change, ecological disturbance, etc.) one needs to provide time-varying
 #' carrying capacity maps.
 #'
-#' Either `K_time_points` or `time` parameter are needed to calculate
-#' interpolation. If interpolation should  be calculated between two carrying
+#' Either `K_time_points` or the `time` parameter is needed to calculate
+#' interpolation. If interpolation should be calculated between two carrying
 #' capacity maps, there is no need to pass the time points, because 1 will
-#' be set as a starting time point and `time` will be used as the ending point.
-#' On the other hand, in the absence of the `time` argument, the last element of
-#' `K_time_points` is considered to be the ending point for the interpolation.
+#' be set as the starting time point and `time` will be used as the ending point.
+#' On the other hand, in the absence of the `time` argument, the maximum element
+#' of `K_time_points` is considered to be the ending point for the interpolation.
 #'
 #'
 #'
@@ -111,6 +111,10 @@ K_check <- function(K_map, K_time_points, time) {
     !is.null(time) || (!is.null(K_time_points)),
     msg = "Either \"K_time_points\" or \"time\" must be specified")
 
+  assert_that(
+    !any(duplicated(K_time_points)),
+    msg = "\"K_time_points\" should contain only unique values")
+
   # number of layers
   nls <- nlyr(K_map)
 
@@ -157,7 +161,7 @@ K_check <- function(K_map, K_time_points, time) {
       "Argument \"time\" is no specified - ",
       "last number from \"K_time_points\" is used as \"time\""
     )
-    time <- K_time_points[ntp]
+    time <- max(K_time_points)
 
   } else {
 
@@ -170,7 +174,7 @@ K_check <- function(K_map, K_time_points, time) {
       K_time_points <- c(1, time) # default time points for 2-layered K_map
     } else {
       assert_that(
-        K_time_points[ntp] == time,
+        max(K_time_points) == time,
         msg = "Last element of \"K_time_points\" should be equal to \"time\"")
     }
   }

R/data.R

@@ -127,6 +127,130 @@ NULL
 #' @srrstats {G5.1} dataset used in examples is exported and documented
 NULL
 
+#' @name K_small_lon_lat.tif
+#' @title Example Of Carrying Capacity Map (Small)
+#' @docType data
+#'
+#' @description
+#' [`SpatRaster`][terra::SpatRaster-class] object that represents a carrying
+#' capacity map projected to WGS 84 (CRS84) from the original raster `K_small`.
+#' This map can be used as a carrying capacity map to initialize data necessary
+#' to perform a simulation. It is compatible with the `n1_small_lon_lat.tif` raster.
+#'
+#' @format [`SpatRaster`][terra::SpatRaster-class] object with 12 rows
+#' and 14 columns containing integer values 0-100 and NA's
+#' (indicating unsuitable areas).
+#'
+#' @source Data generated in-house to serve as an example
+#' (using spatial autocorrelation)
+#'
+#' @examples
+#' system.file("input_maps/K_small_lon_lat.tif", package = "rangr")
+#'
+#' @srrstats {G1.4} uses roxygen documentation
+#' @srrstats {G5.1} dataset used in examples is exported and documented
+NULL
+
+
+#' @name K_small_changing_lon_lat.tif
+#' @title Example Of Changing Carrying Capacity Maps (Small)
+#' @docType data
+#'
+#' @description
+#' [`SpatRaster`][terra::SpatRaster-class] object representing changing carrying
+#' capacity maps projected to WGS 84 (CRS84) from the original raster
+#' `K_small_changing`. These maps can be used as carrying capacity maps to initialize
+#' data necessary to perform a simulation. To use these maps in the initialization
+#' process, the user first has to use [`K_get_interpolation`] to generate a map for
+#' every time step of the simulation. These maps are compatible with the
+#' `n1_small_lon_lat.tif` raster.
+#'
+#' @format [`SpatRaster`][terra::SpatRaster-class] object with 3 layers,
+#' each having 12 rows and 14 columns containing integer values 0-170 and NA's
+#' (indicating unsuitable areas).
+#'
+#' @source Data generated in-house to serve as an example
+#' (using spatial autocorrelation)
+#'
+#' @examples
+#' system.file("input_maps/K_small_changing_lon_lat.tif", package = "rangr")
+#'
+#' @srrstats {G1.4} uses roxygen documentation
+#' @srrstats {G5.1} dataset used in examples is exported and documented
+NULL
+
+
+#' @name K_big_lon_lat.tif
+#' @title Example Of Carrying Capacity Map (Big)
+#' @docType data
+#'
+#' @description
+#' [`SpatRaster`][terra::SpatRaster-class] object representing a carrying
+#' capacity map projected to WGS 84 (CRS84) from the original raster `K_big`.
+#' This map can be used as a carrying capacity map to initialize data necessary
+#' to perform a simulation. It is compatible with the `n1_big_lon_lat.tif` raster.
+#'
+#' @format [`SpatRaster`][terra::SpatRaster-class] object with 74 rows
+#' and 125 columns containing integer values 0-25 and NA's
+#' (indicating unsuitable areas).
+#'
+#' @source Data generated in-house to serve as an example
+#' (using spatial autocorrelation)
+#'
+#' @examples
+#' system.file("input_maps/K_big_lon_lat.tif", package = "rangr")
+#'
+#' @srrstats {G1.4} uses roxygen documentation
+NULL
+
+
+#' @name n1_small_lon_lat.tif
+#' @title Example Of Abundance Map At First Time Step Of The Simulation (Small)
+#' @docType data
+#'
+#' @description
+#' [`SpatRaster`][terra::SpatRaster-class] object representing an abundance map
+#' at the first time step of the simulation projected to WGS 84 (CRS84) from the
+#' original raster `n1_small`. This map can be used as a simulation starting point
+#' to initialize data necessary to perform a simulation. It is compatible with the
+#' `K_small_lon_lat.tif` and `K_small_changing_lon_lat.tif` maps.
+#'
+#' @format [`SpatRaster`][terra::SpatRaster-class] object with 12 rows
+#' and 14 columns containing integer values 0-10 and NA's
+#' (indicating unsuitable areas).
+#'
+#' @source Data generated in-house to serve as an example
+#'
+#' @examples
+#' system.file("input_maps/n1_small_lon_lat.tif", package = "rangr")
+#'
+#' @srrstats {G1.4} uses roxygen documentation
+NULL
+
+
+#' @name n1_big_lon_lat.tif
+#' @title Example Of Abundance Map At First Time Step Of The Simulation (Big)
+#' @docType data
+#'
+#' @description
+#' [`SpatRaster`][terra::SpatRaster-class] object representing an abundance map
+#' at the first time step of the simulation projected to WGS 84 (CRS84) from the
+#' original raster `n1_big`. This map can be used as a simulation starting point
+#' to initialize data necessary to perform a simulation. It is compatible with the
+#' `K_big_lon_lat.tif` map.
+#'
+#' @format [`SpatRaster`][terra::SpatRaster-class] object with 74 rows
+#' and 125 columns containing integer values 0-50 and NA's
+#' (indicating unsuitable areas).
+#'
+#' @source Data generated in-house to serve as an example
+#'
+#' @examples
+#' system.file("input_maps/n1_big_lon_lat.tif", package = "rangr")
+#'
+#' @srrstats {G1.4} uses roxygen documentation
+#' @srrstats {G5.1} dataset used in examples is exported and documented
+NULL
 
 
 #' @title Example Of Observation Points List