From 207214321aae9d4d47683af867722dbf6e458b2f Mon Sep 17 00:00:00 2001
From: "Jentsch, Helge Marc Ole" <helge.marc.ole.jentsch@uni-hamburg.de>
Date: Wed, 24 Mar 2021 20:59:39 +0100
Subject: [PATCH] 2021-03-24 Upadate: - Documentation Updates
Signed-off-by: Jentsch, Helge Marc Ole <helge.marc.ole.jentsch@uni-hamburg.de>
---
DESCRIPTION | 24 ++--
NAMESPACE | 1 -
R/Chelsa_Download_functions.R | 216 ++++++++++++++++-------------
R/WorldClim_download_functions.R | 140 ++++++++++---------
R/auxiliary.R | 68 ++++-----
man/Chelsa.CMIP_5.download.Rd | 47 ++++---
man/Chelsa.CRUts.download.Rd | 34 +++--
man/Chelsa.Clim.download.Rd | 34 +++--
man/Chelsa.lgm.download.Rd | 35 +++--
man/Chelsa.timeseries.download.Rd | 30 ++--
man/WorldClim.CMIP_5.download.Rd | 47 ++++---
man/WorldClim.CMIP_6.download.Rd | 46 +++---
man/WorldClim.HistClim.download.Rd | 44 +++---
man/clipping.tif.Rd | 6 +-
man/combine.raw.in.zip.Rd | 4 +-
man/convert.to.asc.Rd | 2 +-
man/process.raster.int.doub.Rd | 8 +-
man/save.citation.Rd | 15 +-
man/stacking.downloaded.data.Rd | 6 +-
19 files changed, 457 insertions(+), 350 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 1a3ded9..1cd82c1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,16 +15,18 @@ Authors@R: c(person("Helge", "Jentsch",
email = "nadine.kaul@studium.uni-hamburg.de",
role = c("ctb")))
Maintainer: Helge Jentsch <helge.jentsch@studium.uni-hamburg.de>
-Description: ClimDatDownloadR provides functions to download and save
- climate data sets from both Chelsa and WorldClim in their
- various resolution and provided parameters.
- The output is provided as GEOTIFF, ASCII, or netCDF format.
- This work is based on work by Karger et al. (2017)
- <doi:10.1038/sdata.2017.122> (Chelsa), Hijmans et al. (2005)
- <doi:10.1002/joc.1276> (WorldClim 1.4), and Fick and Hijmans (2017)
- <doi:10.1002/joc.5086> (WorldClim 2.1). A applied comparison of the
- two data sets is given by Bobrowski & Schickhoff 2017
- <doi:10.1016/j.ecolmodel.2017.05.021>.
+Description: ClimDatDownloadR provides functions to download, pre-process and
+ manage CHELSA and Worldclim climate data sets in respective available
+ spatial and temporal resolutions. The output is provided as GEOTIFF,
+ ASCII, or netCDF format. The package's main purpose is to simplify and
+ automate the downloading and pre-processing workflows.
+ We are not redistributing the climate data sets.
+ This work is based on work by
+ Karger et al. (2017) <doi:10.1038/sdata.2017.122> (CHELSA),
+ Hijmans et al. (2005) <doi:10.1002/joc.1276> (WorldClim 1.4),
+ and Fick and Hijmans (2017) <doi:10.1002/joc.5086> (WorldClim 2.1).
+ A applied comparison of the two data sets is given by
+ Bobrowski & Schickhoff 2017 <doi:10.1016/j.ecolmodel.2017.05.021>.
YEAR: 2021
License: MIT + file LICENSE
Encoding: UTF-8
@@ -39,7 +41,7 @@ Suggests: knitr, testthat, usethis, rmarkdown
VignetteBuilder: knitr
SystemRequirements: Tested with at least 4 GB RAM.
NeedsCompilation: no
-Packaged: 2021-03-18 22:01:05 UTC; helge
+Packaged: 2021-03-24 19:58:04 UTC; helge
Author: Helge Jentsch [aut, cre],
Maria Bobrowski [aut],
Johannes Weidinger [aut],
diff --git a/NAMESPACE b/NAMESPACE
index 7556526..97aa739 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,7 +11,6 @@ export(WorldClim.HistClim.download)
export(clipping.tif)
export(combine.raw.in.zip)
export(convert.to.asc)
-export(process.raster.int.doub)
export(save.citation)
export(stacking.downloaded.data)
import(RCurl)
diff --git a/R/Chelsa_Download_functions.R b/R/Chelsa_Download_functions.R
index 1f9ce8f..5845294 100644
--- a/R/Chelsa_Download_functions.R
+++ b/R/Chelsa_Download_functions.R
@@ -1,13 +1,12 @@
-#'@title Function for downloading the Chelsa Climate dataset
+#'@title Function for downloading the CHELSA climate dataset (1979-2013)
#'@author Helge Jentsch
-#'@description This function supports a download of the Chelsa Climate dataset. This includes precipitation (mm), temperature (average, maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid,and stacking-tool is included.\cr An output of a .bib-file of the literature is also optional.\cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+#'@description This function supports the download, pre-processing and management of CHELSA climate data comprising of monthly precipitation sums in mm, monthly temperature (average, minimum, maximum) in degrees Celsius, and annual chracteristics (19 bioclimatic variables). The spatial resolution of the downloaded data is 30 arc-seconds.\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.
#'
-#'
-#'@param save.location string. Input where the datasets should be saved. \cr Default: Working Directory.
+#'@param save.location string. Input where the datasets will be saved. \cr Default: Working Directory.
#'@param parameter string (vector). Input of parameters which should be downloaded. \cr Default: \code{c("prec", "temp", "tmax", "tmin", "bio")}
#'@param bio.var integer (vector). Input which monthly data should be downloaded. Only applicable to BIOCLIM variables. For further information see: \url{http://chelsa-climate.org/bioclim/}. \cr Default: \code{c(1:19)}
-#'@param month.var integer (vector). Input which monthly data should be downloaded. Only applicable to precipitation and temperature (average, maximum, minimum). \cr Default: \code{c(1:12O)}
-#'@param version.var string (vector). Input which version of the data set should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.1", "1.2")}
+#'@param month.var integer (vector). Input which monthly data should be downloaded. Only applicable to precipitation and temperature (average, maximum, minimum). \cr Default: \code{c(1:12)}
+#'@param version.var string (vector). Input which version of the dataset should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.2")}
#'@param clipping logical. Input whether the downloaded data should be clipped.\cr If \code{FALSE}: clip.shapefile, buffer, 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)}
@@ -16,16 +15,21 @@
#'@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.\cr 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 data set should be provided in the Working directory. \cr Default: \code{TRUE}
-#'@return Chelsa climate data sets for the period of 1979 - 2013
+#'@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 CHELSA climate datasets for the period of 1979 - 2013
+#'
+#'@note Please note that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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.
+#'
+#'@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
-#' ## NOT RUN
-#' ## Bioclim
-#' # Chelsa.Clim.download(parameter = "bio", bio.var = c(1,12))
-#' ## Precipitation
-#' # Chelsa.Clim.download(parameter = "prec", month.var = c(1,12))
-#' ## NOT RUN
+#' \dontrun{
+#' # Bioclim
+#' Chelsa.Clim.download(parameter = "bio", bio.var = c(1,19))
+#' # Precipitation
+#' Chelsa.Clim.download(parameter = "prec", month.var = c(1,12))
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -223,7 +227,7 @@ Chelsa.Clim.download <- function(save.location = "./",
# buffer is passed
# default: 0. Unit is arc-degrees
buffer = buffer,
- # conversion to ascii format here integrated into the
+ # 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,
@@ -265,7 +269,7 @@ Chelsa.Clim.download <- function(save.location = "./",
# "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_", i, ""),
+ zip.name = paste0("CHELSAClim_", i, ""),
time.stamp.var = call.time)
}
# if delete.raw.data is TRUE ...
@@ -287,7 +291,7 @@ Chelsa.Clim.download <- function(save.location = "./",
# just that bio.var instead of month.var is used.
for(bio in bio.var){
if(version == "1.1"){
- warning("Chelsa BioClim Version 1.1 not available!")
+ warning("CHELSA BioClim Version 1.1 not available!")
next
}
dest.temp <- paste0(temp.temp.save.location,
@@ -377,7 +381,7 @@ Chelsa.Clim.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaClim_", i, ""),
+ zip.name = paste0("CHELSAClim_", i, ""),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -411,25 +415,27 @@ Chelsa.Clim.download <- function(save.location = "./",
# the save.location. If the user's working directory is the desktop
# and no other save.location is specified initially, on the desktop.
if(save.bib.file == TRUE) {
- save.citation(save.location = save.location, dataSetName = "Chelsa")
+ save.citation(save.location = save.location, dataSetName = "CHELSA")
}
# delete all temporary files
unlink(list.files(tempdir(), recursive = T, full.names =T))
}
-#'@title Function for downloading Chelsa CMIP 5 future climatologies data sets for 2050 and 2070
+#'@title Function for downloading CHELSA CMIP 5 future climatologies for the years 2041-2060 and 2061-2080
#'@author Helge Jentsch
-#'@description This function supports a download of the Chelsa CMIP5 future climate data sets. This includes precipitation (mm), temperature (average, maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. An output of a .bib-file of the literature is also optional. For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
-#'@details "The Downscaled data has been produced using climatological aided interpolation based on the 1979-2013 reference climatologies from CHELSA." (Chelsa Climate 2020: \url{http://chelsa-climate.org/future/})
-#'@note For some of the datasets not all models are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of Chelsa Climate (\url{http://chelsa-climate.org/future/}).
+#'@description This function supports the download of CHELSA CMIP5 future climate scenarios comprising of monthly precipitation sums in mm, monthly temperature (average, minimum, maximum) in degrees Celsius, and annual chracteristics (19 bioclimatic variables).\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.
