Merge pull request #17 from jamestsakalos/test-elev

Test elev.R
jamestsakalos · Jul 17, 2023 · f6612fa · f6612fa
2 parents c5ba5f0 + 70f1d06
commit f6612fa
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Showing 33 changed files with 865 additions and 170 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,11 +38,12 @@ Imports:
     climaemet,
     dismo,
     dplyr,
-    elevatr,
+    elevatr (>= 1.0),
     exactextractr,
     geodata,
     glue,
     macroBiome,
+    methods,
     plyr,
     randomForest,
     sf,
@@ -53,12 +54,16 @@ Suggests:
     covr,
     fs,
     knitr,
+    progress,
     raster,
     rmarkdown,
     testthat (>= 3.0.0),
     vdiffr
+Remotes:
+    jhollist/elevatr
 Config/Needs/check: rcmdcheck
 Config/Needs/coverage: covr
 Config/Needs/website: pkgdown
+Config/testthat/edition: 3
 RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
@@ -18,7 +18,6 @@ importFrom(dplyr,group_by)
 importFrom(dplyr,summarize)
 importFrom(elevatr,get_elev_raster)
 importFrom(exactextractr,exact_extract)
-importFrom(geodata,elevation_3s)
 importFrom(geodata,worldclim_tile)
 importFrom(glue,glue)
 importFrom(graphics,axis)
@@ -28,10 +27,12 @@ importFrom(graphics,points)
 importFrom(graphics,strwidth)
 importFrom(graphics,text)
 importFrom(macroBiome,cliHoldridgePoints)
+importFrom(methods,as)
 importFrom(plyr,round_any)
 importFrom(randomForest,importance)
 importFrom(randomForest,randomForest)
 importFrom(randomForest,varImpPlot)
+importFrom(sf,"st_crs<-")
 importFrom(sf,as_Spatial)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)
@@ -42,10 +43,15 @@ importFrom(sp,SpatialPolygonsDataFrame)
 importFrom(stats,aggregate)
 importFrom(stats,sd)
 importFrom(terra,centroids)
+importFrom(terra,colFromCell)
 importFrom(terra,crds)
+importFrom(terra,crs)
 importFrom(terra,extract)
+importFrom(terra,mask)
 importFrom(terra,mosaic)
 importFrom(terra,rast)
+importFrom(terra,rasterize)
+importFrom(terra,rowFromCell)
 importFrom(terra,vect)
 importFrom(terra,writeRaster)
 importFrom(terra,xyFromCell)

diff --git a/R/ce_download.R b/R/ce_download.R
@@ -12,7 +12,7 @@
 #' @param \dots Arguments to control a download from the Internet
 #' `download.file()`.
 #'
-#' @return
+#' @returns
 #' See documentation from [`chelsa()`], [`worldclim()`] and
 #' [`elev()`].
 #'

diff --git a/R/ce_extract.R b/R/ce_extract.R
@@ -287,7 +287,7 @@
 
   # Assigns an 'id' if location_g is empty
   if (is.null(location_g)) {
-    message(
+    warning(
       paste(
         "location_g must be one of",
         paste(setdiff(colnames(location_df),  c("coords.x1", "coords.x2")),
@@ -347,7 +347,7 @@
 #' @template output_c_source_param
 #' @template output_var_param
 #'
-#' @return
+#' @returns
 #' Returns a list storing matrices containing the mean and standard deviation
 #' of the climate and/or elevation data. Each column represents a month, each
 #' row represents a feature of the \code{location} \code{sp}, \code{sf} polygon

diff --git a/R/chelsa.R b/R/chelsa.R
@@ -10,7 +10,7 @@
 #' @param quiet,\dots Arguments to control a download from the Internet
 #' `download.file()`.
 #'
-#' @return
+#' @returns
 #' Returns four subfolders named prec, tmax, tmin and tmean. Each folder
 #' contains 12 GeoTiff (.tif) files, one for each month of the year for the time
 #' period 1981&ndash;2010. Each of the files are downloaded at a spatial

diff --git a/R/data_srtm_tiles.R b/R/data_srtm_tiles.R
@@ -0,0 +1,15 @@
+##' STRM tiles data
+##'
+##' SRTM tiles data.
+##'
+##' @docType data
+##' @format{ An object of class \code{SpatialPolygonsDataFrame} with 872 rows
+##' and 1 columns.}
+##' @details Contains tiles to assist downloading from 'geodata'.
+##' @encoding UTF-8
+##' @keywords datasets
+##' @rdname srtm_tiles
+##' @examples
+##' data("srtm_tiles", package = "climenv")
+##' head(srtm_tiles)
+"srtm_tiles"