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Commit 68c83015 authored by Jentsch, Helge's avatar Jentsch, Helge
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WC CMIP6 Update

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DESCRIPTION
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− 1
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...@@ -45,7 +45,7 @@ Suggests: knitr, testthat, usethis, rmarkdown ...@@ -45,7 +45,7 @@ Suggests: knitr, testthat, usethis, rmarkdown
VignetteBuilder: knitr VignetteBuilder: knitr
SystemRequirements: Tested with at least 4 GB RAM. SystemRequirements: Tested with at least 4 GB RAM.
NeedsCompilation: no NeedsCompilation: no
Packaged: 2023-05-11 12:43:21 UTC; helge Packaged: 2023-06-23 12:34:01 UTC; helge
Author: Helge Jentsch [aut, cre], Author: Helge Jentsch [aut, cre],
Maria Bobrowski [aut], Maria Bobrowski [aut],
Johannes Weidinger [aut], Johannes Weidinger [aut],
......
R/WorldClim_download_functions.R
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− 65
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...@@ -1135,9 +1135,20 @@ WorldClim.CMIP_6.download <- function(save.location = "./", ...@@ -1135,9 +1135,20 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
bio.var = c(1:19), bio.var = c(1:19),
month.var = c(1:12), month.var = c(1:12),
resolution = c("10min", "5min", "2.5min", "30s"), resolution = c("10min", "5min", "2.5min", "30s"),
model.var = c("BCC-CSM2-MR", "CNRM-CM6-1", model.var = c("ACCESS-CM2",
"BCC-CSM2-MR", "CMCC-ESM2",
"CNRM-CM6-1",
"CNRM-ESM2-1", "CanESM5", "CNRM-ESM2-1", "CanESM5",
"GFDL-ESM4", "IPSL-CM6A-LR", "EC-Earth3-Veg",
"FIO-ESM-2-0",
"GFDL-ESM4",
"GISS-E2-1-G",
"HadGEM3-GC31-LL",
"INM-CM5-0",
"IPSL-CM6A-LR",
"MPI-ESM1-2-HR",
"MRI-ESM2-0",
"UKESM1-0-LL",
"MIROC-ES2L", "MIROC6", "MIROC-ES2L", "MIROC6",
"MRI-ESM2-0"), "MRI-ESM2-0"),
emission.scenario.var = c("ssp126", emission.scenario.var = c("ssp126",
...@@ -1193,8 +1204,8 @@ WorldClim.CMIP_6.download <- function(save.location = "./", ...@@ -1193,8 +1204,8 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
# First: Set URL Root -------------------------------------------------------- # First: Set URL Root --------------------------------------------------------
# https://geodata.ucdavis.edu/cmip6/30s/ACCESS-CM2/ssp126/wc2.1_30s_tmin_ACCESS-CM2_ssp126_2021-2040.tif
URL.1 <- "http://biogeo.ucdavis.edu/data/worldclim/v2.1/fut/" URL.1 <- "https://geodata.ucdavis.edu/cmip6/"
# Second: Parameters --------------------------------------------------------- # Second: Parameters ---------------------------------------------------------
for(parm in parameter){ for(parm in parameter){
...@@ -1258,15 +1269,17 @@ WorldClim.CMIP_6.download <- function(save.location = "./", ...@@ -1258,15 +1269,17 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
# temp.temp.save.location <- normalizePath(temp.temp.save.location, # temp.temp.save.location <- normalizePath(temp.temp.save.location,
# winslash = "/") # winslash = "/")
dest.temp <- paste0(temp.temp.save.location, "WC_", res, "_", dest.temp <- paste0(temp.temp.save.location, "WC_", res, "_",
gcm, "_", rcp.temp, "_", year.temp, "_Bulk.zip") gcm, "_", rcp.temp, "_", year.temp, "_Bulk.tif")
URL.3 <- paste0("wc2.1_",res.temp,"_",parm.temp, "_", gcm, "_", URL.3 <- paste0("",gcm, "/",rcp.temp, "/",
rcp.temp, "_", year.temp) "wc2.1_",res.temp,"_",parm.temp, "_", gcm, "_", rcp.temp, "_", year.temp)
print(URL.3) print(URL.3)
if(!file.exists(dest.temp)){ if(!file.exists(dest.temp)){
# create a variable for the later requested Download-URL to avoid # create a variable for the later requested Download-URL to avoid
