diff --git a/DESCRIPTION b/DESCRIPTION
index 8af0e5477bdd1f15b50ec1ac91adc4437b18989e..6f52079d06333433bbfbbb043deefd247085ac22 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: ClimDatDownloadR
Type: Package
Title: Downloads Climate Data from Chelsa and WorldClim
-Version: 0.1.7-3
+Version: 0.1.7-4
Authors@R: c(person("Helge", "Jentsch",
email = "helge.marc.ole.jentsch@uni-hamburg.de",
role = c("aut", "cre"),
@@ -45,7 +45,7 @@ Suggests: knitr, testthat, usethis, rmarkdown
VignetteBuilder: knitr
SystemRequirements: Tested with at least 4 GB RAM.
NeedsCompilation: no
-Packaged: 2023-07-18 09:50:31 UTC; helge
+Packaged: 2023-08-14 18:54:05 UTC; helge
Author: Helge Jentsch [aut, cre],
Maria Bobrowski [aut],
Johannes Weidinger [aut],
diff --git a/R/Chelsa_Download_functions.R b/R/Chelsa_Download_functions.R
index 76904d3abaf479bdf9deafc898e798bf885f40df..d1cdd2303a923b905d84c404f8c4f39b89f38d67 100644
--- a/R/Chelsa_Download_functions.R
+++ b/R/Chelsa_Download_functions.R
@@ -1138,7 +1138,6 @@ Chelsa.lgm.download <- function(save.location = "./",
#'@param clip.extent numeric (vector). Input vector with four numeric values. This is following the input order c("xleft", "xright", "ybottom", "ytop").\cr Default: \code{c(-180, 180, -90, 90)}
#'@param buffer numeric. Input of decimal degrees of buffer around the shapefile and/or extent. \cr Default: \code{0}
#'@param convert.files.to.asc logical. Input whether files should be converted into the ASCII format.\cr If \code{TRUE}: a new subdirectory is created and the rawdata is saved there. \cr If \code{clipping} is \code{TRUE}: the clipped raster files are also saved as ASCII grids. \cr Default: \code{FALSE}
-#'@param stacking.data logical. Input whether the downloaded data should be stacked as a netCDF-rasterstack. \cr Default: \code{FALSE}
#'@param combine.raw.zip logical. Should the downloaded raw-data be "zipped". \cr Default: \code{FALSE}
#'@param delete.raw.data logical. Should the downloaded raw-data be deleted. If \code{combine.raw.zip} is \code{TRUE}: raw-data is still available in the zipped file. \cr Default: \code{FALSE}
#'@param save.bib.file logical. Whether a BibTex-citation file of the dataset should be provided in the Working directory. \cr Default: \code{TRUE}
@@ -1166,7 +1165,7 @@ Chelsa.lgm.download <- function(save.location = "./",
#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
#'
#'
-#'@export
+#'
Chelsa.timeseries.download <- function(save.location = "./",
parameter = c("prec", "tmax", "tmin"),
start.year.var = 1979,
diff --git a/R/Chelsa_new_download_functions.R b/R/Chelsa_new_download_functions.R
index 8ec635c3ff0a80b92b7e705aec31d88b2970144b..743b7a763c65d712898afae118f9e0a60b8d8400 100644
--- a/R/Chelsa_new_download_functions.R
+++ b/R/Chelsa_new_download_functions.R
@@ -874,4 +874,650 @@ Chelsa.CMIP_6.download <- function(save.location = "./",
close(PGB)
# delete all temporary files
unlink(list.files(tempdir(), recursive = T, full.names =T))
-}
\ No newline at end of file
+}
+
+#'@title CHELSA Timeseries Download
+#'@author Helge Jentsch
+#'@description This function supports a download of the CHELSA Timeseries dataset (Jan. 1979 - Dec. 2013). This includes precipitation sums (mm) and temperature (average, maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/timeseries/}.\cr To allow pre-processing, clipping and buffering, conversion to ASCII-grids and stacking options are included.\cr Optional an output of a .bib-file of the cited literature can be retrieved.\cr For user convenience, saving directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+#'
+#'@note Please note that the downloaded data for temperature are processed to °C with one significant decimal without offset and factor. Processing and conversion to other file-formats on a global dataset may take some time.
+#'
+#'@param save.location string. Input where the datasets should be saved. \cr Default: Working Directory.
