diff --git a/DESCRIPTION b/DESCRIPTION
index e9aba15850e79489f17d740591779741ddc89ee0..22f14303bc10b08f81f80d0e3046e0609c1bfb63 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: ClimDatDownloadR
Type: Package
Title: Downloads Climate Data from Chelsa and WorldClim
-Version: 0.1.7
+Version: 0.1.7-2
Authors@R: c(person("Helge", "Jentsch",
email = "helge.marc.ole.jentsch@uni-hamburg.de",
role = c("aut", "cre"),
@@ -38,14 +38,14 @@ License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.6), terra (>= 1.7-18)
Imports: curl (>= 4.3.2), httr (>= 1.4.1), ncdf4 (>= 1.17), RCurl (>=
- 1.98), raster (>= 3.1-5), RefManageR (>= 1.2.12), stringr (>=
- 1.4.0), sf (>= 0.9-4), sp (>= 1.4-1), utils
+ 1.98), RefManageR (>= 1.2.12), stringr (>= 1.4.0), sf (>=
+ 0.9-4), sp (>= 1.4-1), utils
RoxygenNote: 7.2.3
Suggests: knitr, testthat, usethis, rmarkdown
VignetteBuilder: knitr
SystemRequirements: Tested with at least 4 GB RAM.
NeedsCompilation: no
-Packaged: 2023-06-23 12:34:01 UTC; helge
+Packaged: 2023-07-05 14:07:57 UTC; helge
Author: Helge Jentsch [aut, cre],
Maria Bobrowski [aut],
Johannes Weidinger [aut],
diff --git a/NAMESPACE b/NAMESPACE
index 6753522662b39ada7c5efa2c2581bacb8bab2bab..0976af3b3f3c6c701b307c758584d102cdf68bc8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,7 +4,6 @@ export(Chelsa.CMIP_5.download)
export(Chelsa.CMIP_6.download)
export(Chelsa.CRUts.download)
export(Chelsa.Clim.download)
-export(Chelsa.Clim.download.deprecated)
export(Chelsa.lgm.download)
export(Chelsa.timeseries.download)
export(WorldClim.CMIP_5.download)
@@ -21,7 +20,6 @@ export(stacking.downloaded.data)
import(RCurl)
import(httr)
import(ncdf4)
-import(raster)
import(sf)
import(sp)
import(stringr)
diff --git a/R/Chelsa_Download_functions.R b/R/Chelsa_Download_functions.R
index 65863267f0b1e0f9aecd7eed3c819c5fab5f6b20..f4224b54df61dd985dc7759cb05290e99d161927 100644
--- a/R/Chelsa_Download_functions.R
+++ b/R/Chelsa_Download_functions.R
@@ -34,11 +34,10 @@
#'@import stringr
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
#'
-#'@export
Chelsa.Clim.download.deprecated<- function(save.location = "./",
parameter = c("prec", "temp", "tmax", "tmin", "bio"),
bio.var = c(1:19),
@@ -181,15 +180,14 @@ Chelsa.Clim.download.deprecated<- function(save.location = "./",
quiet = FALSE,
cacheOK = FALSE)
if(i != "prec"){
- raster.temp <- raster(dest.temp)
-
+ raster.temp <- terra::rast(dest.temp)
gc()
- raster.temp <- clamp(raster.temp, lower = -1000,
+ raster.temp <- terra::clamp(raster.temp, lower = -1000,
useValues = FALSE)
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
gc()
- writeRaster(raster.temp,
+ terra::writeRaster(raster.temp,
dest.temp,
overwrite = TRUE)
rm(raster.temp)
@@ -313,29 +311,29 @@ Chelsa.Clim.download.deprecated<- function(save.location = "./",
quiet = FALSE)
if(bio <= 11){
- raster.temp <- raster(dest.temp)
+ raster.temp <- terra::rast(dest.temp)
# raster.values <- values(raster.temp)
# raster.values[raster.values==-32768] <- NA
# values(raster.temp) <- raster.values
# rm(raster.values)
gc()
- raster.temp <- clamp(raster.temp, lower = -1000,
+ raster.temp <- terra::clamp(raster.temp, lower = -1000,
useValues = FALSE)
- gain(raster.temp) <- 0.1
- writeRaster(raster.temp,
+ raster.temp <- process.raster.int.doub(raster.temp)
+ terra::writeRaster(raster.temp,
dest.temp,
overwrite = TRUE)
rm(raster.temp)
gc()
}else{
- raster.temp <- raster(paste0(temp.temp.save.location, "CHELSA_",
+ raster.temp <- terra::rast(paste0(temp.temp.save.location, "CHELSA_",
i, "_", bio, vers, ".tif"))
gc()
- raster.temp <- clamp(raster.temp, lower = -1000,