# requireing multiple changes, if the link changes. # requireing multiple changes, if the link changes.
URL.temp <- paste0(URL.1, URL.2,URL.3, ".zip") URL.temp <- paste0(URL.1,
URL.2,
URL.3, ".tif")
# check if URL is available # check if URL is available
# if(url.exists(URL.temp)){ # if(url.exists(URL.temp)){
if(RCurl::url.exists(url = URL.temp)){ if(RCurl::url.exists(url = URL.temp)){
...@@ -1295,63 +1308,89 @@ WorldClim.CMIP_6.download <- function(save.location = "./", ...@@ -1295,63 +1308,89 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
next() next()
} }
} }
# Unzip the files of the Bulk-Download-Zip-File # # Unzip the files of the Bulk-Download-Zip-File
files.list <- list.files(temp.temp.save.location, # files.list <- list.files(temp.temp.save.location,
pattern = ".zip", # pattern = ".zip",
# full.names = T)
# for (file in files.list) {
# unzip(file,
# exdir = stringr::str_sub(temp.temp.save.location,
# start = 0,
# end = stringr::str_length(temp.temp.save.location)-1)
# )
# file.copy(from = paste0(list.files(temp.temp.save.location,
# pattern = paste0(URL.3, ".tif"),
# recursive = TRUE,
# full.names = TRUE))[1],
# to = paste0(temp.temp.save.location,
# URL.3,"_stacked_RAW.tif"),
# overwrite = TRUE)
# if(dir.exists(paste0(temp.temp.save.location,"//share"))){
# unlink(paste0(temp.temp.save.location,"//share"),
# recursive = TRUE)
#
# }
# tif.list <- list.files(temp.temp.save.location,
# pattern = "stacked_RAW.tif",
# recursive = TRUE,
# full.names = TRUE)
# print(tif.list)
# if (!is.null(tif.list)){
# if(length(tif.list)==1){
# raster.temp <- raster::unstack(raster::stack(tif.list))
# if(parm != "bio"){
# for(layer.month in month.var){
# writeRaster(x = raster.temp[[layer.month]],
# filename = paste0(temp.temp.save.location,
# URL.3,"_",layer.month,".tif"),
# overwrite = TRUE
# )
# }
# }else{
# for(layer.bio in bio.var){
# writeRaster(x = raster.temp[[layer.bio]],
# filename = paste0(temp.temp.save.location,
# URL.3,"_",layer.bio,".tif"),
# overwrite = TRUE
# )
# }
# }
# }
# unlink(tif.list)
# }
# if(keep.raw.zip == FALSE){
# print(file)
# unlink(file)
# }
# }
temp.bulkfile <- list.files(path = temp.temp.save.location,
pattern = "Bulk.tif",
full.names = T) full.names = T)
for (file in files.list) { temp.rast <- rast(temp.bulkfile)
unzip(file, if(parm == "bio"){
exdir = stringr::str_sub(temp.temp.save.location, temp.rast <- temp.rast[[bio.var]]
start = 0,
end = stringr::str_length(temp.temp.save.location)-1)
)
file.copy(from = paste0(list.files(temp.temp.save.location,
pattern = paste0(URL.3, ".tif"),
recursive = TRUE,
full.names = TRUE))[1],
to = paste0(temp.temp.save.location,
URL.3,"_stacked_RAW.tif"),
overwrite = TRUE)
if(dir.exists(paste0(temp.temp.save.location,"//share"))){
unlink(paste0(temp.temp.save.location,"//share"),
recursive = TRUE)
}
tif.list <- list.files(temp.temp.save.location,
pattern = "stacked_RAW.tif",
recursive = TRUE,
full.names = TRUE)
print(tif.list)
if (!is.null(tif.list)){
if(length(tif.list)==1){
raster.temp <- raster::unstack(raster::stack(tif.list))