+#'@param parameter string (vector). Input of parameters which should be downloaded. \cr Default: \code{c("prec", "tmax", "tmin")}
+#'@param start.year.var integer. Input year the download timeseries starts. \cr Default: 1979 (minimum)
+#'@param start.month.var integer. Input month the download timeseries starts. \cr Default: 1 (minimum)
+#'@param end.year.var integer. Input year the download timeseries ends. \cr Default: 2013 (maximum)
+#'@param end.month.var integer. Input month the download timeseries ends. \cr Default: 12 (maximum)
+#'@param include.month.var integer (vector). Input which monthly data should be downloaded. \cr Default: \code{c(1:12)}
+#'@param version.var string (vector). Input which version of the dataset should be downloaded. Multiple selection is _not_ possible. Select between version _1.2_ and _2.1_.\cr Default: \code{c("1.2")}
+#'@param clipping logical. Input whether the downloaded data should be clipped.\cr If \code{FALSE}: \code{clip.shapefile}, \code{buffer}, \code{clip.extent} will be ignored. \cr Default: \code{FALSE}
+#'@param clip.shapefile string. Input which shapefile should be used for clipping. \cr Default: \code{NULL}
+#'@param clip.extent numeric (vector). Input vector with four numeric values. This is following the input order c("xleft", "xright", "ybottom", "ytop").\cr Default: \code{c(-180, 180, -90, 90)}
+#'@param buffer numeric. Input of decimal degrees of buffer around the shapefile and/or extent. \cr Default: \code{0}
+#'@param convert.files.to.asc logical. Input whether files should be converted into the ASCII format.\cr If \code{TRUE}: a new subdirectory is created and the rawdata is saved there. \cr If \code{clipping} is \code{TRUE}: the clipped raster files are also saved as ASCII grids. \cr Default: \code{FALSE}
+#'@param combine.raw.zip logical. Should the downloaded raw-data be "zipped". \cr Default: \code{FALSE}
+#'@param delete.raw.data logical. Should the downloaded raw-data be deleted. If \code{combine.raw.zip} is \code{TRUE}: raw-data is still available in the zipped file. \cr Default: \code{FALSE}
+#'@param save.bib.file logical. Whether a BibTex-citation file of the dataset should be provided in the Working directory. \cr Default: \code{TRUE}
+#'
+#'@return Custom dataset of CHELSA Timeseries for a chosen timeseries.
+#'
+#'@references D. N. Karger, O. Conrad, J. B{\"o}hner , et al. "Climatologies at high resolution for the earth's land surface areas". In: _Scientific Data_ 4.1 (Sep. 2017). DOI: 10.1038/sdata.2017.122. <URL: https://doi.org/10.1038/sdata.2017.122>.
+#'@references D. N. Karger, O. Conrad, J. B{\"o}hner , et al. _Data from: Climatologies at high resolution for the earth's land surface areas_. En. 2018. DOI: 10.5061/DRYAD.KD1D4. <URL: http://datadryad.org/stash/dataset/doi:10.5061/dryad.kd1d4>.
+#'
+#'@examples
+#' \dontrun{
+#' Chelsa.timeseries.download(parameter = "prec",
+#' start.year.var = 2000,
+#' start.month.var = 1,
+#' end.year.var = 2002,
+#' end.month.var = 12,
+#' version.var = "1.2",
+#' include.month.var = c(1,12))
+#' }
+#'
+#'@import stringr
+#'@import RCurl
+#'@import ncdf4
+#'@import terra
+#'@import httr
+#'@importFrom utils unzip download.file setTxtProgressBar txtProgressBar
+#'
+#'
+#'@export
+Chelsa.timeseries.download <- function(save.location = "./",
+ parameter = c("prec", "temp", "tmax", "tmin"),
+ start.year.var = 1979,
+ start.month.var = 1,
+ end.year.var = 2013,
+ end.month.var = 12,
+ include.month.var = c(1:12),
+ version.var = c("1.2"),
+ clipping = FALSE,
+ clip.shapefile = NULL,
+ buffer = 0,
+ clip.extent = c(-180, 180, -90, 90),
+ convert.files.to.asc = FALSE,
+ combine.raw.zip = FALSE,
+ delete.raw.data = FALSE,
+ save.bib.file = TRUE){
+ gc()
+ call.time <- stringr::str_replace_all(stringr::str_replace_all(paste0(Sys.time()),
+ pattern = ":",
+ replacement = "-"),
+ pattern = " ",
+ replacement = "_")
+ # initial check -----------------------------------------------------------
+ # normalize Path for easier application later
+ save.location <- normalizePath(save.location,
+ winslash = "/")
+ if(length(version.var) != 1) stop("Version variable 'version.var' should only have either '1.2' or '2.1'.")
+ if(!is.null(version.var) & version.var == "1.2"){
+ # Check which parameters are put in and if the connected
+ # month/bio-variables are correctly input
+ if(is.element("prec", parameter)|
+ is.element("tmax", parameter)|
+ is.element("temp", parameter)|
+ is.element("tmin", parameter)){
+ include.month.var <- c(include.month.var)
+ if(!is.numeric(include.month.var)) stop()
+ include.month.var <- str_pad(include.month.var,
+ 2,
+ 'left',
+ pad = "0")
+ # print(include.month.var)
+ }
+ if(start.year.var < 1979 | end.year.var > 2013 | end.year.var < 1979 | start.year.var > 2013) {
+ stop("Timeseries only available from 01.1979 to 12.2013. \n Please check input!")
+ }
+ # check for consistent timeseries
+ if(end.year.var < start.year.var) stop("Endyear is before the startyear. Please correct the input!")
+ if(start.year.var == end.year.var){
+ if(start.month.var > end.month.var) stop("End is before the start. Please correct the input!")