+#'
+#'@details "The downscaled data has been produced using climatological aided interpolation based on the 1979-2013 reference climatologies from CHELSA." (CHELSA Climate 2020: \url{http://chelsa-climate.org/future/})
+#'
+#'@note Please note that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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.\cr For some of the datasets not all models and rcps are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of CHELSA Climate (\url{http://chelsa-climate.org/future/}). Please note, that the downloaded data for temperature and the therefore also the first eleven bioclim-variables are processed to °C 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", "temp", "tmax", "tmin", "bio")}
#'@param bio.var integer (vector). Input which monthly data should be downloaded. Only applicable to BIOCLIM variables. For further information see: \url{http://chelsa-climate.org/bioclim/}. \cr Default: \code{c(1:19)}
#'@param month.var integer (vector). Input which monthly data should be downloaded. Only applicable to Precipitation and Temperature (average, maximum, minimum). \cr Default: \code{c(1:12)}
#'@param emission.scenario.var string (vector). Input which emission scenario dataset should be downloaded. Provided are the representative concentration pathways (RCP) 2.6, 4.5, 6.0, and 8.5.\cr Default: \code{c("rcp26", "rcp45", "rcp60", "rcp85")}
-#'@param time.interval.var string (vector). Input for which time interval data should be downloaded. Chelsa provides downscaled CMIP5 climatologies for 2050 and 2070. Multiple inputs possible.\cr Default: \code{c("2041-2060", "2061-2080")}
+#'@param time.interval.var string (vector). Input for which time interval data should be downloaded. CHELSA provides downscaled CMIP5 climatologies for 2050 and 2070. Multiple inputs possible.\cr Default: \code{c("2041-2060", "2061-2080")}
#'@param model.var string (vector). Input which future model dataset should be downloaded. For more information see: \url{http://chelsa-climate.org/future/}.\cr For some of the datasets not all downloads are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. For an overview please try "warnings()" after execution. \cr Default: \code{c("ACCESS1-0", "bcc-csm1-1", "BNU-ESM", "CanESM2", "CCSM4", "CESM1-BGC", } \cr \code{"CESM1-CAM5", "CMCC-CESM", "CMCC-CM", "CMCC-CMS", "CNRM-CM5", "CSIRO-Mk3-6-0",} \cr \code{ "CSIRO-Mk3L-1-2", "EC-EARTH", "FGOALS-g2", "FIO-ESM", "GFDL-CM3", "GFDL-ESM2G", } \cr \code{"GFDL-ESM2M","GISS-E2-H", "GISS-E2-H-CC", "GISS-E2-R", "GISS-E2-R-CC", "HadGEM2-AO",} \cr \code{"HadGEM2-CC", "HadGEM2-ES", "inmcm4", "IPSL-CM5A-LR", "IPSL-CM5A-MR","MIROC-ESM",} \cr \code{"MIROC-ESM-CHEM","MIROC5", "MPI-ESM-LR", "MPI-ESM-MR", "MRI-CGCM3", "MRI-ESM1",} \cr \code{ "NorESM1-M","NorESM1-ME")}
#'@param clipping logical. Input whether the downloaded data should be clipped.\cr If \code{FALSE} \code{clip.shapefile}, buffer, 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}
@@ -439,25 +445,28 @@ Chelsa.Clim.download <- function(save.location = "./",
#'@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 the \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 data set should be provided in the Working directory. \cr Default: \code{TRUE}
+#'@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 Downscaled Chelsa CMIP5 climatologies for 2050 and 2070.
+#'@return Downscaled CHELSA CMIP5 climatologies for 2050 and 2070.
+#'
+#'@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
-#' ## NOT RUN
-#' ## Bioclim
-#' # Chelsa.CMIP_5.download(parameter = "bio",
-#' # bio.var = c(1,12),
-#' # emission.scenario.var = "rcp26",
-#' # time.interval.var = "2041-2060",
-#' # model.var = "MPI-ESM-LR")
-#' ## Precipitation
-#' # Chelsa.CMIP_5.download(parameter = "prec",
-#' # month.var = c(1,12),
-#' # emission.scenario.var = "rcp26",
-#' # time.interval.var = "2041-2060",
-#' # model.var = "MPI-ESM-LR")
-#' ## NOT RUN
+#' \dontrun{
+#' # Bioclim
+#' Chelsa.CMIP_5.download(parameter = "bio",
+#' bio.var = c(1,19),
+#' emission.scenario.var = "rcp26",
+#' time.interval.var = "2041-2060",
+#' model.var = "MPI-ESM-LR")
+#' # Precipitation
+#' Chelsa.CMIP_5.download(parameter = "prec",
+#' month.var = c(1,12),
+#' emission.scenario.var = "rcp26",
+#' time.interval.var = "2041-2060",
+#' model.var = "MPI-ESM-LR")
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -591,8 +600,6 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
raster.temp <- clamp(raster.temp, lower = -1000,
useValues = FALSE)
gc()
-
- # raster.temp <- process.raster.int.doub(raster.temp)
gain(raster.temp) <- 0.1
gc()
writeRaster(raster.temp,
@@ -638,7 +645,7 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaCMIP5_", i, ""),
+ zip.name = paste0("CHELSACMIP5_", i, ""),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -724,7 +731,7 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaCMIP5_", i, ""),
+ zip.name = paste0("CHELSACMIP5_", i, ""),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -748,14 +755,16 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
}
}
# Saving BIB File ---------------------------------------------------------
- if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "Chelsa")
+ if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "CHELSA")
}
-#'@title Function for downloading Chelsa Last Glacial Maximum datasets
+#'@title Function for downloading CHELSA Last Glacial Maximum datasets
#'@author Helge Jentsch
-#'@description This function supports a download of the Chelsa Last Glacial Maximum Climate datasets (21.000 years ago). This includes precipitation (mm), temperature (average, maximum, minimum; °C), bioclimatic parameters, and a global digital elevation model. For further information, please regard \url{http://chelsa-climate.org/last-glacial-maximum-climate/}.\cr For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
-#'@details "The CHELSA LGM data is based on a implementation of the CHELSA algorithm on PMIP3 data." (Chelsa Climate 2020: \url{http://chelsa-climate.org/last-glacial-maximum-climate/})
-#'@note For some of the datasets not all models are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of Chelsa Climate (\url{http://chelsa-climate.org/last-glacial-maximum-climate/}).
+#'@description This function supports a download of the CHELSA Last Glacial Maximum Climate datasets (21.000 BP). This includes monthly precipitation sums in mm, monthly temperature (average, maximum, minimum) in degree Celsius, annual characteristics (19 bioclimatic parameters), and a global digital elevation model. For further information, please regard \url{http://chelsa-climate.org/last-glacial-maximum-climate/}.\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.
+#'
+#'@details "The CHELSA LGM data is based on a implementation of the CHELSA algorithm on PMIP3 data." (CHELSA Climate 2020: \url{http://chelsa-climate.org/last-glacial-maximum-climate/})
+#'
+#'@note Please note that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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.\cr For some of the datasets not all models are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of CHELSA Climate (\url{http://chelsa-climate.org/last-glacial-maximum-climate/}).
#'
#'
#'@param save.location string. Input where the datasets should be saved. \cr Default: Working Directory.
@@ -772,21 +781,24 @@ Chelsa.CMIP_5.download <- function(save.location = "./",
#'@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 the "combine.raw.zip"-option 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 Chelsa-dataset should be provided in the Working directory. \cr Default: \code{TRUE}
+#'@param save.bib.file logical. Whether a BibTex-citation file of the CHELSA dataset should be provided in the Working directory. \cr Default: \code{TRUE}
#'
#'@return Downscaled global climatological data from the last glacial maximum.
#'
+#'@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
-#' ## NOT RUN
-#' ## Bioclim
-#' # Chelsa.lgm.download(parameter = "bio",
-#' # bio.var = c(1,12),
-#' # model.var = "MPI-ESM-P")
-#' ## Precipitation
-#' # Chelsa.lgm.download(parameter = "prec",
-#' # month.var = c(1,12),
-#' # model.var = "MPI-ESM-P")
-#' ## NOT RUN
+#' \dontrun{
+#' # Bioclim
+#' Chelsa.lgm.download(parameter = "bio",
+#' bio.var = c(1,19),
+#' model.var = "MPI-ESM-P")
+#' # Precipitation
+#' Chelsa.lgm.download(parameter = "prec",
+#' month.var = c(1,12),
+#' model.var = "MPI-ESM-P")
+#' }
#'
#'
#'@import stringr
@@ -869,7 +881,7 @@ Chelsa.lgm.download <- function(save.location = "./",
temp.save.location <- paste0(save.location, "/", i, "/")
for (model in model.var) {
- # download of the requested data sets -------------------------------------
+ # download of the requested datasets -------------------------------------
temp.temp.save.location <- paste0(temp.save.location,
str_replace_all(interm,
pattern = "/",
@@ -989,7 +1001,7 @@ Chelsa.lgm.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaLGM_", i, ""),
+ zip.name = paste0("CHELSALGM_", i, ""),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -1070,7 +1082,7 @@ Chelsa.lgm.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaLGM_", i, ""),
+ zip.name = paste0("CHELSALGM_", i, ""),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -1093,24 +1105,26 @@ Chelsa.lgm.download <- function(save.location = "./",
if(!dir.exists(paste0(save.location, "/elev"))){
dir.create(paste0(save.location, "/elev"))
}
- if(!dir.exists(paste0(save.location, "/elev/Chelsa_LGM_Elevation_Grid"))){
- dir.create(paste0(save.location, "/elev/Chelsa_LGM_Elevation_Grid"))
+ if(!dir.exists(paste0(save.location, "/elev/CHELSA_LGM_Elevation_Grid"))){
+ dir.create(paste0(save.location, "/elev/CHELSA_LGM_Elevation_Grid"))
}
- if(!file.exists(paste0(save.location, "/elev/Chelsa_LGM_Elevation_Grid/", "CHELSA_PMIP_dem_global.tif"))){
+ if(!file.exists(paste0(save.location, "/elev/CHELSA_LGM_Elevation_Grid/", "CHELSA_PMIP_dem_global.tif"))){
download.file(url = "https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V1/pmip3/DEM/high_longlat.tif",
- destfile = paste0(save.location, "/elev/Chelsa_LGM_Elevation_Grid/", "CHELSA_PMIP_dem_global.tif"),
+ destfile = paste0(save.location, "/elev/CHELSA_LGM_Elevation_Grid/", "CHELSA_PMIP_dem_global.tif"),
overwrite = TRUE,
mode = 'wb',
quiet = FALSE)
}
}
# Saving BIB File
- if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "Chelsa")
+ if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "CHELSA")
}
-#'@title Chelsa Timeseries Download
+#'@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 (mm) and temperature (average, maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/timeseries/}.\cr For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+#'@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")}
@@ -1129,17 +1143,20 @@ Chelsa.lgm.download <- function(save.location = "./",
#'@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.