+ raster.temp <- terra::clamp(raster.temp, lower = -1000,
useValues = FALSE)
gc()
- writeRaster(raster.temp,
+ terra::writeRaster(raster.temp,
paste0(temp.temp.save.location, "CHELSA_",
i, "_", bio, vers, ".tif"),
overwrite = TRUE)
@@ -471,7 +469,7 @@ Chelsa.Clim.download.deprecated<- function(save.location = "./",
#'@import stringr
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@import httr
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
@@ -596,15 +594,15 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
quiet = FALSE)
if(i != "prec"){
gc()
- raster.temp <- raster(dest.temp)
- raster.temp <- clamp(raster.temp, lower = -1000,
+ raster.temp <- terra::rast(dest.temp)
+ raster.temp <- terra::clamp(raster.temp, lower = -1000,
useValues = FALSE)
gc()
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(dest.temp)
gc()
- writeRaster(raster.temp,
- dest.temp,
- overwrite = TRUE)
+ terra::writeRaster(x = raster.temp,
+ filename = dest.temp,
+ overwrite = TRUE)
rm(raster.temp)
gc()
}
@@ -675,22 +673,22 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
mode = 'wb',
quiet = FALSE)
- raster.temp <- raster(dest.temp)
+ raster.temp <- terra::rast(dest.temp)
# raster.values <- values(raster.temp)
# raster.values[raster.values==-32768] <- NA
# values(raster.temp) <- raster.values
# rm(raster.values); gc()
- raster.temp <- clamp(raster.temp,
+ raster.temp <- terra::clamp(raster.temp,
lower = -1000,
useValues = FALSE)
gc()
if(bio <= 11){
gc()
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
}
- writeRaster(raster.temp,
- dest.temp,
- overwrite = TRUE)
+ terra::writeRaster(x = raster.temp,
+ filename = dest.temp,
+ overwrite = TRUE)
rm(raster.temp)
gc()
}else{
@@ -806,7 +804,7 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
#'@import stringr
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
#'
@@ -937,30 +935,30 @@ Chelsa.lgm.download <- function(save.location = "./",
mode = 'wb',
quiet = FALSE)
if(i != "prec"){
- raster.temp <- raster(dest.temp)
+ raster.temp <- terra::rast(dest.temp)
- raster.temp <- clamp(raster.temp, lower = -1000, useValues= FALSE)
+ raster.temp <- terra::clamp(raster.temp, lower = -1000, useValues= FALSE)
gc()
# Conversion Float
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
# umrechnung Kelvin - Celsius
gc()
- offs(raster.temp) <- -273.15
-
- writeRaster(raster.temp,
- dest.temp,
+ raster.temp <- process.raster.offset(raster.layer= raster.temp)
+ terra::writeRaster(x = raster.temp,
+ filename = dest.temp,
overwrite = TRUE)
rm(raster.temp)
gc()
}else{
# for precipitation as http://chelsa-climate.org/last-glacial-maximum-climate/ says
- raster.temp <- raster(dest.temp)
- raster.temp <- clamp(raster.temp, upper = 30000, useValues= FALSE)
+ raster.temp <- terra::rast(dest.temp)
+ raster.temp <- terra::clamp(raster.temp, upper = 30000, useValues= FALSE)
gc()
- gain(raster.temp) <- 0.1
- writeRaster(raster.temp,
- dest.temp,
+ raster.temp <- process.raster.int.doub(raster.temp)
+
+ terra::writeRaster(x = raster.temp,
+ filename = dest.temp,
overwrite = TRUE)
rm(raster.temp)
gc()
@@ -1033,17 +1031,17 @@ Chelsa.lgm.download <- function(save.location = "./",
mode = 'wb',
quiet = FALSE)
# Casting into floats and deleting NA values
- raster.temp <- raster(dest.temp)
- raster.temp <- clamp(raster.temp, lower = -1000, useValues= FALSE)
+ raster.temp <- terra::rast(dest.temp)
+ raster.temp <- terra::clamp(raster.temp, upper = -1000, useValues= FALSE)
gc()
if(bio <= 11){
# values(raster.temp) <- as.numeric(values(raster.temp)/10)
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