+ }
+
+ ts_string <- seq.Date(as.Date(paste(start.year.var,
+ start.month.var, "01", sep = "-")),
+ as.Date(paste(end.year.var,
+ end.month.var, "01", sep = "-")),
+ by = "month")
+ ts_string <- format.Date(ts_string, format = "%Y_%m")
+ # ts_string <- str_sub(ts_string, 1, end = str_length(ts_string)-3)
+ # ts_string <- str_replace_all(ts_string, pattern = "-", replacement = "_")
+
+ if(length(include.month.var)!=12){
+ ts.string.temp <- c()
+ for (incl.month in include.month.var) {
+ # print(incl.month)
+ ts.string.temp <- c(ts.string.temp,
+ ts_string[grep(pattern = paste0("_", incl.month)
+ , ts_string)]
+ )
+ }
+ ts_string <- ts.string.temp
+ }
+ }
+ if(!is.null(version.var) & version.var == "2.1"){
+ # Check which parameters are put in and if the connected
+ # month/bio-variables are correctly input
+ if(is.element("prec", parameter)|
+ is.element("tmax", parameter)|
+ is.element("temp", parameter)|
+ is.element("tmin", parameter)){
+ include.month.var <- c(include.month.var)
+ if(!is.numeric(include.month.var)) stop()
+ include.month.var <- str_pad(include.month.var,
+ 2,
+ 'left',
+ pad = "0")
+ # print(include.month.var)
+ }
+ if(start.year.var < 1979 | end.year.var > 2019 | end.year.var < 1979 | start.year.var > 2019) {
+ stop("Timeseries only available from 02.1979 to 12.2019. \n Please check input!")
+ }
+ # check for consistent timeseries
+ if(end.year.var < start.year.var) stop("Endyear is before the startyear. Please correct the input!")
+ if(start.year.var == end.year.var){
+ if(start.month.var > end.month.var) stop("End is before the start. Please correct the input!")
+ }
+
+ ts_string <- seq.Date(as.Date(paste(start.year.var,
+ start.month.var, "01", sep = "-")),
+ as.Date(paste(end.year.var,
+ end.month.var, "01", sep = "-")),
+ by = "month")
+ ts_string <- format.Date(ts_string, format = "%m_%Y")
+ # ts_string <- str_sub(ts_string, 1, end = str_length(ts_string)-3)
+ # ts_string <- str_replace_all(ts_string, pattern = "-", replacement = "_")
+
+ if(length(include.month.var)!=12){
+ ts.string.temp <- c()
+ for (incl.month in include.month.var) {
+ # print(incl.month)
+ ts.string.temp <- c(ts.string.temp,
+ ts_string[grep(pattern = paste0("_", incl.month)
+ , ts_string)]
+ )
+ }
+ ts_string <- ts.string.temp
+ }
+ }
+
+ # Preparations ------------------------------------------------------------
+ # parameter
+ parameter <- base::sort(parameter)
+ DLTparameter <- c(base::rep(parameter[parameter!="bio"],
+ base::length(ts_string)))
+ DLTparameter <- base::sort(DLTparameter)
+ # variables
+ DLTvariable <- NULL
+ for(parm in parameter){
+ DLTvariable <- c(DLTvariable,
+ switch(parm,
+ "prec" = ts_string,
+ "tmax" = ts_string,
+ "temp" = ts_string,
+ "tmin" = ts_string,
+ stop()
+ )
+ )
+ }
+ # Combine search into large dataframe -------------------------------------
+ dataDF <- data.frame("parameter" = base::sort(DLTparameter),
+ "variable" = DLTvariable
+ )
+ if(length(version.var)==1){
+ dataDF$version <- base::rep(version.var, length(DLTvariable))
+ }
+
+ # v1.2
+ if(is.element("1.2", dataDF$version)){
+ # dataDF$parmLong[dataDF$version == "1.2"] <- base::paste0(dataDF$parameter[dataDF$version == "1.2"],"10")
+
+ dataDF$parmLong[dataDF$version == "1.2"] <-
+ base::paste0(dataDF$parameter[dataDF$version == "1.2"])
+ dataDF$parmLong[dataDF$version == "1.2" & dataDF$parameter == "prec"] <-
+ base::paste0("prec")
+ dataDF$parmLong[dataDF$version == "1.2" & dataDF$parameter == "tmean"] <-
+ base::paste0("tmean")
+ dataDF$parmLong[dataDF$version == "1.2" & dataDF$parameter == "tmax"] <-
+ base::paste0("tmax")
+ dataDF$parmLong[dataDF$version == "1.2" & dataDF$parameter == "tmin"] <-
+ base::paste0("tmin")
+
+ dataDF$parameter[dataDF$version == "1.2" & dataDF$parameter == "temp"] <- base::paste0("tmean")
+ # dataDF$years[dataDF$version =="1.2"] <- "_1979-2013"
+ # dataDF$years[dataDF$version == "1.2" &
+ # (dataDF$parameter == "prec" | dataDF$parameter == "bio")] <- base::paste0("")
+
+ # Adding the URL stings
+ # https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V1/timeseries/tmax/CHELSA_tmax_1979_01_V1.2.1.tif
+ dataDF$URL[dataDF$version == "1.2" & dataDF$parameter != "bio"] <-
+ # https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V1/timeseries/