if(parm != "bio"){
for(layer.month in month.var){
writeRaster(x = raster.temp[[layer.month]],
filename = paste0(temp.temp.save.location,
URL.3,"_",layer.month,".tif"),
overwrite = TRUE
)
}
}else{ }else{
for(layer.bio in bio.var){ temp.rast <- temp.rast[[month.var]]
writeRaster(x = raster.temp[[layer.bio]],
filename = paste0(temp.temp.save.location,
URL.3,"_",layer.bio,".tif"),
overwrite = TRUE
)
} }
for(lyr.temp in seq(1, terra::nlyr(temp.rast), 1)){
lyrName <- names(temp.rast[[lyr.temp]])
lyrName <- paste0(stringr::str_sub(temp.bulkfile, end = -9),
lyrName,
".tif")
terra::writeRaster(temp.rast[[lyr.temp]],
filename = lyrName,
overwrite = TRUE)
} }
}
unlink(tif.list) if(!dir.exists(paths = paste0(temp.temp.save.location, "/Bulk/"))){
} dir.create(paste0(temp.temp.save.location, "/Bulk/"))
if(keep.raw.zip == FALSE){
print(file)
unlink(file)
}
} }
# print(ls()) file.copy(from = temp.bulkfile,
to = paste0(temp.temp.save.location, "/Bulk/", basename(temp.bulkfile)))
unlink(temp.bulkfile,
force = T)
# Hier weiter mit alle-betreffenden Bearbeitungen # Hier weiter mit alle-betreffenden Bearbeitungen
# print(list.files(temp.temp.save.location, pattern = ".tif", full.names = FALSE)) # print(list.files(temp.temp.save.location, pattern = ".tif", full.names = FALSE))
...@@ -1430,6 +1469,8 @@ WorldClim.CMIP_6.download <- function(save.location = "./", ...@@ -1430,6 +1469,8 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
include.dirs = FALSE, include.dirs = FALSE,
full.names = T), full.names = T),
force = TRUE) force = TRUE)
unlink(x = paste0(temp.temp.save.location,"/Bulk/"),
recursive = T)
} }
# if no subdirectories and files are to be found in the 2nd order # if no subdirectories and files are to be found in the 2nd order
# subdirectory the directory will be deleted for a better overview of # subdirectory the directory will be deleted for a better overview of
......
man/WorldClim.CMIP_6.download.Rd
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...@@ -10,8 +10,10 @@ WorldClim.CMIP_6.download( ...@@ -10,8 +10,10 @@ WorldClim.CMIP_6.download(
bio.var = c(1:19), bio.var = c(1:19),
month.var = c(1:12), month.var = c(1:12),
resolution = c("10min", "5min", "2.5min", "30s"), resolution = c("10min", "5min", "2.5min", "30s"),
model.var = c("BCC-CSM2-MR", "CNRM-CM6-1", "CNRM-ESM2-1", "CanESM5", "GFDL-ESM4", model.var = c("ACCESS-CM2", "BCC-CSM2-MR", "CMCC-ESM2", "CNRM-CM6-1", "CNRM-ESM2-1",
"IPSL-CM6A-LR", "MIROC-ES2L", "MIROC6", "MRI-ESM2-0"), "CanESM5", "EC-Earth3-Veg", "FIO-ESM-2-0", "GFDL-ESM4", "GISS-E2-1-G",
"HadGEM3-GC31-LL", "INM-CM5-0", "IPSL-CM6A-LR", "MPI-ESM1-2-HR", "MRI-ESM2-0",
"UKESM1-0-LL", "MIROC-ES2L", "MIROC6", "MRI-ESM2-0"),
emission.scenario.var = c("ssp126", "ssp245", "ssp370", "ssp585"), emission.scenario.var = c("ssp126", "ssp245", "ssp370", "ssp585"),
time.interval.var = c("2021-2040", "2041-2060", "2061-2080", "2081-2100"), time.interval.var = c("2021-2040", "2041-2060", "2061-2080", "2081-2100"),
clipping = FALSE, clipping = FALSE,
......
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