+#'@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
-#' ## NOT RUN
-#' # Chelsa.timeseries.download(parameter = "prec",
-#' # start.year.var = 2000,
-#' # start.month.var = 1,
-#' # end.year.var = 2002,
-#' # end.month.var = 12,
-#' # include.month.var = c(1,12))
-#' ## END
+#' \dontrun{
+#' Chelsa.timeseries.download(parameter = "prec",
+#' start.year.var = 2000,
+#' start.month.var = 1,
+#' end.year.var = 2002,
+#' end.month.var = 12,
+#' include.month.var = c(1,12))
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -1346,7 +1363,7 @@ Chelsa.timeseries.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaTimeseries_", i, ""),
+ zip.name = paste0("CHELSATimeseries_", i, ""),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -1367,12 +1384,14 @@ Chelsa.timeseries.download <- function(save.location = "./",
}
}
# Saving BIB File
- if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "Chelsa")
+ if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "CHELSA")
}
-#'@title Chelsa CRU Timeseries Download
+#'@title CHELSA CRU Timeseries Download
#'@author Helge Jentsch
-#'@description This function supports a download of the Chelsa CRU Timeseries dataset (Jan. 1901 - Dec. 2016). This includes precipitation (mm) and temperature (maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/chelsacruts/}.\cr For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+#'@description This function supports a download of the CHELSA CRU Timeseries dataset (Jan. 1901 - Dec. 2016). This includes precipitation sums in mm and temperature (maximum, minimum) in degree Celsius. For further information, please regard \url{http://chelsa-climate.org/chelsacruts/}.\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 is 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")}
@@ -1389,19 +1408,24 @@ Chelsa.timeseries.download <- function(save.location = "./",
#'@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}
+#'@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 CRU Timeseries for a chosen timeseries.
+#'
#'
-#'@return Custom dataset of Chelsa CRU 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>.
+#'@references D. N. Karger and N. E. Zimmermann. _CHELSAcruts - High resolution temperature and precipitation timeseries for the 20th century and beyond_. 2018. DOI: http://dx.doi.org/10.16904/envidat.159.
#'
#'@examples
-#' ## NOT RUN
-#' # Chelsa.CRUts.download(parameter = "prec",
-#' # start.year.var = 2000,
-#' # start.month.var = 1,
-#' # end.year.var = 2002,
-#' # end.month.var = 12,
-#' # include.month.var = c(1,12))
-#' ## END
+#' \dontrun{
+#' Chelsa.CRUts.download(parameter = "prec",
+#' start.year.var = 2000,
+#' start.month.var = 1,
+#' end.year.var = 2002,
+#' end.month.var = 12,
+#' include.month.var = c(1,12))
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -1444,7 +1468,7 @@ Chelsa.CRUts.download <- function(save.location = "./",
is.element("tmax", parameter)|is.element("tmin", parameter)){
include.month.var <- c(include.month.var)
if(!is.numeric(include.month.var)) {
- stop(paste0("Chelsa CRU timeseries is only available for ",
+ stop(paste0("CHELSA CRU timeseries is only available for ",
"precipitation and temperature maximum and minimum"))
}
include.month.var <- str_pad(include.month.var, 2, 'left', pad = "0")
@@ -1618,7 +1642,7 @@ Chelsa.CRUts.download <- function(save.location = "./",
}
if(combine.raw.zip == TRUE){
combine.raw.in.zip(save.location = temp.temp.save.location,
- zip.name = paste0("ChelsaCRUts_", i, "_V.1.0"),
+ zip.name = paste0("CHELSACRUts_", i, "_V.1.0"),
time.stamp.var = call.time)
}
if(delete.raw.data == TRUE){
@@ -1639,5 +1663,5 @@ Chelsa.CRUts.download <- function(save.location = "./",
}
# Saving BIB File
- if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "Chelsa")
+ if(save.bib.file == TRUE) save.citation(save.location = save.location, dataSetName = "CHELSA")
}
diff --git a/R/WorldClim_download_functions.R b/R/WorldClim_download_functions.R
index 8325c82..6bdf99e 100644
--- a/R/WorldClim_download_functions.R
+++ b/R/WorldClim_download_functions.R
@@ -1,14 +1,16 @@
-#'@title Function for downloading the WorldClim Historical Climate dataset
+#'@title Function for downloading the WorldClim historical climate dataset
#'@author Helge Jentsch
-#'@description This function supports a download of the WorldClim Historical Climate dataset. \cr This includes precipitation (mm), temperature (average, maximum, minimum; °C), solar radiation (kJ m-2 day-1), wind speed (m s-1), water vapor pressure (kPa) and bioclimatic parameters. Also an elevation raster is provided. \cr For convenience also a clipping-, conversion to ASCII-grid, and stacking-tool is included in this function. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
-#'@note Please note, that solar radiation, wind speed, water vapor pressure, bioclimatic parameters, and elevation raster are only provided by the WorldClim Version 2.1 (current version).
+#'@description This function supports the download, pre-processing and management of the WorldClim historical climate dataset.\cr This comprises of monthly precipitation sums (mm), temperature (average, maximum, minimum; °C), monthly solar radiation sums (kJ m-2 day-1), wind speed (m s-1), water vapor pressure (kPa), and annual chracteristics (19 bioclimatic variables). Also an elevation raster is provided.\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 solar radiation, wind speed, water vapor pressure, bioclimatic parameters, and elevation raster are only provided by the WorldClim Version 2.1 (current version).
+#'@note Please note also that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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 depending on the spatial resolution.
#'
#'@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", "temp", "tmax","tmin", "srad", "wind", "vapr", "bio", "elev").}
#'@param bio.var integer (vector). Input which monthly data should be downloaded. Only applicable to BIOCLIM variables. For further information see: \url{https://www.worldclim.org/data/bioclim.html}. \cr Default: \code{c(1:19)}
#'@param month.var integer (vector). Input which monthly data should be downloaded. \cr Default: \code{c(1:12)}
#'@param resolution string (vector). Ranging from a 10 arc-minute resolution over 5 and 2.5 arc-minute to 30 arc-second resolution.\cr Default: \code{c("10m", "5m", "2.5m", "30s")}
-#'@param version.var string (vector). Input which version of the data set should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.4", "2.1")}
+#'@param version.var string (vector). Input which version of the dataset should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.4", "2.1")}
#'@param clipping logical. Input whether the downloaded data should be clipped. See \code{\link{clipping.tif}} for more information. \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)}
@@ -17,23 +19,27 @@
#'@param stacking.data logical. Input whether the downloaded data should be stacked as a netCDF-rasterstack. See \code{\link{stacking.downloaded.data}} for more information. \cr Default: \code{FALSE}
#'@param keep.raw.zip logical. Should the downloaded raw-data be provided as "zip"-file. See \code{\link{combine.raw.in.zip}} for more information. \cr Default: \code{FALSE}
#'@param delete.raw.data logical. Should the downloaded raw-data be deleted. \cr If the "combine.raw.zip"-option 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. See \code{\link{save.citation}} for more information. \cr Default: \code{TRUE}
+#'@param save.bib.file logical. Whether a BibTex-citation file of the dataset should be provided in the Working directory. See \code{\link{save.citation}} for more information. \cr Default: \code{TRUE}
+#'
+#'@return WorldClim climate datasets for the period of 1960-1990 (for v1.4) and/or 1970-2000 (for v2.1).
#'
-#'@return WorldClim climate data sets for the period of 1960-1990 (for v1.4) and/or 1970-2000 (for v2.1).
+#'@references R. J. Hijmans, S. E. Cameron, J. L. Parra, et al. "Very high resolution interpolated climate surfaces for global land areas". In: _International Journal of Climatology_ 25.15 (2005), pp. 1965-1978. DOI: 10.1002/joc.1276. <URL: https://doi.org/10.1002/joc.1276>.
+#'@references S. E. Fick and R. J. Hijmans. "WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas". In: _International Journal of Climatology_ 37.12 (Okt. 2017), pp. 4302-4315. DOI: 10.1002/joc.5086. <URL:https://doi.org/10.1002/joc.5086>.
#'
#'@examples
-#' ## NOT RUN
-#' ## Bioclim
-#' # WorldClim.HistClim.download(parameter = "bio,
-#' # bio.var = c(1,12),
-#' # resolution = "10min",
-#' # version.var = c("1.4", "2.1"))
-#' ## Precipitation
-#' # WorldClim.HistClim.download(parameter = "prec",
-#' # month.var = c(1,12),
-#' # resolution = "10min",
-#' # version.var = c("1.4", "2.1"))
-#' ## NOT RUN
+#' \dontrun{
+#' # Bioclim
+#' WorldClim.HistClim.download(parameter = "bio",
+#' bio.var = c(1,12),
+#' resolution = "10min",
+#' version.var = c("1.4", "2.1"))
+#' # Precipitation
+#' WorldClim.HistClim.download(parameter = "prec",
+#' month.var = c(1,12),
+#' resolution = "10min",
+#' version.var = c("1.4", "2.1")
+#' )
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -481,7 +487,7 @@ WorldClim.HistClim.download <- function(save.location = "./",
# buffer is passed
# default: 0. Unit is arc-degrees
buffer = buffer,
- # conversion to ascii format here integrated into the
+ # conversion to ASCII format here integrated into the
# clipping function. Since it can be assumed that
# they should be converted later on anyway.
convert.files.to.asc = convert.files.to.asc,
@@ -555,10 +561,12 @@ WorldClim.HistClim.download <- function(save.location = "./",
}
-#'@title Function for downloading the WorldClim v1.4 CMIP5 Future Climate dataset
+#'@title Function for downloading the WorldClim v1.4 CMIP5 future climate dataset
#'@author Helge Jentsch
-#'@description This function supports a download of the WorldClim v1.4 CMIP5 Future Climate dataset. This includes precipitation (mm), temperature (maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
-#'@note Please note, that this dataset is regarded to as "outdated" by the WorldClim creators. The download of the current dataset "CMIP6" is also provided by this package with the \code{\link{WorldClim.CMIP_6.download}} function.
+#'@description This function supports the download, pre-processing and management of the WorldClim v1.4 CMIP5 future climate dataset.\cr This comprises of monthly precipitation sums (mm), temperature (maximum, minimum; °C), and annual chracteristics (19 bioclimatic variables).\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 this dataset is regarded to as "outdated" by the WorldClim creators. The download of the current dataset "CMIP6" is also provided by this package with the \code{\link{WorldClim.CMIP_6.download}} function.
+#'@note Please note also that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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 depending on the spatial resolution.
#'
#'@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", "bio")}
@@ -576,27 +584,29 @@ WorldClim.HistClim.download <- function(save.location = "./",
#'@param stacking.data logical. Input whether the downloaded data should be stacked as a netCDF-rasterstack.\cr Default: \code{FALSE}
#'@param keep.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.\cr If the \code{combine.raw.zip}-option 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}
+#'@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 WorldClim 1.4 CMIP5 Future climate datasets for the periods of 2041-2060 and/or 2061-2080.