+ paste0("https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V1/timeseries/",
+ # tmax
+ dataDF$parameter[dataDF$version == "1.2" & dataDF$parameter != "bio"],
+ # /CHELSA_
+ "/CHELSA_",
+ # tmax
+ dataDF$parameter[dataDF$version == "1.2" & dataDF$parameter != "bio"],
+ # _
+ "_",
+ # 1979_01
+ dataDF$variable[dataDF$version == "1.2" & dataDF$parameter != "bio"],
+ #_V1.2.1.tif
+ "_V1.2.1.tif")
+ }
+
+ # v2.1
+ if(is.element("2.1", dataDF$version)){
+ dataDF$parmLong[dataDF$version == "2.1" &
+ dataDF$parameter == "prec"] <- base::paste0("pr")
+ dataDF$parmLong[dataDF$version == "2.1" &
+ dataDF$parameter == "temp"] <- base::paste0("tas")
+ dataDF$parmLong[dataDF$version == "2.1" &
+ dataDF$parameter == "tmin"] <- base::paste0("tasmin")
+ dataDF$parmLong[dataDF$version == "2.1" &
+ dataDF$parameter == "tmax"] <- base::paste0("tasmax")
+ # dataDF$years[dataDF$version =="2.1"] <- "_1981-2010"
+
+
+ # https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V2/GLOBAL/monthly/tas/CHELSA_tas_11_2007_V.2.1.tif
+ dataDF$URL[dataDF$version == "2.1" & dataDF$parameter != "bio"] <-
+ paste0("https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V2/GLOBAL/monthly/",
+ dataDF$parmLong[dataDF$version == "2.1" & dataDF$parameter != "bio"],
+ "/CHELSA_",
+ dataDF$parmLong[dataDF$version == "2.1" & dataDF$parameter != "bio"],
+ "_",
+ dataDF$variable[dataDF$version == "2.1" & dataDF$parameter != "bio"],
+ "_V.2.1.tif")
+ }
+ write.table(x = dataDF,
+ file = normalizePath(paste0(save.location, "/", call.time, "_downloadDataframe.csv"), winslash = "/"),
+ sep = ";",
+ dec = ".",
+ row.names = F,
+ append = F)
+ # Check if URL exists!
+ for(urlexists in dataDF$URL){ # loop through all URLs
+ if(!RCurl::url.exists(urlexists)){ # if not, print warning!
+ cat(paste(urlexists,
+ " does not exist, please check the website of Chelsa. \n")
+ )
+ if(urlexists == dataDF$URL[1]){
+ cat(paste("\t If any of these download warnings was prompted incorrectly, we apprecheate a feedback on this at helge.marc.ole.jentsch@uni-hamburg.de\n")
+ )}
+ next
+ }
+ }
+ # print the amount of data to be downloaded and processed.
+ print(paste0(getDownloadSize(dataDF$URL), " MB will be downloaded."))
+ # Progressbar setup
+ PGBsum <- nrow(dataDF) + length(unique(dataDF$parameter)) + 1
+ PGB <- utils::txtProgressBar(min = 0, max = PGBsum, style = 3)
+ PGBstate <- 0
+ # Preparation of save location stack
+ locationSack <- NULL
+ # loop through every instance and save the location.
+ # HINT FOR RUNTIME IMPROVEMENT!!!
+ for(parm in dataDF$parameter){
+ if (!dir.exists(paste0(save.location, "/", parm))){
+ dir.create(paste0(save.location, "/", parm))
+ }
+ if("1.2" %in% dataDF$version){
+ if (!dir.exists(paste0(save.location, "/", parm, "/ChelsaV1.2Timeseries"))){
+ dir.create(paste0(save.location, "/", parm, "/ChelsaV1.2Timeseries"))
+ }
+ locationSack <- c(locationSack, paste0(save.location, "/", parm, "/ChelsaV1.2Timeseries/"))
+ }
+ if("2.1" %in% dataDF$version){
+ if (!dir.exists(paste0(save.location, "/", parm, "/ChelsaV2.1Timeseries"))){
+ dir.create(paste0(save.location, "/", parm, "/ChelsaV2.1Timeseries"))
+ }
+ locationSack <- c(locationSack, paste0(save.location, "/", parm, "/ChelsaV2.1Timeseries/"))
+ }
+ }
+ print(locationSack)
+
+ dataDF$filepath[dataDF$version == "1.2"] <-
+ paste0(save.location,"/",
+ dataDF$parameter, "/ChelsaV1.2Timeseries",
+ "/CHELSA_", dataDF$parmLong , "_", dataDF$variable, dataDF$years,
+ "_V1.2.tif")
+ dataDF$filepath[dataDF$version == "2.1"] <-
+ paste0(save.location,"/",
+ dataDF$parameter, "/ChelsaV2.1Timeseries",
+ "/CHELSA_", dataDF$parmLong , "_", dataDF$variable, dataDF$years,
+ "_V2.1.tif")
+ # check for file existance - if not already present - download file
+ for(fileexists in dataDF$filepath){
+ if(!file.exists(fileexists)){
+ unlink(list.files(tempdir(), recursive = TRUE, full.names = TRUE))
+ download.file(url = dataDF$URL[dataDF$filepath == fileexists],
+ destfile = fileexists,
+ # overwrite is TRUE otherwise a error is caused
+ overwrite = TRUE,
+ # From the description file:
+ # The choice of binary transfer (mode = "wb" or "ab")
+ # is important on Windows, since unlike Unix-alikes
+ # it does distinguish between text and binary files and
+ # for text transfers changes
+ # \n line endings to \r\n (aka ‘CRLF’).