}
- writeRaster(raster.temp,
- dest.temp,
- overwrite = TRUE)
+ terra::writeRaster(x = raster.temp,
+ filename = dest.temp,
+ overwrite = TRUE)
rm(raster.temp)
gc()
}else{
@@ -1163,7 +1161,7 @@ Chelsa.lgm.download <- function(save.location = "./",
#'@import stringr
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@import httr
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
@@ -1303,22 +1301,16 @@ Chelsa.timeseries.download <- function(save.location = "./",
if(i != "prec"){
- raster.temp <- raster(dest.file)
- # raster.values <- values(raster.temp)
- # raster.values[raster.values==-32768] <- NA
- # values(raster.temp) <- raster.values
- # rm(raster.values)
+ raster.temp <- terra::rast(dest.file)
- raster.temp <- clamp(raster.temp, lower = -1000, useValues = FALSE)
+ raster.temp <- terra::clamp(raster.temp, lower = -1000, useValues = FALSE)
gc()
- # values(raster.temp) <- as.numeric(values(raster.temp)/10)
- # values(raster.temp) <- as.numeric(values(raster.temp)-273.15)
- gain(raster.temp) <- 0.1
- offs(raster.temp) <- -273.15
+ raster.temp <- process.raster.int.doub(raster.temp)
+ raster.temp <- process.raster.offset(raster.layer = raster.temp)
- writeRaster(raster.temp,
- dest.file,
+ terra::writeRaster(x = raster.temp,
+ filename = dest.file,
overwrite = TRUE)
rm(raster.temp)
gc()
@@ -1432,7 +1424,7 @@ Chelsa.timeseries.download <- function(save.location = "./",
#'@import stringr
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@import httr
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
@@ -1592,11 +1584,11 @@ Chelsa.CRUts.download <- function(save.location = "./",
mustWork = T),
"/temp_gdalwarped.tif")
# gdalUtils::gdalwarp(dest.temp, raster.temp.file.dest)
- raster.temp <- raster(raster.temp.file.dest)
- raster.temp <- clamp(raster.temp, lower = -1000, useValues = FALSE)
- gain(raster.temp) <- 0.1
- writeRaster(raster.temp,
- dest.temp,
+ raster.temp <- terra::rast(raster.temp.file.dest)
+ raster.temp <- terra::clamp(raster.temp, lower = -1000, useValues = FALSE)
+ raster.temp <- process.raster.int.doub(raster.temp)
+ terra::writeRaster(x = raster.temp,
+ filename = dest.temp,
overwrite = TRUE)
rm(raster.temp)
gc()
diff --git a/R/WorldClim_download_functions.R b/R/WorldClim_download_functions.R
index 4389b860de7c771ad6234c2418425e87c38f0eae..d2272a0e5e1eaac108cab81569b496b2f38ea5d0 100644
--- a/R/WorldClim_download_functions.R
+++ b/R/WorldClim_download_functions.R
@@ -288,43 +288,42 @@ WorldClim.HistClim.download <- function(save.location = "./",
for (month in month.var) {
if(parm.temp != "prec"){
if(res.temp != "30s"){
- raster.temp <- raster(
+ raster.temp <- terra::rast(
list.files(path = temp.temp.save.location,
pattern = paste0(parm.temp, month,".bil"),
full.names = T)
)
}else{
- raster.temp <- raster(
+ raster.temp <- terra::rast(
list.files(path = temp.temp.save.location,
pattern = paste0(parm.temp, "_", month,".bil"),
full.names = T)
)
}
gc()
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
gc()
}else{
if(res.temp != "30s"){
- raster.temp <- raster(
+ raster.temp <- terra::rast(
list.files(path = temp.temp.save.location,
pattern = paste0(parm.temp, month,".bil"),
full.names = T)
)
}else{
- raster.temp <- raster(
+ raster.temp <- terra::rast(
list.files(path = temp.temp.save.location,
pattern = paste0(parm.temp, "_", month,".bil"),
full.names = T)
)
}
}
- writeRaster(raster.temp,
+ terra::writeRaster(raster.temp,
filename = paste0(temp.temp.save.location,
"WC_",vers, "_",
res, "_", parm.temp, "_",
str_pad(c(1:12)[month], 2, 'left', pad = "0"),
".tif"),
- format = "GTiff",
overwrite = TRUE)