#'
-#'@return WorldClim 1.4 CMIP5 Future climate data sets for the periods of 2041-2060 and/or 2061-2080.
+#'@references R. J. Hijmans, S. E. Cameron, J. L. Parra, et al. "Very high resolution interpolated climate surfaces for global land areas". In: _International Journal of Climatology_ 25.15 (2005), pp. 1965-1978. DOI: 10.1002/joc.1276. <URL: https://doi.org/10.1002/joc.1276>.
#'
#'@examples
-#' ## NOT RUN
-#' ## Bioclim
-#' # WorldClim.CMIP_5.download(parameter = "bio",
-#' # bio.var = c(1,12),
-#' # resolution = "10min",
-#' # model.var = "MPI-ESM-LR",
-#' # emission.scenario.var = "rcp26",
-#' # time.interval.var = "2050")
-#' ## Precipitation
-#' # WorldClim.CMIP_5.download(parameter = "prec",
-#' # month.var = c(1,12),
-#' # resolution = "10min",
-#' # model.var = "MPI-ESM-LR",
-#' # emission.scenario.var = "rcp26",
-#' # time.interval.var = "2050")
-#' ## NOT RUN
+#' \dontrun{
+#' # Bioclim
+#' WorldClim.CMIP_5.download(parameter = "bio",
+#' bio.var = c(1,12),
+#' resolution = "10min",
+#' model.var = "MPI-ESM-LR",
+#' emission.scenario.var = "rcp26",
+#' time.interval.var = "2050")
+#' # Precipitation
+#' WorldClim.CMIP_5.download(parameter = "prec",
+#' month.var = c(1,12),
+#' resolution = "10min",
+#' model.var = "MPI-ESM-LR",
+#' emission.scenario.var = "rcp26",
+#' time.interval.var = "2050")
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -974,7 +984,7 @@ WorldClim.CMIP_5.download <- function(save.location = "./",
# buffer is passed
# default: 0. Unit is arc-degrees
buffer = buffer,
- # conversion to ascii format here integrated into the
+ # 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,
@@ -1046,9 +1056,11 @@ WorldClim.CMIP_5.download <- function(save.location = "./",
}
-#'@title Function for downloading the WorldClim v2.1 CMIP6 Future Climate dataset
+#'@title Function for downloading the WorldClim v2.1 CMIP6 future climate dataset
#'@author Helge Jentsch
-#'@description This function supports a download of the WorldClim v2.1 CMIP6 Future Climate dataset. This includes precipitation (mm), temperature (maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+#'@description This function supports the download, pre-processing and management of the WorldClim v2.1 CMIP6 future climate dataset.\cr This comprises of monthly precipitation sums (mm), temperature (maximum, minimum; °C), and annual chracteristics (19 bioclimatic variables).\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 and the therefore also the first eleven bioclim-variables 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 depending on the spatial resolution.
#'
#'@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", "bio")}
@@ -1066,27 +1078,29 @@ WorldClim.CMIP_5.download <- function(save.location = "./",
#'@param stacking.data logical. Input whether the downloaded data should be stacked as a netCDF-rasterstack. \cr Default: \code{FALSE}
#'@param keep.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 the "combine.raw.zip"-option 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}
+#'@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 WorldClim 2.1 CMIP6 Future climate datasets for the periods of 2021-2040, 2041-2060, 2061-2080 and/or 2081-2100.
#'
-#'@return WorldClim 2.1 CMIP6 Future climate data sets for the periods of 2021-2040, 2041-2060, 2061-2080 and/or 2081-2100.
+#'@references S. E. Fick and R. J. Hijmans. "WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas". In: _International Journal of Climatology_ 37.12 (Okt. 2017), pp. 4302-4315. DOI: 10.1002/joc.5086. <URL:https://doi.org/10.1002/joc.5086>.
#'
#'@examples
-#' ## NOT RUN
-#' ## Bioclim
-#' # WorldClim.CMIP_6.download(parameter = "bio",
-#' # bio.var = c(1,12),
-#' # resolution = "10min",
-#' # model.var = "MIROC6",
-#' # emission.scenario.var = "ssp126",
-#' # time.interval.var = "2021-2040")
-#' ## Precipitation
-#' # WorldClim.CMIP_6.download(parameter = "prec",
-#' # month.var = c(1,12),
-#' # resolution = "10min",
-#' # model.var = "MIROC6",
-#' # emission.scenario.var = "ssp126",
-#' # time.interval.var = "2021-2040")
-#' ## END
+#' \dontrun{
+#' # Bioclim
+#' WorldClim.CMIP_6.download(parameter = "bio",
+#' bio.var = c(1,12),
+#' resolution = "10min",
+#' model.var = "MIROC6",
+#' emission.scenario.var = "ssp126",
+#' time.interval.var = "2021-2040")
+#' # Precipitation
+#' WorldClim.CMIP_6.download(parameter = "prec",
+#' month.var = c(1,12),
+#' resolution = "10min",
+#' model.var = "MIROC6",
+#' emission.scenario.var = "ssp126",
+#' time.interval.var = "2021-2040")
+#' }
#'
#'@import stringr
#'@import RCurl
@@ -1336,7 +1350,7 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
# buffer is passed
# default: 0. Unit is arc-degrees
buffer = buffer,
- # conversion to ascii format here integrated into the
+ # 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,
@@ -1388,7 +1402,7 @@ WorldClim.CMIP_6.download <- function(save.location = "./",
}
# if delete.raw.data is TRUE ...
if(delete.raw.data == TRUE){
- # All .tif raster files in the current 2nd order subdirectory are
+ # All tif files in the current 2nd order subdirectory are
# unlinked (deleted).
unlink(list.files(temp.temp.save.location,
pattern = ".tif",
diff --git a/R/auxiliary.R b/R/auxiliary.R
index 3d0d35b..15dfacc 100644
--- a/R/auxiliary.R
+++ b/R/auxiliary.R
@@ -1,6 +1,6 @@
#'@title Clipping .tif-raster files in one specified directory
#'@author Helge Jentsch
-#'@description This function clips all .tif-raster files in a specified directory (clip.save.location) to an extent given by a shapefile or user input with the possibility of adding a buffer. Furthermore an option for conversion to ASCII format is given.
+#'@description This function clips all .tif-raster files at a defined extent (e.g., shapefile or coordinates). Additionally, a buffer can be specified and added to the clipping extent. For user convenience, clipped rasters will be saved to a specified directory (clip.save.location). Furthermore, an option for conversion to ASCII format is given.
#'
#'@param clip.save.location string (directory path). The directory where .tif-raster files are saved. \cr Default: \code{"./"} (Working directory)
#'@param clip.shapefile string (file path to a ESRI shapefile with the file extension ".shp"). \cr Extent of this shapefile is used to clip the .tif-raster files if no buffer is specified. \cr Default: \code{NULL}
@@ -9,15 +9,15 @@
#'@param convert.files.to.asc logical. Input whether the clipped output should be converted into ASCII-Grids. \cr Default: \code{FALSE}
#'@param time.stamp.var string. Timestamp to create unique directories for multiple run outputs. \cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}
#'
-#'@return This function returns, depending on the parameter \code{convert.files.to.asc} whether it is ASCII- or GEOTIFF-format, clipped raster files to a new directory. This directory is dynamically created.
+#'@return This function returns, depending on the parameter \code{convert.files.to.asc} whether it is ASCII or tif format, clipped raster files to a new directory. This directory is automatically created.
#'
#'@import raster
#'@import stringr
#'@import sp
#'@import sf
#'
-#'@examples
-#'#clipping.tif(clip.save.location = system.file("pictures/", package = "rgdal"))
+#' @examples
+#' clipping.tif(clip.save.location = system.file("pictures/", package = "rgdal"))
#'
#'@export
clipping.tif <- function(clip.save.location = "./",
@@ -142,7 +142,7 @@ clipping.tif <- function(clip.save.location = "./",
#'@title Converting .tif-raster files in one specified directory into ASCII-Grids
#'@author Helge Jentsch
-#'@description This function Converts all .tif-raster files in a specified directory into an ASCII-File format in a new directory named "ASCII_files" with a unique timestamp of the current system time.
+#'@description This function converts and saves all .tif-raster files to ASCII-file format to a specified location and creates a new folder named "ASCII_files" with a unique timestamp of the current system time.
#'
#'@param save.location string (directory path). The directory where .tif-raster files are saved. \cr Default: \code{"./"} (Working directory)
#'@param time.stamp.var string. Timestamp to create unique directories for multiple run outputs. \cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}
@@ -191,12 +191,12 @@ convert.to.asc <- function(save.location = "./",
#'@title Stacking .tif-raster files in one specified directory
#'@author Helge Jentsch
-#'@description This function stacks all .tif-raster files in a specified directory and saves the Raster*stack File as netCDF-file in the specified directory.
+#'@description This function stacks all .tif-raster files of a specified directory and saves the stacked layers as a netCDF-file in that directory.
#'
-#'@param stack.save.location string (directory path). The directory where .tif-raster files are saved. Rasterfiles must be in a Geographic Coordinate System (in Arc-Degrees) \cr Default: \code{"./"} (Working directory)
+#'@param stack.save.location string (directory path). The directory where .tif-raster files are saved. Raster-files must be in a Geographic Coordinate System (in arc-degrees) \cr Default: \code{"./"} (Working directory)
#'@param stack.clipped logical. Input whether clipped data should be stacked and saved as netCDF as well. \cr Default: \code{FALSE}
#'@param parameter.var string. Input whether bioclim or climatic parameters are the input for the stacking process. \cr Default: \code{NULL}
-#'@param variable.numbers numeric (vector). Input how the stack variables should be called. By default just a sequence from 1 to the number of ".tif"-files are used.\cr Default: \code{c(1:length(list.files("./", pattern = ".tif")))}
+#'@param variable.numbers numeric (vector). Input how the stack variables should be called. By default just a sequence from 1 to the number of tif-raster files are used.\cr Default: \code{c(1:length(list.files("./", pattern = ".tif")))}
#'@param stack.time.series logical. Input whether a timeseries should be stacked. \cr Default: \code{FALSE}
#'@param time.series string (vector). String input of timeseries vector. \cr Default: \code{NULL}
#'@param time.stamp.var string. Timestamp to create unique directories for multiple run outputs.\cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}
@@ -371,29 +371,35 @@ stacking.downloaded.data <- function(stack.save.location = "./",
#'@title Save the citation of the downloaded dataset
#'@author Helge Jentsch
#'
-#'@description Saves the citation of the downloaded dataset into a BibTex-file in the Working Directory.