+ mode = 'wb',
+ # to show progression bar
+ quiet = TRUE,
+ cacheOK = FALSE)
+ }
+ setTxtProgressBar(PGB, PGBstate+1)
+ PGBstate <- PGBstate+1
+ }
+
+
+ if(is.element("1.2", dataDF$version)){
+ # https://chelsa-climate.org/wp-admin/download-page/CHELSA_tech_specification.pdf
+ rescaleDF_V12 <- dataDF[dataDF$version == "1.2" &
+ dataDF$parameter != "prec"
+ ,]
+
+ if(nrow(rescaleDF_V12)>0){
+ for(rescale_i in 1:nrow(rescaleDF_V12)){
+ gc()
+ tempRast <- terra::rast(rescaleDF_V12$filepath[rescale_i])
+ tempRast <- process.raster.int.doub(tempRast)
+ tempFilePath <- tempfile(tmpdir = tempdir(), fileext = ".tif")
+ terra::writeRaster(x = tempRast,
+ filename = tempFilePath
+ )
+ terra::writeRaster(x = terra::rast(x = tempFilePath),
+ filename = rescaleDF_V12$filepath[rescale_i],
+ overwrite = TRUE)
+ rm(tempFilePath)
+ gc()
+ }
+ rm(rescale_i)
+ unlink(list.files(tempdir(), recursive = T, full.names =T))
+ }
+ }
+ if(is.element("2.1", dataDF$version)){
+ # https://chelsa-climate.org/wp-admin/download-page/CHELSA_tech_specification_V2.pdf
+ rescaleDF_V21 <- dataDF[dataDF$version == "2.1",]
+ if(nrow(rescaleDF_V21)>0){
+ for(rescale_i in 1:nrow(rescaleDF_V21)){
+ gc()
+ tempRast <- terra::rast(rescaleDF_V21$filepath[rescale_i])
+ tempRast <- process.raster.int.doub(tempRast)
+ tempFilePath <- tempfile(tmpdir = tempdir(), fileext = ".tif")
+ terra::writeRaster(x = tempRast,
+ filename = tempFilePath
+ )
+ terra::writeRaster(x = terra::rast(x = tempFilePath),
+ filename = rescaleDF_V21$filepath[rescale_i],
+ overwrite = TRUE)
+ rm(tempFilePath)
+ gc()
+ }
+ rm(rescale_i)
+ unlink(list.files(tempdir(), recursive = T, full.names =T))
+ }
+ offsetDF_V21 <- dataDF[dataDF$version == "2.1" &
+ dataDF$parameter != "prec"]
+ if(nrow(offsetDF_V21)>0){
+ for(rescale_i in 1:nrow(offsetDF_V21)){
+ gc()
+ tempRast <- terra::rast(offsetDF_V21$filepath[rescale_i])
+ tempRast <- process.raster.offset(tempRast)
+ tempFilePath <- tempfile(tmpdir = tempdir(), fileext = ".tif")
+ terra::writeRaster(x = tempRast,
+ filename = tempFilePath
+ )
+ terra::writeRaster(x = terra::rast(x = tempFilePath),
+ filename = offsetDF_V21$filepath[rescale_i],
+ overwrite = TRUE)
+ rm(tempFilePath)
+ gc()
+ }
+ rm(rescale_i)
+ unlink(list.files(tempdir(), recursive = T, full.names =T))
+ }
+ }
+ locationSack <- unique(locationSack)
+ for (temp.temp.save.location in locationSack) {
+ run <- grep(temp.temp.save.location, locationSack)
+ for(i in run){
+ # print(ls())
+ # variable.numbers <- dataDF$variable[dataDF$parameter == parameter[i]]
+ # stop()
+ # if clipping is TRUE ...
+ if(clipping == TRUE){
+ # the function "clipping.tif" (found in the auxiliary.R-File)
+ # is executed. The clip.save.location is the same location as the
+ # "current" save location
+ clipping.tif(clip.save.location = temp.temp.save.location,
+ # the clip-shapefile is passed
+ # default "NULL" does not produce error
+ clip.shapefile = clip.shapefile,
+ # Clip.extent is passed
+ # default "c(-180, 180, -90, 90)" does not produce errors
+ # simply clips the whole world.
+ clip.extent = clip.extent,
+ # buffer is passed
+ # default: 0. Unit is arc-degrees
+ buffer = buffer,
+ # conversion to ASCII format here integrated into the
+ # clipping function. Since it can be assumed that
+ # they should be converted lateron anyway.
+ convert.files.to.asc = convert.files.to.asc,
+ time.stamp.var = call.time)
+ }
+ # if converting.files.to.asc is TRUE ...
+ if(convert.files.to.asc == TRUE){
+ # the function "convert.to.asc" (found in the auxiliary.R-File)
+ # is executed. The save.location is the same location as the
+ # "current" save location. Also another new subdirectory will
+ # be created with the name "ASCII" .
+ convert.to.asc(save.location = temp.temp.save.location,
+ time.stamp.var = call.time)
+ }
+ # if stacking.data is TRUE ...
+ # if(stacking.data == TRUE){
+ # # the function "stacking.downloaded.data"
+ # # (found in the auxiliary.R-File) is executed.
+ # # The save.location is the same location as the
+ # # "current" save location.