}
unlink(c(list.files(temp.temp.save.location, pattern = ".bil",
@@ -333,7 +332,7 @@ WorldClim.HistClim.download <- function(save.location = "./",
full.names = TRUE)))
}else{
for (bio in bio.var) {
- raster.temp <- raster(
+ raster.temp <- terra::rast(
list.files(temp.temp.save.location,
pattern = paste0(parm.temp, bio, ".bil"),
full.names = T)
@@ -341,22 +340,21 @@ WorldClim.HistClim.download <- function(save.location = "./",
if(bio <= 11){
if(res.temp != "30s"){
gc()
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
gc()
}else{
# crop
gc()
- gain(raster.temp) <- 0.1
+ raster.temp <- process.raster.int.doub(raster.temp)
gc()
}
}
- writeRaster(raster.temp,
+ terra::writeRaster(raster.temp,
filename = paste0(temp.temp.save.location,
"WC_",vers, "_",
res, "_", parm.temp, "_",
str_pad(c(1:19)[bio], 2, 'left', pad = "0"),
".tif"),
- format = "GTiff",
overwrite = TRUE)
}
unlink(c(list.files(temp.temp.save.location, pattern = ".bil",
@@ -623,7 +621,7 @@ WorldClim.HistClim.download <- function(save.location = "./",
#'@importFrom curl curl_fetch_memory
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
#'@export
@@ -895,22 +893,22 @@ WorldClim.CMIP_5.download <- function(save.location = "./",
if(parm.temp != "prec"){
for (file.conversion.num in 1:length(keep.files)) {
if(res.temp != "30s"){
- raster.temp <- raster(keep.files[file.conversion.num])
+ raster.temp <- terra::rast(keep.files[file.conversion.num])
gc()
- gain(raster.temp) <- .1
- writeRaster(x = raster.temp,
+ raster.temp <- process.raster.int.doub(raster.temp)
+ terra::writeRaster(x = raster.temp,
filename = keep.files[file.conversion.num],
overwrite = TRUE)
rm(raster.temp)
gc()
}else{
- raster.temp <- raster(keep.files[file.conversion.num])
+ raster.temp <- terra::rast(keep.files[file.conversion.num])
# crop
gc()
- gain(raster.temp) <- .1
+ raster.temp <- process.raster.int.doub(raster.temp)
gc()
# save
- writeRaster(x = raster.temp,
+ terra::writeRaster(x = raster.temp,
filename = keep.files[file.conversion.num],
overwrite = TRUE)
rm(raster.temp)
@@ -960,22 +958,19 @@ WorldClim.CMIP_5.download <- function(save.location = "./",
print(file.conversion.temp)
if(file.conversion.temp <= 11){
if(res.temp != "30s"){
+ raster.temp <- terra::rast(keep.files[file.conversion.num])
gc()
- raster.temp <- raster(keep.files[file.conversion.num])
- gain(raster.temp) <- .1
- writeRaster(x = raster.temp,
+ raster.temp <- process.raster.int.doub(raster.temp)
+ terra::writeRaster(x = raster.temp,
filename = keep.files[file.conversion.num],
overwrite = TRUE)
rm(raster.temp)
gc()
}else{
- raster.temp <- raster(keep.files[file.conversion.num])
- # crop
- gc()
- gain(raster.temp) <- .1
+ raster.temp <- terra::rast(keep.files[file.conversion.num])
gc()
- # save
- writeRaster(x = raster.temp,
+ raster.temp <- process.raster.int.doub(raster.temp)
+ terra::writeRaster(x = raster.temp,
filename = keep.files[file.conversion.num],
overwrite = TRUE)
rm(raster.temp)
@@ -1123,7 +1118,7 @@ WorldClim.CMIP_5.download <- function(save.location = "./",
#'@import stringr
#'@import RCurl
#'@import ncdf4
-#'@import raster
+#'@import terra
#'@importFrom utils download.file unzip setTxtProgressBar txtProgressBar
#'@importFrom curl curl_fetch_memory
@@ -1197,11 +1192,6 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
# if(!is.numeric(bio.var)) stop()
# bio.var <- str_pad(bio.var, 2, 'left', pad = "0")
}
- if(is.element("30s", resolution)){
- warning("Data at 30-seconds spatial resolution is expected to be available soon.", call. = TRUE, immediate. = TRUE)
- }
- # analog the elevation can be regarded.