+#'@description Saves the citation of the downloaded dataset into a BibTex-file in the working directory.
#'
#'@param save.location string (directory path). Where the BibTex-file will be saved. \cr Default: \code{"./"} (Working Directory)
#'@param dataSetName string (vector). Specifies which dataset was downloaded or which citation should be saved. \cr Default: \code{c("Chelsa1.2", "WorldClim1.4", "WorldClim2.1")} (all available datasets)
#'
-#'@return BIBtex-file with biliography of the downloaded dataset
-#'@note DISCLAIMER: No warranty or liability! The citations are provided without any warranty of any kind whatsoever, either expressed or implied, including warranties of merchantability and fitness for a particular purpose. The author should not be responsible for any incomplete citation of datasets or climate data products downloaded through this package.
+#'@return BibTex-file with biliography of the downloaded dataset
+#'@note DISCLAIMER: No warranty or liability! The citations are provided without any warranty of any kind whatsoever, either expressed or implied, including warranties of merchantability and fitness for a particular purpose. The package author will not be responsible for any incomplete citation of datasets or climate data products downloaded through this package.
#'
#'@importFrom RefManageR ReadCrossRef
#'@importFrom RefManageR ReadBib
#'@importFrom RefManageR WriteBib
#'@importFrom utils download.file
#'
+#'@examples
+#' \dontrun{
+#' save.citation(dataSetName = "Chelsa")
+#' save.citation(dataSetName = "WorldClim1.4")
+#' save.citation(dataSetName = "WorldClim2.1")
+#' }
#'@export
save.citation <- function(save.location = "./",
- dataSetName= c("Chelsa",
+ dataSetName= c("CHELSA",
"WorldClim1.4",
"WorldClim2.1")){
gc()
# requireNamespace("RefManageR")
save.location <- paste0(normalizePath(save.location, winslash = "/"), "/")
- if(dataSetName == "Chelsa"){
+ if(dataSetName == "CHELSA"){
print("Please regard 'https://chelsa-climate.org/downloads/' for correct citations.")
if(!file.exists(paste0(save.location, "chelsa_citation.bib"))){
# citation_ <- RefManageR::ReadCrossRef("")
@@ -451,9 +457,9 @@ save.citation <- function(save.location = "./",
#'@title Combines all .tif-raster files into a .zip-file
#'@author Helge Jentsch
-#'@description Combines all .tif-raster files of one directory into a .zip-file with a custom name.
+#'@description Combines and saves all .tif-raster files to a .zip-file, whereas name and saving location can be specified.
#'
-#'@param save.location string (directory path). The directory where .tif-raster files are saved and the created/updated .zip file should be saved. \cr Default: \code{"./"} (Working directory)
+#'@param save.location string (directory path). The directory where .tif-raster files are saved and the created/updated .zip file will be saved. \cr Default: \code{"./"} (Working directory)
#'@param zip.name string. Input how the .zip-file should be named. \cr Default: \code{"RAWDATA"}
#'@param unique.name logical. Should the .zip-file be named uniquely? If TRUE the current system time is added as a timestamp to create unique directories for multiple run outputs. \cr Default: \code{TRUE}
#'@param time.stamp.var string. Input of current system time or, if called within another function the initial time of the execution. \cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}
@@ -503,42 +509,42 @@ combine.raw.in.zip <- function(save.location = "./",
#'@title Preprocessing data to get real values
#'@author Helge Jentsch
-#'@description Takes input Raster* File, crops it, processes the integer values into double values, mosaiks the cropped and processed data, and returns the mosaiked Rasterfile
+#'@description Takes input RasterLayer, crops it, processes the integer values into double values, mosaiks the cropped and processed data, and returns the mosaiked Rasterfile
#'
-#'@param raster.file Raster*File to be processed
+#'@param raster.layer RasterLayer to be processed
#'
-#'@return Rasterfile
+#'@return RasterLayer
#'
#'@import raster
#'@import sp
-#'@export
-process.raster.int.doub <- function(raster.file = NULL)
+#'
+process.raster.int.doub <- function(raster.layer = NULL)
{
gc()
- if(is.null(raster.file)){
- stop("raster.file is NULL")
+ if(is.null(raster.layer)){
+ stop("raster.layer is NULL")
}
- if(class(raster.file)[1] != "RasterLayer"){
- stop("raster.file is not a 'RasterLayer'")
+ if(class(raster.layer)[1] != "RasterLayer"){
+ stop("raster.layer is not a 'RasterLayer'")
}
- extent_rasterfile <- extent(raster.file)
+ extent_rasterfile <- extent(raster.layer)
# crop
- tl <- crop(raster.file, extent(extent_rasterfile@xmin,
+ tl <- crop(raster.layer, extent(extent_rasterfile@xmin,
(extent_rasterfile@xmin+extent_rasterfile@xmax)/2,
(extent_rasterfile@ymin+extent_rasterfile@ymax)/2,
extent_rasterfile@ymax)
)
- bl <- crop(raster.file, extent(extent_rasterfile@xmin,
+ bl <- crop(raster.layer, extent(extent_rasterfile@xmin,
(extent_rasterfile@xmin+extent_rasterfile@xmax)/2,
extent_rasterfile@ymin,
(extent_rasterfile@ymin+extent_rasterfile@ymax)/2)
)
- tr <- crop(raster.file, extent((extent_rasterfile@xmin+extent_rasterfile@xmax)/2,
+ tr <- crop(raster.layer, extent((extent_rasterfile@xmin+extent_rasterfile@xmax)/2,
extent_rasterfile@xmax,
(extent_rasterfile@ymin+extent_rasterfile@ymax)/2,
extent_rasterfile@ymax)
)
- br <- crop(raster.file, extent((extent_rasterfile@xmin+extent_rasterfile@xmax)/2,
+ br <- crop(raster.layer, extent((extent_rasterfile@xmin+extent_rasterfile@xmax)/2,
extent_rasterfile@xmax,
extent_rasterfile@ymin,
(extent_rasterfile@ymin+extent_rasterfile@ymax)/2)
@@ -561,6 +567,6 @@ process.raster.int.doub <- function(raster.file = NULL)
bottom <- mosaic(bl,br, fun = "mean")
rm(bl, br)
gc()
- raster.file <- mosaic(top, bottom, fun = "mean")
- return(raster.file)
+ raster.layer <- mosaic(top, bottom, fun = "mean")
+ return(raster.layer)
}
diff --git a/man/Chelsa.CMIP_5.download.Rd b/man/Chelsa.CMIP_5.download.Rd
index 49748f2..f117c22 100644
--- a/man/Chelsa.CMIP_5.download.Rd
+++ b/man/Chelsa.CMIP_5.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/Chelsa_Download_functions.R
\name{Chelsa.CMIP_5.download}
\alias{Chelsa.CMIP_5.download}
-\title{Function for downloading Chelsa CMIP 5 future climatologies data sets for 2050 and 2070}
+\title{Function for downloading CHELSA CMIP 5 future climatologies for the years 2041-2060 and 2061-2080}
\usage{
Chelsa.CMIP_5.download(
save.location = "./",
@@ -40,7 +40,7 @@ Chelsa.CMIP_5.download(
\item{emission.scenario.var}{string (vector). Input which emission scenario dataset should be downloaded. Provided are the representative concentration pathways (RCP) 2.6, 4.5, 6.0, and 8.5.\cr Default: \code{c("rcp26", "rcp45", "rcp60", "rcp85")}}
-\item{time.interval.var}{string (vector). Input for which time interval data should be downloaded. Chelsa provides downscaled CMIP5 climatologies for 2050 and 2070. Multiple inputs possible.\cr Default: \code{c("2041-2060", "2061-2080")}}
+\item{time.interval.var}{string (vector). Input for which time interval data should be downloaded. CHELSA provides downscaled CMIP5 climatologies for 2050 and 2070. Multiple inputs possible.\cr Default: \code{c("2041-2060", "2061-2080")}}
\item{model.var}{string (vector). Input which future model dataset should be downloaded. For more information see: \url{http://chelsa-climate.org/future/}.\cr For some of the datasets not all downloads are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. For an overview please try "warnings()" after execution. \cr Default: \code{c("ACCESS1-0", "bcc-csm1-1", "BNU-ESM", "CanESM2", "CCSM4", "CESM1-BGC", } \cr \code{"CESM1-CAM5", "CMCC-CESM", "CMCC-CM", "CMCC-CMS", "CNRM-CM5", "CSIRO-Mk3-6-0",} \cr \code{ "CSIRO-Mk3L-1-2", "EC-EARTH", "FGOALS-g2", "FIO-ESM", "GFDL-CM3", "GFDL-ESM2G", } \cr \code{"GFDL-ESM2M","GISS-E2-H", "GISS-E2-H-CC", "GISS-E2-R", "GISS-E2-R-CC", "HadGEM2-AO",} \cr \code{"HadGEM2-CC", "HadGEM2-ES", "inmcm4", "IPSL-CM5A-LR", "IPSL-CM5A-MR","MIROC-ESM",} \cr \code{"MIROC-ESM-CHEM","MIROC5", "MPI-ESM-LR", "MPI-ESM-MR", "MRI-CGCM3", "MRI-ESM1",} \cr \code{ "NorESM1-M","NorESM1-ME")}}
@@ -60,36 +60,41 @@ Chelsa.CMIP_5.download(
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted. If the \code{combine.raw.zip} is \code{TRUE}: raw-data is still available in the zipped file. \cr Default: \code{FALSE}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the data set should be provided in the Working directory. \cr Default: \code{TRUE}}
+\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{
-Downscaled Chelsa CMIP5 climatologies for 2050 and 2070.
+Downscaled CHELSA CMIP5 climatologies for 2050 and 2070.
}
\description{
-This function supports a download of the Chelsa CMIP5 future climate data sets. This includes precipitation (mm), temperature (average, maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. An output of a .bib-file of the literature is also optional. For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+This function supports the download of CHELSA CMIP5 future climate scenarios comprising of monthly precipitation sums in mm, monthly temperature (average, minimum, maximum) in degrees Celsius, and annual chracteristics (19 bioclimatic variables).\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.
}
\details{
-"The Downscaled data has been produced using climatological aided interpolation based on the 1979-2013 reference climatologies from CHELSA." (Chelsa Climate 2020: \url{http://chelsa-climate.org/future/})
+"The downscaled data has been produced using climatological aided interpolation based on the 1979-2013 reference climatologies from CHELSA." (CHELSA Climate 2020: \url{http://chelsa-climate.org/future/})
}
\note{
-For some of the datasets not all models are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of Chelsa Climate (\url{http://chelsa-climate.org/future/}).