+ # if(clipping==TRUE){
+ # stacking.downloaded.data(stack.save.location = temp.temp.save.location,
+ # parameter.var = parameter[i],
+ # variable.numbers = variable.numbers,
+ # stack.clipped = TRUE,
+ # time.stamp.var = call.time)
+ # }else{
+ # stacking.downloaded.data(stack.save.location = temp.temp.save.location,
+ # parameter.var = parameter[i],
+ # variable.numbers = variable.numbers,
+ # stack.clipped = FALSE,
+ # time.stamp.var = call.time)
+ # }
+ # }
+ # if combine.raw.zip is TRUE ...
+ if(combine.raw.zip == TRUE){
+ # the function "combine.raw.in.zip"
+ # (found in the auxiliary.R-File) is executed.
+ # The save.location is the same location as the
+ # "current" save location. The name of the zip-file is also
+ # passed with the current parameter in it.
+ combine.raw.in.zip(save.location = temp.temp.save.location,
+ zip.name = paste0("CHELSAClim_", parameter[i], ""),
+ time.stamp.var = call.time)
+ }
+ # if delete.raw.data is TRUE ...
+ if(delete.raw.data == TRUE){
+ # All .tif raster files in the current 2nd order subdirectory are
+ # unlinked (deleted).
+ unlink(list.files(temp.temp.save.location,
+ pattern = ".tif",
+ include.dirs = FALSE,
+ full.names = T),
+ force = TRUE)
+ }
+ }
+ # delete all temporary files
+ unlink(list.files(tempdir(), recursive = T, full.names =T))
+ setTxtProgressBar(PGB, PGBstate+1)
+ PGBstate <- PGBstate+1
+ }
+ if(save.bib.file == TRUE) {
+ save.citation(save.location = save.location, dataSetName = "CHELSA")
+ }
+ setTxtProgressBar(PGB, PGBstate+1)
+ close(PGB)
+ # delete all temporary files
+ unlink(list.files(tempdir(), recursive = T, full.names =T))
+}
+# stop()
+# # Parameter and directories -----------------------------------------------
+# # work through paramerters
+# for(i in parameter){
+# # clear up the temporary directory
+# unlink(list.files(tempdir(), recursive = T, full.names=T))
+#
+# # create intermediate strings for later use
+# interm <- switch(i,
+# "prec" = "prec/",
+# "temp" = "tmean/",
+# "tmax" = "tmax/",
+# "tmin" = "tmin/",
+# # "bio" = "bio/",
+# stop())
+#
+# variable.numbers <- switch(i,
+# # "bio" = bio.var,
+# "tmin" = include.month.var,
+# "tmax" = include.month.var,
+# "temp" = include.month.var,
+# "prec" = include.month.var,
+# stop())
+#
+# # create new directory
+# if(!dir.exists(paste0(save.location, "/", i))){
+# dir.create(paste0(save.location, "/", i), showWarnings = FALSE)
+# }
+# temp.save.location <- paste0(save.location, "/", i, "/")
+# # to go analog to the functions before
+# temp.temp.save.location <- paste0(temp.save.location,
+# stringr::str_replace_all(interm,
+# pattern = "/",
+# "_"),
+# "timeseries","/")
+# # print(str_sub(temp.temp.save.location, end=-2))
+# if(!dir.exists(temp.temp.save.location)){
+# dir.create(str_sub(temp.temp.save.location, end=-2))
+# }
+#
+# # temp.temp.save.location <- normalizePath(temp.temp.save.location,
+# # winslash = "/")
+# # if(i == "temp"){
+# # i <- "tmean"
+# # }
+# # print(interm)
+# # Download ----------------------------------------------------------------
+# # if(i != "bio"){
+# for (year_month in ts_string){
+# URL.temp <-
+# paste0("https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V1/timeseries/",
+# interm, "CHELSA_", i,"_",year_month,
+# "_V1.2.1.tif")
+# # check if URL is available
+# if(!http_error(URL.temp)){
+# # clear up the temporary directory
+# unlink(list.files(tempdir(), recursive = T, full.names=T))
+#
+# dest.file <- paste0(temp.temp.save.location, "CHELSA_", i,
+# "_", year_month, "_V1.2.1.tif")
+# if(!file.exists(dest.file)){
+# # download file to save location
+# download.file(url = URL.temp,
+# destfile = dest.file,
+# overwrite = TRUE,
+# mode = 'wb',
+# quiet = FALSE)
+#
+#
+# if(i != "prec"){
+# raster.temp <- terra::rast(dest.file)
+#
+# raster.temp <- terra::clamp(raster.temp, lower = -1000, useValues = FALSE)
+# gc()
+#
+# raster.temp <- process.raster.int.doub(raster.temp)
+# raster.temp <- process.raster.offset(raster.layer = raster.temp)
+#
+# terra::writeRaster(x = raster.temp,
+# filename = dest.file,
+# overwrite = TRUE)
+# rm(raster.temp)
+# gc()
+# }
+# }
+# }else{
+# # Warning message
+# warning(paste0("File does not exist. Did not download: \n", URL.temp, "\n\n"),
+# call. = TRUE, immediate. = FALSE)
+# }
+# if(year_month == ts_string[length(ts_string)] &
+# length(list.files(temp.temp.save.location,
+# pattern = ".tif",
+# include.dirs = FALSE)) != 0){
+# if(clipping == TRUE){
+# clipping.tif(clip.save.location = temp.temp.save.location,
+# clip.shapefile = clip.shapefile,
+# clip.extent = clip.extent,
+# convert.files.to.asc = convert.files.to.asc,
+# buffer = buffer,
+# time.stamp.var = call.time)
+# }
+# if(convert.files.to.asc == TRUE){
+# convert.to.asc(temp.temp.save.location,
+# time.stamp.var = call.time)
+# }
+# if(stacking.data == TRUE){
+# if(clipping==TRUE){