-
# First: Set URL Root --------------------------------------------------------
# https://geodata.ucdavis.edu/cmip6/30s/ACCESS-CM2/ssp126/wc2.1_30s_tmin_ACCESS-CM2_ssp126_2021-2040.tif
@@ -1242,14 +1232,6 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
"30s" = "30s",
next
)
- # if(res.temp == "30s") {
- # warning(
- # # "Processing might take a while since 30s resolution is downloaded for the whole world",
- # "30 second data is not yet available. Please check WorldClim website. Skipping 30s data!",
- # call. = TRUE,
- # immediate. = TRUE)
- # next
- # }
URL.2 <- paste0(res.temp, "/")
# Forth: Global Circulation Model --------------------------------------
for(gcm in model.var){
@@ -1282,9 +1264,18 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
URL.3, ".tif")
# check if URL is available
# if(url.exists(URL.temp)){
- if(RCurl::url.exists(url = URL.temp)){
+ # if(RCurl::urlExists(url = URL.temp)){
+ URLstatus <- curl::curl_fetch_memory(url = URL.temp)$status
+ if(URLstatus == 200){
# clear up the temporary directory
unlink(list.files(tempdir(), recursive = T, full.names=T))
+ if(res.temp == "30s"){
+ options(timeout = max(2400, getOption("timeout")))
+ }else{
+ if(getOption("timeout") != 60){
+ options(timeout = max(60, getOption("timeout")))
+ }
+ }
# download file to save location
download.file(url = URL.temp,
destfile = dest.temp,
diff --git a/build/vignette.rds b/build/vignette.rds
index d21735aa51ea825212c5d138535de4e413ab1afa..5cf6f94285e0877160cddd496bcf89146c0336f4 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/ClimDatDownloadR.html b/inst/doc/ClimDatDownloadR.html
index 011fb535ead0bf281c9c079ff052d4f4e9e95bbd..feb20ea7dbf307b224299f2782994594ab36431b 100644
--- a/inst/doc/ClimDatDownloadR.html
+++ b/inst/doc/ClimDatDownloadR.html
@@ -353,7 +353,15 @@ first, if not already done. Then you can activate the package with the
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># install.packages("ClimDatDownloadR", dependencies = TRUE)</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ClimDatDownloadR)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#> Loading required package: terra</span></span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> terra 1.7.23</span></span></code></pre></div>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#> terra 1.7.39</span></span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,</span></span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#> which was just loaded, will retire in October 2023.</span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#> Please refer to R-spatial evolution reports for details, especially</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">#> https://r-spatial.org/r/2023/05/15/evolution4.html.</span></span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">#> It may be desirable to make the sf package available;</span></span>
+<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#> package maintainers should consider adding sf to Suggests:.</span></span>
+<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#> The sp package is now running under evolution status 2</span></span>
+<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#> (status 2 uses the sf package in place of rgdal)</span></span></code></pre></div>
<p>Very well, now that you have the package installed and attached,
let’s start with the data sets of the climatologies of Chelsa and
WorldClim.</p>