+Please note that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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.\cr For some of the datasets not all models and rcps are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of CHELSA Climate (\url{http://chelsa-climate.org/future/}). Please note, that the downloaded data for temperature and the therefore also the first eleven bioclim-variables are processed to °C without offset and factor. Processing and conversion to other file-formats on a global dataset may take some time.
}
\examples{
-## NOT RUN
-## Bioclim
-# Chelsa.CMIP_5.download(parameter = "bio",
-# bio.var = c(1,12),
-# emission.scenario.var = "rcp26",
-# time.interval.var = "2041-2060",
-# model.var = "MPI-ESM-LR")
-## Precipitation
-# Chelsa.CMIP_5.download(parameter = "prec",
-# month.var = c(1,12),
-# emission.scenario.var = "rcp26",
-# time.interval.var = "2041-2060",
-# model.var = "MPI-ESM-LR")
-## NOT RUN
+\dontrun{
+# Bioclim
+Chelsa.CMIP_5.download(parameter = "bio",
+ bio.var = c(1,19),
+ emission.scenario.var = "rcp26",
+ time.interval.var = "2041-2060",
+ model.var = "MPI-ESM-LR")
+# Precipitation
+Chelsa.CMIP_5.download(parameter = "prec",
+ month.var = c(1,12),
+ emission.scenario.var = "rcp26",
+ time.interval.var = "2041-2060",
+ model.var = "MPI-ESM-LR")
+}
+
+}
+\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>.
}
\author{
Helge Jentsch
diff --git a/man/Chelsa.CRUts.download.Rd b/man/Chelsa.CRUts.download.Rd
index a425a26..34e7dc8 100644
--- a/man/Chelsa.CRUts.download.Rd
+++ b/man/Chelsa.CRUts.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/Chelsa_Download_functions.R
\name{Chelsa.CRUts.download}
\alias{Chelsa.CRUts.download}
-\title{Chelsa CRU Timeseries Download}
+\title{CHELSA CRU Timeseries Download}
\usage{
Chelsa.CRUts.download(
save.location = "./",
@@ -54,24 +54,34 @@ Chelsa.CRUts.download(
\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}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the dataset should be provided in the Working directory. \cr Default: \code{TRUE}}
+\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 CRU Timeseries for a chosen timeseries.
+Custom dataset of CHELSA CRU Timeseries for a chosen timeseries.
}
\description{
-This function supports a download of the Chelsa CRU Timeseries dataset (Jan. 1901 - Dec. 2016). This includes precipitation (mm) and temperature (maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/chelsacruts/}.\cr For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, 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 CRU Timeseries dataset (Jan. 1901 - Dec. 2016). This includes precipitation sums in mm and temperature (maximum, minimum) in degree Celsius. For further information, please regard \url{http://chelsa-climate.org/chelsacruts/}.\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 is 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{
-## NOT RUN
-# Chelsa.CRUts.download(parameter = "prec",
-# start.year.var = 2000,
-# start.month.var = 1,
-# end.year.var = 2002,
-# end.month.var = 12,
-# include.month.var = c(1,12))
-## END
+\dontrun{
+Chelsa.CRUts.download(parameter = "prec",
+ start.year.var = 2000,
+ start.month.var = 1,
+ end.year.var = 2002,
+ end.month.var = 12,
+ 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 and N. E. Zimmermann. _CHELSAcruts - High resolution temperature and precipitation timeseries for the 20th century and beyond_. 2018. DOI: http://dx.doi.org/10.16904/envidat.159.
}
\author{
Helge Jentsch
diff --git a/man/Chelsa.Clim.download.Rd b/man/Chelsa.Clim.download.Rd
index 01d575e..24eff11 100644
--- a/man/Chelsa.Clim.download.Rd
+++ b/man/Chelsa.Clim.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/Chelsa_Download_functions.R
\name{Chelsa.Clim.download}
\alias{Chelsa.Clim.download}
-\title{Function for downloading the Chelsa Climate dataset}
+\title{Function for downloading the CHELSA climate dataset (1979-2013)}
\usage{
Chelsa.Clim.download(
save.location = "./",
@@ -22,15 +22,15 @@ Chelsa.Clim.download(
)
}
\arguments{
-\item{save.location}{string. Input where the datasets should be saved. \cr Default: Working Directory.}
+\item{save.location}{string. Input where the datasets will be saved. \cr Default: Working Directory.}
\item{parameter}{string (vector). Input of parameters which should be downloaded. \cr Default: \code{c("prec", "temp", "tmax", "tmin", "bio")}}
\item{bio.var}{integer (vector). Input which monthly data should be downloaded. Only applicable to BIOCLIM variables. For further information see: \url{http://chelsa-climate.org/bioclim/}. \cr Default: \code{c(1:19)}}
-\item{month.var}{integer (vector). Input which monthly data should be downloaded. Only applicable to precipitation and temperature (average, maximum, minimum). \cr Default: \code{c(1:12O)}}
+\item{month.var}{integer (vector). Input which monthly data should be downloaded. Only applicable to precipitation and temperature (average, maximum, minimum). \cr Default: \code{c(1:12)}}
-\item{version.var}{string (vector). Input which version of the data set should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.1", "1.2")}}
+\item{version.var}{string (vector). Input which version of the dataset should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.2")}}
\item{clipping}{logical. Input whether the downloaded data should be clipped.\cr If \code{FALSE}: clip.shapefile, buffer, clip.extent will be ignored. \cr Default: \code{FALSE}}
@@ -48,22 +48,30 @@ Chelsa.Clim.download(
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted.\cr If \code{combine.raw.zip} is \code{TRUE}: raw-data is still available in the zipped file. \cr Default: \code{FALSE}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the data set should be provided in the Working directory. \cr Default: \code{TRUE}}
+\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{
-Chelsa climate data sets for the period of 1979 - 2013
+CHELSA climate datasets for the period of 1979 - 2013
}
\description{
-This function supports a download of the Chelsa Climate dataset. This includes precipitation (mm), temperature (average, maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid,and stacking-tool is included.\cr An output of a .bib-file of the literature is also optional.\cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+This function supports the download, pre-processing and management of CHELSA climate data comprising of monthly precipitation sums in mm, monthly temperature (average, minimum, maximum) in degrees Celsius, and annual chracteristics (19 bioclimatic variables). The spatial resolution of the downloaded data is 30 arc-seconds.\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 and the therefore also the first eleven bioclim-variables 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{
-## NOT RUN
-## Bioclim
-# Chelsa.Clim.download(parameter = "bio", bio.var = c(1,12))
-## Precipitation
-# Chelsa.Clim.download(parameter = "prec", month.var = c(1,12))
-## NOT RUN
+\dontrun{
+# Bioclim
+Chelsa.Clim.download(parameter = "bio", bio.var = c(1,19))
+# Precipitation
+Chelsa.Clim.download(parameter = "prec", 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>.
}
\author{
Helge Jentsch
diff --git a/man/Chelsa.lgm.download.Rd b/man/Chelsa.lgm.download.Rd
index 72db015..454108b 100644
--- a/man/Chelsa.lgm.download.Rd
+++ b/man/Chelsa.lgm.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/Chelsa_Download_functions.R
\name{Chelsa.lgm.download}
\alias{Chelsa.lgm.download}
-\title{Function for downloading Chelsa Last Glacial Maximum datasets}
+\title{Function for downloading CHELSA Last Glacial Maximum datasets}
\usage{
Chelsa.lgm.download(
save.location = "./",
@@ -52,33 +52,38 @@ Chelsa.lgm.download(
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted. If the "combine.raw.zip"-option is \code{TRUE}, raw-data is still available in the zipped file.\cr Default: \code{FALSE}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the Chelsa-dataset should be provided in the Working directory. \cr Default: \code{TRUE}}
+\item{save.bib.file}{logical. Whether a BibTex-citation file of the CHELSA dataset should be provided in the Working directory. \cr Default: \code{TRUE}}
}
\value{
Downscaled global climatological data from the last glacial maximum.
}
\description{
-This function supports a download of the Chelsa Last Glacial Maximum Climate datasets (21.000 years ago). This includes precipitation (mm), temperature (average, maximum, minimum; °C), bioclimatic parameters, and a global digital elevation model. For further information, please regard \url{http://chelsa-climate.org/last-glacial-maximum-climate/}.\cr For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, 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 Last Glacial Maximum Climate datasets (21.000 BP). This includes monthly precipitation sums in mm, monthly temperature (average, maximum, minimum) in degree Celsius, annual characteristics (19 bioclimatic parameters), and a global digital elevation model. For further information, please regard \url{http://chelsa-climate.org/last-glacial-maximum-climate/}.\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.
}
\details{
-"The CHELSA LGM data is based on a implementation of the CHELSA algorithm on PMIP3 data." (Chelsa Climate 2020: \url{http://chelsa-climate.org/last-glacial-maximum-climate/})
+"The CHELSA LGM data is based on a implementation of the CHELSA algorithm on PMIP3 data." (CHELSA Climate 2020: \url{http://chelsa-climate.org/last-glacial-maximum-climate/})
}
\note{
-For some of the datasets not all models are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of Chelsa Climate (\url{http://chelsa-climate.org/last-glacial-maximum-climate/}).
+Please note that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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.\cr For some of the datasets not all models are available. For the ones that are not supported the data will not be downloaded and a warning will be prompted. See parameter \code{model.var} for more information or check the website of CHELSA Climate (\url{http://chelsa-climate.org/last-glacial-maximum-climate/}).
}
\examples{
-## NOT RUN
-## Bioclim
-# Chelsa.lgm.download(parameter = "bio",
-# bio.var = c(1,12),
-# model.var = "MPI-ESM-P")
-## Precipitation
-# Chelsa.lgm.download(parameter = "prec",
-# month.var = c(1,12),
-# model.var = "MPI-ESM-P")
-## NOT RUN
+\dontrun{
+# Bioclim
+Chelsa.lgm.download(parameter = "bio",
+ bio.var = c(1,19),
+ model.var = "MPI-ESM-P")
+# Precipitation
+Chelsa.lgm.download(parameter = "prec",
+ month.var = c(1,12),
+ model.var = "MPI-ESM-P")
+}
+
+}
+\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>.
}
\author{
Helge Jentsch
diff --git a/man/Chelsa.timeseries.download.Rd b/man/Chelsa.timeseries.download.Rd
index a10dc3c..9fe70f5 100644
--- a/man/Chelsa.timeseries.download.Rd
+++ b/man/Chelsa.timeseries.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/Chelsa_Download_functions.R
\name{Chelsa.timeseries.download}
\alias{Chelsa.timeseries.download}
-\title{Chelsa Timeseries Download}
+\title{CHELSA Timeseries Download}
\usage{
Chelsa.timeseries.download(
save.location = "./",
@@ -57,21 +57,29 @@ 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 (mm) and temperature (average, maximum, minimum; °C) parameters. For further information, please regard \url{http://chelsa-climate.org/timeseries/}.\cr For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, 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.