+# stacking.downloaded.data(stack.save.location = temp.temp.save.location,
+# parameter.var = i,
+# variable.numbers = variable.numbers,
+# stack.clipped = TRUE,
+# stack.time.series = TRUE,
+# time.series = ts_string,
+# time.stamp.var = call.time)
+# }else{
+# stacking.downloaded.data(stack.save.location = temp.temp.save.location,
+# parameter.var = i,
+# variable.numbers = variable.numbers,
+# stack.time.series = TRUE,
+# time.series = ts_string,
+# time.stamp.var = call.time)
+# }
+# }
+# if(combine.raw.zip == TRUE){
+# combine.raw.in.zip(save.location = temp.temp.save.location,
+# zip.name = paste0("CHELSATimeseries_", i, ""),
+# time.stamp.var = call.time)
+# }
+# if(delete.raw.data == TRUE){
+# unlink(list.files(temp.temp.save.location,
+# pattern = ".tif",
+# include.dirs = FALSE, full.names = T), force = TRUE)
+# }
+# }
+# }
+#
+# # Clean up, if no data was downloaded. ------------------------------------
+#
+#
+# if(length(list.files(temp.temp.save.location,
+# include.dirs = TRUE)) == 0){
+# unlink(str_sub(temp.temp.save.location, 1, end = str_length(temp.temp.save.location)-1),
+# force = T, recursive = TRUE)
+# }
+# }
+# # Saving BIB File
+# if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "CHELSA")
+# }
diff --git a/R/auxiliary.R b/R/auxiliary.R
index 2ffa22a1172c982cf6606367a5fd7d2822fcb8e4..21b6a1de80457044b011fbd5b211bb67a2183ff8 100644
--- a/R/auxiliary.R
+++ b/R/auxiliary.R
@@ -592,6 +592,10 @@ getDownloadSize <- function(URLVector){
filesizes <- sum(filesizes,fileISize)
# return(Downloadsize)
}
+ availDiscSpaceMB <- as.numeric(stringr::str_remove(base::system("wmic logicaldisk get freespace", inter=TRUE)[2], pattern = " \r"))/1024/1024
+ # if(availDiscSpaceMB < round(filesizes*0.000001, 2)){
+ # print(paste0(round(filesizes*0.000001, 2),"MB will be downloaded. These is only ", availDiscSpaceMB, "MB available. Please consider another download location."))
+ # }
return(round(filesizes*0.000001, 2))
# Download size in MB
diff --git a/inst/doc/ClimDatDownloadR.html b/inst/doc/ClimDatDownloadR.html
index feb20ea7dbf307b224299f2782994594ab36431b..65ebe23b7f71e9a1de9ef525837c057ae3202d93 100644
--- a/inst/doc/ClimDatDownloadR.html
+++ b/inst/doc/ClimDatDownloadR.html
@@ -350,18 +350,18 @@ provided by <a href="http://chelsa-climate.org/">Chelsa</a> and <a href="https:/
<p>To start, you’ll have to install the package and it’s dependencies
first, if not already done. Then you can activate the package with the
<code>library</code>-function.</p>
-<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 1.7.39</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>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="co"># install.packages("ClimDatDownloadR", dependencies = TRUE)</span></span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">library</span>(ClimDatDownloadR)</span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="co">#> Loading required package: terra</span></span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="co">#> terra 1.7.39</span></span>
+<span id="cb1-5"><a href="#cb1-5" 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" 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" 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" 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" 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" tabindex="-1"></a><span class="co">#> package maintainers should consider adding sf to Suggests:.</span></span>
+<span id="cb1-11"><a href="#cb1-11" 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" 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>
diff --git a/man/Chelsa.timeseries.download.Rd b/man/Chelsa.timeseries.download.Rd
index 9fe70f541dee69df390ba13cb955cf1a3b8fca3e..7880adea7e81d0f9066e4da3c53df13d9fa52dc2 100644
--- a/man/Chelsa.timeseries.download.Rd
+++ b/man/Chelsa.timeseries.download.Rd
@@ -1,23 +1,43 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Chelsa_Download_functions.R
+% Please edit documentation in R/Chelsa_Download_functions.R,
+% R/Chelsa_new_download_functions.R
\name{Chelsa.timeseries.download}
\alias{Chelsa.timeseries.download}
\title{CHELSA Timeseries Download}
\usage{
Chelsa.timeseries.download(
save.location = "./",
- parameter = c("prec", "tmax", "tmin"),
+ parameter = c("prec", "temp", "tmax", "tmin"),
start.year.var = 1979,
start.month.var = 1,
end.year.var = 2013,
end.month.var = 12,
include.month.var = c(1:12),
+ version.var = c("1.2"),
+ clipping = FALSE,
+ clip.shapefile = NULL,
+ buffer = 0,
+ clip.extent = c(-180, 180, -90, 90),
+ convert.files.to.asc = FALSE,
+ combine.raw.zip = FALSE,
+ delete.raw.data = FALSE,
+ save.bib.file = TRUE
+)
+
+Chelsa.timeseries.download(
+ save.location = "./",
+ parameter = c("prec", "temp", "tmax", "tmin"),
+ start.year.var = 1979,
+ start.month.var = 1,
+ end.year.var = 2013,