}
\examples{
-## NOT RUN
-# Chelsa.timeseries.download(parameter = "prec",
-# start.year.var = 2000,
-# start.month.var = 1,
-# end.year.var = 2002,
-# end.month.var = 12,
-# include.month.var = c(1,12))
-## END
+\dontrun{
+Chelsa.timeseries.download(parameter = "prec",
+ start.year.var = 2000,
+ start.month.var = 1,
+ end.year.var = 2002,
+ end.month.var = 12,
+ 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>.
}
\author{
Helge Jentsch
diff --git a/man/WorldClim.CMIP_5.download.Rd b/man/WorldClim.CMIP_5.download.Rd
index cb0b30f..887757c 100644
--- a/man/WorldClim.CMIP_5.download.Rd
+++ b/man/WorldClim.CMIP_5.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/WorldClim_download_functions.R
\name{WorldClim.CMIP_5.download}
\alias{WorldClim.CMIP_5.download}
-\title{Function for downloading the WorldClim v1.4 CMIP5 Future Climate dataset}
+\title{Function for downloading the WorldClim v1.4 CMIP5 future climate dataset}
\usage{
WorldClim.CMIP_5.download(
save.location = "./",
@@ -60,35 +60,40 @@ WorldClim.CMIP_5.download(
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted.\cr If the \code{combine.raw.zip}-option is \code{TRUE}, raw-data is still available in the zipped file.\cr Default: \code{FALSE}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the dataset should be provided in the Working directory.\cr Default: \code{TRUE}}
+\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{
-WorldClim 1.4 CMIP5 Future climate data sets for the periods of 2041-2060 and/or 2061-2080.
+WorldClim 1.4 CMIP5 Future climate datasets for the periods of 2041-2060 and/or 2061-2080.
}
\description{
-This function supports a download of the WorldClim v1.4 CMIP5 Future Climate dataset. This includes precipitation (mm), temperature (maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+This function supports the download, pre-processing and management of the WorldClim v1.4 CMIP5 future climate dataset.\cr This comprises of monthly precipitation sums (mm), temperature (maximum, minimum; °C), and annual chracteristics (19 bioclimatic variables).\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 this dataset is regarded to as "outdated" by the WorldClim creators. The download of the current dataset "CMIP6" is also provided by this package with the \code{\link{WorldClim.CMIP_6.download}} function.
+Please note that this dataset is regarded to as "outdated" by the WorldClim creators. The download of the current dataset "CMIP6" is also provided by this package with the \code{\link{WorldClim.CMIP_6.download}} function.
+
+Please note also that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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 depending on the spatial resolution.
}
\examples{
-## NOT RUN
-## Bioclim
-# WorldClim.CMIP_5.download(parameter = "bio",
-# bio.var = c(1,12),
-# resolution = "10min",
-# model.var = "MPI-ESM-LR",
-# emission.scenario.var = "rcp26",
-# time.interval.var = "2050")
-## Precipitation
-# WorldClim.CMIP_5.download(parameter = "prec",
-# month.var = c(1,12),
-# resolution = "10min",
-# model.var = "MPI-ESM-LR",
-# emission.scenario.var = "rcp26",
-# time.interval.var = "2050")
-## NOT RUN
+\dontrun{
+# Bioclim
+WorldClim.CMIP_5.download(parameter = "bio",
+ bio.var = c(1,12),
+ resolution = "10min",
+ model.var = "MPI-ESM-LR",
+ emission.scenario.var = "rcp26",
+ time.interval.var = "2050")
+# Precipitation
+WorldClim.CMIP_5.download(parameter = "prec",
+ month.var = c(1,12),
+ resolution = "10min",
+ model.var = "MPI-ESM-LR",
+ emission.scenario.var = "rcp26",
+ time.interval.var = "2050")
+}
+}
+\references{
+R. J. Hijmans, S. E. Cameron, J. L. Parra, et al. "Very high resolution interpolated climate surfaces for global land areas". In: _International Journal of Climatology_ 25.15 (2005), pp. 1965-1978. DOI: 10.1002/joc.1276. <URL: https://doi.org/10.1002/joc.1276>.
}
\author{
Helge Jentsch
diff --git a/man/WorldClim.CMIP_6.download.Rd b/man/WorldClim.CMIP_6.download.Rd
index 6de1593..94a3eee 100644
--- a/man/WorldClim.CMIP_6.download.Rd
+++ b/man/WorldClim.CMIP_6.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/WorldClim_download_functions.R
\name{WorldClim.CMIP_6.download}
\alias{WorldClim.CMIP_6.download}
-\title{Function for downloading the WorldClim v2.1 CMIP6 Future Climate dataset}
+\title{Function for downloading the WorldClim v2.1 CMIP6 future climate dataset}
\usage{
WorldClim.CMIP_6.download(
save.location = "./",
@@ -58,32 +58,38 @@ WorldClim.CMIP_6.download(
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted. If the "combine.raw.zip"-option is \code{TRUE}, raw-data is still available in the zipped file. \cr Default: \code{FALSE}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the dataset should be provided in the Working directory. \cr Default: \code{TRUE}}
+\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{
-WorldClim 2.1 CMIP6 Future climate data sets for the periods of 2021-2040, 2041-2060, 2061-2080 and/or 2081-2100.
+WorldClim 2.1 CMIP6 Future climate datasets for the periods of 2021-2040, 2041-2060, 2061-2080 and/or 2081-2100.
}
\description{
-This function supports a download of the WorldClim v2.1 CMIP6 Future Climate dataset. This includes precipitation (mm), temperature (maximum, minimum; °C), and bioclimatic parameters. For convenience also a clipping-, conversion to ascii-grid, and stacking-tool is included. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+This function supports the download, pre-processing and management of the WorldClim v2.1 CMIP6 future climate dataset.\cr This comprises of monthly precipitation sums (mm), temperature (maximum, minimum; °C), and annual chracteristics (19 bioclimatic variables).\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 and the therefore also the first eleven bioclim-variables 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 depending on the spatial resolution.
}
\examples{
-## NOT RUN
-## Bioclim
-# WorldClim.CMIP_6.download(parameter = "bio",
-# bio.var = c(1,12),
-# resolution = "10min",
-# model.var = "MIROC6",
-# emission.scenario.var = "ssp126",
-# time.interval.var = "2021-2040")
-## Precipitation
-# WorldClim.CMIP_6.download(parameter = "prec",
-# month.var = c(1,12),
-# resolution = "10min",
-# model.var = "MIROC6",
-# emission.scenario.var = "ssp126",
-# time.interval.var = "2021-2040")
-## END
+\dontrun{
+# Bioclim
+WorldClim.CMIP_6.download(parameter = "bio",
+ bio.var = c(1,12),
+ resolution = "10min",
+ model.var = "MIROC6",
+ emission.scenario.var = "ssp126",
+ time.interval.var = "2021-2040")
+# Precipitation
+WorldClim.CMIP_6.download(parameter = "prec",
+ month.var = c(1,12),
+ resolution = "10min",
+ model.var = "MIROC6",
+ emission.scenario.var = "ssp126",
+ time.interval.var = "2021-2040")
+}
+}
+\references{
+S. E. Fick and R. J. Hijmans. "WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas". In: _International Journal of Climatology_ 37.12 (Okt. 2017), pp. 4302-4315. DOI: 10.1002/joc.5086. <URL:https://doi.org/10.1002/joc.5086>.
}
\author{
Helge Jentsch
diff --git a/man/WorldClim.HistClim.download.Rd b/man/WorldClim.HistClim.download.Rd
index a0c9e3d..a2a532c 100644
--- a/man/WorldClim.HistClim.download.Rd
+++ b/man/WorldClim.HistClim.download.Rd
@@ -2,7 +2,7 @@
% Please edit documentation in R/WorldClim_download_functions.R
\name{WorldClim.HistClim.download}
\alias{WorldClim.HistClim.download}
-\title{Function for downloading the WorldClim Historical Climate dataset}
+\title{Function for downloading the WorldClim historical climate dataset}
\usage{
WorldClim.HistClim.download(
save.location = "./",
@@ -33,7 +33,7 @@ WorldClim.HistClim.download(
\item{resolution}{string (vector). Ranging from a 10 arc-minute resolution over 5 and 2.5 arc-minute to 30 arc-second resolution.\cr Default: \code{c("10m", "5m", "2.5m", "30s")}}
-\item{version.var}{string (vector). Input which version of the data set should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.4", "2.1")}}
+\item{version.var}{string (vector). Input which version of the dataset should be downloaded. Multiple selection is possible. \cr Default: \code{c("1.4", "2.1")}}
\item{clipping}{logical. Input whether the downloaded data should be clipped. See \code{\link{clipping.tif}} for more information. \cr If \code{FALSE}: \code{clip.shapefile}, \code{buffer}, \code{clip.extent} will be ignored. \cr Default: \code{FALSE}}
@@ -51,31 +51,39 @@ WorldClim.HistClim.download(
\item{delete.raw.data}{logical. Should the downloaded raw-data be deleted. \cr If the "combine.raw.zip"-option is \code{TRUE}: raw-data is still available in the zipped file. \cr Default: \code{FALSE}}
-\item{save.bib.file}{logical. Whether a bibTex-citation file of the dataset should be provided in the Working directory. See \code{\link{save.citation}} for more information. \cr Default: \code{TRUE}}
+\item{save.bib.file}{logical. Whether a BibTex-citation file of the dataset should be provided in the Working directory. See \code{\link{save.citation}} for more information. \cr Default: \code{TRUE}}
}
\value{
-WorldClim climate data sets for the period of 1960-1990 (for v1.4) and/or 1970-2000 (for v2.1).
+WorldClim climate datasets for the period of 1960-1990 (for v1.4) and/or 1970-2000 (for v2.1).
}
\description{
-This function supports a download of the WorldClim Historical Climate dataset. \cr This includes precipitation (mm), temperature (average, maximum, minimum; °C), solar radiation (kJ m-2 day-1), wind speed (m s-1), water vapor pressure (kPa) and bioclimatic parameters. Also an elevation raster is provided. \cr For convenience also a clipping-, conversion to ASCII-grid, and stacking-tool is included in this function. \cr An output of a .bib-file of the literature is also optional. \cr For a clear working environment, directories will be created automatically. Also options to "zip" and/or delete the RAW-files are included.
+This function supports the download, pre-processing and management of the WorldClim historical climate dataset.\cr This comprises of monthly precipitation sums (mm), temperature (average, maximum, minimum; °C), monthly solar radiation sums (kJ m-2 day-1), wind speed (m s-1), water vapor pressure (kPa), and annual chracteristics (19 bioclimatic variables). Also an elevation raster is provided.\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 solar radiation, wind speed, water vapor pressure, bioclimatic parameters, and elevation raster are only provided by the WorldClim Version 2.1 (current version).
+Please note that solar radiation, wind speed, water vapor pressure, bioclimatic parameters, and elevation raster are only provided by the WorldClim Version 2.1 (current version).
+
+Please note also that the downloaded data for temperature and the therefore also the first eleven bioclim-variables 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 depending on the spatial resolution.
}
\examples{
-## NOT RUN
-## Bioclim
-# WorldClim.HistClim.download(parameter = "bio,
-# bio.var = c(1,12),
-# resolution = "10min",
-# version.var = c("1.4", "2.1"))
-## Precipitation
-# WorldClim.HistClim.download(parameter = "prec",
-# month.var = c(1,12),
-# resolution = "10min",
-# version.var = c("1.4", "2.1"))
-## NOT RUN
+\dontrun{
+# Bioclim
+WorldClim.HistClim.download(parameter = "bio",
+ bio.var = c(1,12),
+ resolution = "10min",
+ version.var = c("1.4", "2.1"))
+# Precipitation
+WorldClim.HistClim.download(parameter = "prec",
+ month.var = c(1,12),
+ resolution = "10min",
+ version.var = c("1.4", "2.1")
+ )
+}
+
+}
+\references{
+R. J. Hijmans, S. E. Cameron, J. L. Parra, et al. "Very high resolution interpolated climate surfaces for global land areas". In: _International Journal of Climatology_ 25.15 (2005), pp. 1965-1978. DOI: 10.1002/joc.1276. <URL: https://doi.org/10.1002/joc.1276>.
+S. E. Fick and R. J. Hijmans. "WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas". In: _International Journal of Climatology_ 37.12 (Okt. 2017), pp. 4302-4315. DOI: 10.1002/joc.5086. <URL:https://doi.org/10.1002/joc.5086>.
}
\author{
Helge Jentsch
diff --git a/man/clipping.tif.Rd b/man/clipping.tif.Rd
index fc12395..efe927a 100644
--- a/man/clipping.tif.Rd
+++ b/man/clipping.tif.Rd
@@ -28,13 +28,13 @@ clipping.tif(
\item{time.stamp.var}{string. Timestamp to create unique directories for multiple run outputs. \cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}}
}
\value{
-This function returns, depending on the parameter \code{convert.files.to.asc} whether it is ASCII- or GEOTIFF-format, clipped raster files to a new directory. This directory is dynamically created.
+This function returns, depending on the parameter \code{convert.files.to.asc} whether it is ASCII or tif format, clipped raster files to a new directory. This directory is automatically created.
}
\description{
-This function clips all .tif-raster files in a specified directory (clip.save.location) to an extent given by a shapefile or user input with the possibility of adding a buffer. Furthermore an option for conversion to ASCII format is given.
+This function clips all .tif-raster files at a defined extent (e.g., shapefile or coordinates). Additionally, a buffer can be specified and added to the clipping extent. For user convenience, clipped rasters will be saved to a specified directory (clip.save.location). Furthermore, an option for conversion to ASCII format is given.
}
\examples{
-#clipping.tif(clip.save.location = system.file("pictures/", package = "rgdal"))
+clipping.tif(clip.save.location = system.file("pictures/", package = "rgdal"))
}
\author{
diff --git a/man/combine.raw.in.zip.Rd b/man/combine.raw.in.zip.Rd
index 1be13f2..12c0576 100644
--- a/man/combine.raw.in.zip.Rd
+++ b/man/combine.raw.in.zip.Rd
@@ -14,7 +14,7 @@ combine.raw.in.zip(
)
}
\arguments{
-\item{save.location}{string (directory path). The directory where .tif-raster files are saved and the created/updated .zip file should be saved. \cr Default: \code{"./"} (Working directory)}
+\item{save.location}{string (directory path). The directory where .tif-raster files are saved and the created/updated .zip file will be saved. \cr Default: \code{"./"} (Working directory)}
\item{zip.name}{string. Input how the .zip-file should be named. \cr Default: \code{"RAWDATA"}}
@@ -23,7 +23,7 @@ combine.raw.in.zip(
\item{time.stamp.var}{string. Input of current system time or, if called within another function the initial time of the execution. \cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}}
}
\description{
-Combines all .tif-raster files of one directory into a .zip-file with a custom name.
+Combines and saves all .tif-raster files to a .zip-file, whereas name and saving location can be specified.
}
\author{
Helge Jentsch
diff --git a/man/convert.to.asc.Rd b/man/convert.to.asc.Rd
index ffb3b28..4f80056 100644
--- a/man/convert.to.asc.Rd
+++ b/man/convert.to.asc.Rd
@@ -19,7 +19,7 @@ convert.to.asc(
This function returns ASCII-format raster files to a new directory. This directory is dynamically created.
}
\description{
-This function Converts all .tif-raster files in a specified directory into an ASCII-File format in a new directory named "ASCII_files" with a unique timestamp of the current system time.
+This function converts and saves all .tif-raster files to ASCII-file format to a specified location and creates a new folder named "ASCII_files" with a unique timestamp of the current system time.
}
\examples{
convert.to.asc(save.location = system.file("pictures/", package = "rgdal"))
diff --git a/man/process.raster.int.doub.Rd b/man/process.raster.int.doub.Rd
index eb460d4..d9063bd 100644
--- a/man/process.raster.int.doub.Rd
+++ b/man/process.raster.int.doub.Rd
@@ -4,16 +4,16 @@
\alias{process.raster.int.doub}
\title{Preprocessing data to get real values}
\usage{
-process.raster.int.doub(raster.file = NULL)
+process.raster.int.doub(raster.layer = NULL)
}
\arguments{
-\item{raster.file}{Raster*File to be processed}
+\item{raster.layer}{RasterLayer to be processed}
}
\value{
-Rasterfile
+RasterLayer
}
\description{
-Takes input Raster* File, crops it, processes the integer values into double values, mosaiks the cropped and processed data, and returns the mosaiked Rasterfile
+Takes input RasterLayer, crops it, processes the integer values into double values, mosaiks the cropped and processed data, and returns the mosaiked Rasterfile
}
\author{
Helge Jentsch
diff --git a/man/save.citation.Rd b/man/save.citation.Rd
index 478d55c..0d7ce7d 100644
--- a/man/save.citation.Rd
+++ b/man/save.citation.Rd
@@ -6,7 +6,7 @@
\usage{
save.citation(
save.location = "./",
- dataSetName = c("Chelsa", "WorldClim1.4", "WorldClim2.1")
+ dataSetName = c("CHELSA", "WorldClim1.4", "WorldClim2.1")
)
}
\arguments{
@@ -15,13 +15,20 @@ save.citation(
\item{dataSetName}{string (vector). Specifies which dataset was downloaded or which citation should be saved. \cr Default: \code{c("Chelsa1.2", "WorldClim1.4", "WorldClim2.1")} (all available datasets)}
}
\value{
-BIBtex-file with biliography of the downloaded dataset
+BibTex-file with biliography of the downloaded dataset
}
\description{
-Saves the citation of the downloaded dataset into a BibTex-file in the Working Directory.
+Saves the citation of the downloaded dataset into a BibTex-file in the working directory.
}
\note{
-DISCLAIMER: No warranty or liability! The citations are provided without any warranty of any kind whatsoever, either expressed or implied, including warranties of merchantability and fitness for a particular purpose. The author should not be responsible for any incomplete citation of datasets or climate data products downloaded through this package.
+DISCLAIMER: No warranty or liability! The citations are provided without any warranty of any kind whatsoever, either expressed or implied, including warranties of merchantability and fitness for a particular purpose. The package author will not be responsible for any incomplete citation of datasets or climate data products downloaded through this package.
+}
+\examples{
+\dontrun{
+save.citation(dataSetName = "Chelsa")
+save.citation(dataSetName = "WorldClim1.4")
+save.citation(dataSetName = "WorldClim2.1")
+}
}
\author{
Helge Jentsch
diff --git a/man/stacking.downloaded.data.Rd b/man/stacking.downloaded.data.Rd
index 081b96e..9514eba 100644
--- a/man/stacking.downloaded.data.Rd
+++ b/man/stacking.downloaded.data.Rd
@@ -17,13 +17,13 @@ stacking.downloaded.data(
)
}
\arguments{
-\item{stack.save.location}{string (directory path). The directory where .tif-raster files are saved. Rasterfiles must be in a Geographic Coordinate System (in Arc-Degrees) \cr Default: \code{"./"} (Working directory)}
+\item{stack.save.location}{string (directory path). The directory where .tif-raster files are saved. Raster-files must be in a Geographic Coordinate System (in arc-degrees) \cr Default: \code{"./"} (Working directory)}
\item{stack.clipped}{logical. Input whether clipped data should be stacked and saved as netCDF as well. \cr Default: \code{FALSE}}
\item{parameter.var}{string. Input whether bioclim or climatic parameters are the input for the stacking process. \cr Default: \code{NULL}}
-\item{variable.numbers}{numeric (vector). Input how the stack variables should be called. By default just a sequence from 1 to the number of ".tif"-files are used.\cr Default: \code{c(1:length(list.files("./", pattern = ".tif")))}}
+\item{variable.numbers}{numeric (vector). Input how the stack variables should be called. By default just a sequence from 1 to the number of tif-raster files are used.\cr Default: \code{c(1:length(list.files("./", pattern = ".tif")))}}
\item{stack.time.series}{logical. Input whether a timeseries should be stacked. \cr Default: \code{FALSE}}
@@ -32,7 +32,7 @@ stacking.downloaded.data(
\item{time.stamp.var}{string. Timestamp to create unique directories for multiple run outputs.\cr Default: \code{stringr::str_replace_all(stringr::str_replace_all(paste0(} \cr \code{Sys.time()),pattern = ":",replacement = "-"))}}
}
\description{
-This function stacks all .tif-raster files in a specified directory and saves the Raster*stack File as netCDF-file in the specified directory.
+This function stacks all .tif-raster files of a specified directory and saves the stacked layers as a netCDF-file in that directory.
}
\author{
Helge Jentsch
--
GitLab