+ end.month.var = 12,
+ include.month.var = c(1:12),
+ version.var = c("1.2"),
clipping = FALSE,
clip.shapefile = NULL,
buffer = 0,
clip.extent = c(-180, 180, -90, 90),
convert.files.to.asc = FALSE,
- stacking.data = FALSE,
combine.raw.zip = FALSE,
delete.raw.data = FALSE,
save.bib.file = TRUE
@@ -38,6 +58,8 @@ Chelsa.timeseries.download(
\item{include.month.var}{integer (vector). Input which monthly data should be downloaded. \cr Default: \code{c(1:12)}}
+\item{version.var}{string (vector). Input which version of the dataset should be downloaded. Multiple selection is _not_ possible. Select between version _1.2_ and _2.1_.\cr Default: \code{c("1.2")}}
+
\item{clipping}{logical. Input whether the downloaded data should be clipped.\cr If \code{FALSE}: \code{clip.shapefile}, \code{buffer}, \code{clip.extent} will be ignored. \cr Default: \code{FALSE}}
\item{clip.shapefile}{string. Input which shapefile should be used for clipping. \cr Default: \code{NULL}}
@@ -48,8 +70,6 @@ Chelsa.timeseries.download(
\item{convert.files.to.asc}{logical. Input whether files should be converted into the ASCII format.\cr If \code{TRUE}: a new subdirectory is created and the rawdata is saved there. \cr If \code{clipping} is \code{TRUE}: the clipped raster files are also saved as ASCII grids. \cr Default: \code{FALSE}}
-\item{stacking.data}{logical. Input whether the downloaded data should be stacked as a netCDF-rasterstack. \cr Default: \code{FALSE}}
-
\item{combine.raw.zip}{logical. Should the downloaded raw-data be "zipped". \cr Default: \code{FALSE}}
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted. If \code{combine.raw.zip} is \code{TRUE}: raw-data is still available in the zipped file. \cr Default: \code{FALSE}}
@@ -57,12 +77,18 @@ Chelsa.timeseries.download(
\item{save.bib.file}{logical. Whether a BibTex-citation file of the dataset should be provided in the Working directory. \cr Default: \code{TRUE}}
}
\value{
+Custom dataset of CHELSA Timeseries for a chosen timeseries.
+
Custom dataset of CHELSA Timeseries for a chosen timeseries.
}
\description{
+This function supports a download of the CHELSA Timeseries dataset (Jan. 1979 - Dec. 2013). This includes precipitation sums (mm) and temperature (average, maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/timeseries/}.\cr To allow pre-processing, clipping and buffering, conversion to ASCII-grids and stacking options are included.\cr Optional an output of a .bib-file of the cited literature can be retrieved.\cr For user convenience, saving directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+
This function supports a download of the CHELSA Timeseries dataset (Jan. 1979 - Dec. 2013). This includes precipitation sums (mm) and temperature (average, maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/timeseries/}.\cr To allow pre-processing, clipping and buffering, conversion to ASCII-grids and stacking options are included.\cr Optional an output of a .bib-file of the cited literature can be retrieved.\cr For user convenience, saving directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
}
\note{
+Please note that the downloaded data for temperature are processed to °C with one significant decimal without offset and factor. Processing and conversion to other file-formats on a global dataset may take some time.
+
Please note that the downloaded data for temperature are processed to °C with one significant decimal without offset and factor. Processing and conversion to other file-formats on a global dataset may take some time.
}
\examples{
@@ -75,10 +101,24 @@ Chelsa.timeseries.download(parameter = "prec",
include.month.var = c(1,12))
}
+\dontrun{
+Chelsa.timeseries.download(parameter = "prec",
+ start.year.var = 2000,
+ start.month.var = 1,
+ end.year.var = 2002,
+ end.month.var = 12,
+ version.var = "1.2",
+ include.month.var = c(1,12))
+}
+
}
\references{
D. N. Karger, O. Conrad, J. B{\"o}hner , et al. "Climatologies at high resolution for the earth's land surface areas". In: _Scientific Data_ 4.1 (Sep. 2017). DOI: 10.1038/sdata.2017.122. <URL: https://doi.org/10.1038/sdata.2017.122>.
+D. N. Karger, O. Conrad, J. B{\"o}hner , et al. _Data from: Climatologies at high resolution for the earth's land surface areas_. En. 2018. DOI: 10.5061/DRYAD.KD1D4. <URL: http://datadryad.org/stash/dataset/doi:10.5061/dryad.kd1d4>.
+
+D. N. Karger, O. Conrad, J. B{\"o}hner , et al. "Climatologies at high resolution for the earth's land surface areas". In: _Scientific Data_ 4.1 (Sep. 2017). DOI: 10.1038/sdata.2017.122. <URL: https://doi.org/10.1038/sdata.2017.122>.
+
D. N. Karger, O. Conrad, J. B{\"o}hner , et al. _Data from: Climatologies at high resolution for the earth's land surface areas_. En. 2018. DOI: 10.5061/DRYAD.KD1D4. <URL: http://datadryad.org/stash/dataset/doi:10.5061/dryad.kd1d4>.
}
\author{