Nothing
R/worldclim.R
In geodata: Download Geographic Data
Defines functions
cmip6_tile
cmip6_world
.check_cmip6
.cmip6_world_old
worldclim_global
worldclim_country
worldclim_tile
.wcerad21
.wcerad
.get_id
.wccruts
Documented in
cmip6_tile
cmip6_world
worldclim_country
worldclim_global
worldclim_tile
.wccruts <- function(lon, lat, path, ...) {
}
.get_id <- function(lon, lat) {
r <- rast(res=5)
id <- unique(cellFromXY(r, cbind(lon,lat)))
if (any(is.na(id))) stop("invalid coordinates (lon/lat reversed?)")
path <- system.file(package="geodata")
tiles <- readRDS(file.path(path, "ex/tiles.rds"))
if (!(id %in% tiles)) {
stop("there is no weather data for this location (not on land?)")
}
id
}
.wcerad <- function(lon, lat, path, ...) {
path <- .get_path(path, "climate")
ids <- .get_id(lon, lat)
#ids <- unique(cellFromXY(r, cbind(lon,lat)))
pth <- file.path(path, "wcdera")
for (id in ids) {
fname <- paste0("wcdera_", id, ".nc")
outfname <- file.path(pth, fname)
if (!file.exists(outfname)) {
dir.create(pth, showWarnings=FALSE)
turl <- .wc_url(paste0("day/nc/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
}
sds(outfname)
}
.wcerad21 <- function(lon, lat, path, ...) {
path <- .get_path(path, "climate")
id <- .get_id(lon, lat)
pth <- file.path(path, "wcdera")
fname <- paste0("wcdera_", id, ".nc")
outfname <- file.path(pth, gsub("_", "21_", fname))
if (!file.exists(outfname)) {
dir.create(pth, showWarnings=FALSE)
turl <- .wc_url(paste0("day/nc21/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
sds(outfname)
}
worldclim_tile <- function(var, lon, lat, path, version="2.1", ...) {
stopifnot(var %in% c("tavg", "tmin", "tmax", "prec", "bio", "bioc", "elev", "wind", "vapr", "srad"))
version <- as.character(version)
stopifnot(version %in% c("2.1"))
if (var == "bioc") var <- "bio"
path <- .get_path(path, "climate")
r <- rast(res=30)
id <- cellFromXY(r, cbind(lon,lat))
if (is.na(id)) stop("invalid coordinates (lon/lat reversed?)")
pth <- file.path(path, "wc2.1_tiles")
dir.create(pth, showWarnings=FALSE)
fname <- paste0("tile_", id, "_wc2.1_30s_", var, ".tif")
outfname <- file.path(pth, fname)
if (!file.exists(outfname)) {
turl <- .wc_url(paste0("tiles/tile/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
rast(outfname)
}
worldclim_country <- function(country, var, path, version="2.1", ...) {
stopifnot(var %in% c("tavg", "tmin", "tmax", "prec", "bio", "bioc", "elev", "wind", "vapr", "srad"))
version <- as.character(version)
stopifnot(version %in% c("2.1"))
if (var == "bioc") var <- "bio"
iso <- .getCountryISO(country)
path <- .get_path(path, "climate")
pth <- file.path(path, "wc2.1_country")
dir.create(pth, showWarnings=FALSE)
fname <- paste0(iso, "_wc2.1_30s_", var, ".tif")
outfname <- file.path(pth, fname)
if (!file.exists(outfname)) {
turl <- .wc_url(paste0("tiles/iso/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
rast(outfname)
}
worldclim_global <- function(var, res, path, version="2.1", ...) {
res <- as.character(res)
version <- as.character(version)
stopifnot(res %in% c("2.5", "5", "10", "0.5"))
stopifnot(var %in% c("tavg", "tmin", "tmax", "prec", "bio", "bioc", "elev", "wind", "vapr", "srad"))
stopifnot(version %in% c("2.1"))
if (var == "bioc") var <- "bio"
path <- .get_path(path, "climate")
fres <- ifelse(res=="0.5", "30s", paste0(res, "m"))
path <- file.path(path, paste0("wc2.1_", fres, "/"))
dir.create(path, showWarnings=FALSE)
zip <- paste0("wc2.1_", fres, "_", var, ".zip")
if (var == "elev") {
ff <- paste0("wc2.1_", fres, "_elev.tif")
} else {
nf <- if (var == "bio") 1:19 else formatC(1:12, width=2, flag=0)
ff <- paste0("wc2.1_", fres, "_", var, "_", nf, ".tif")
}
pzip <- file.path(path, zip)
ff <- file.path(path, ff)
if (!all(file.exists(ff))) {
turl <- .wc_url(paste0("base/", zip))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, pzip, ...)) return(NULL)
fz <- try(utils::unzip(pzip, exdir=path), silent=TRUE)
try(file.remove(pzip), silent=TRUE)
if (inherits(fz, "try-error")) {
message("download failed")
return(NULL)
}
}
rast(ff)
}
.cmip6_world_old <- function(model, ssp, time, var, res, path, ...) {
res <- as.character(res)
stopifnot(res %in% c("2.5", "5", "10"))
stopifnot(var %in% c("tmin", "tmax", "prec", "bio", "bioc"))
ssp <- as.character(ssp)
stopifnot(ssp %in% c("126", "245", "370", "585"))
stopifnot(model %in% c("BCC-CSM2-MR", "CanESM5", "CNRM-CM6-1", "CNRM-ESM2-1", "GFDL-ESM4", "IPSL-CM6A-LR", "MIROC-ES2L", "MIROC6", "MRI-ESM2-0"))
stopifnot(time %in% c("2021-2040", "2041-2060", "2061-2080"))
# some combinations do not exist. Catch these here.
if (var == "bio") var <- "bioc"
path <- .get_path(path, "climate")
fres <- ifelse(res==0.5, "30s", paste0(res, "m"))
path <- file.path(path, paste0("wc2.1_", fres, "/"))
dir.create(path, showWarnings=FALSE)
outf <- paste0("wc2.1_", fres, "_", var, "_", model, "_ssp", ssp, "_", time, ".tif")
poutf <- file.path(path, outf)
if (!file.exists(poutf)) {
if (!file.exists(outf)) {
url <- .wc_url(paste0("cmip6/", fres, "/", model, "/ssp", ssp, "/", outf))
if (is.null(url)) return(NULL)
if(!.downloadDirect(url, poutf, ...)) return(NULL)
}
}
rast(poutf)
}
.cmods <- c('ACCESS-CM2', 'ACCESS-ESM1-5', 'AWI-CM-1-1-MR', 'BCC-CSM2-MR', 'CanESM5', 'CanESM5-CanOE', 'CMCC-ESM2', 'CNRM-CM6-1', 'CNRM-CM6-1-HR', 'CNRM-ESM2-1', 'EC-Earth3-Veg', 'EC-Earth3-Veg-LR', 'FIO-ESM-2-0', 'GFDL-ESM4', 'GISS-E2-1-G', 'GISS-E2-1-H', 'HadGEM3-GC31-LL', 'INM-CM4-8', 'INM-CM5-0', 'IPSL-CM6A-LR', 'MIROC-ES2L', 'MIROC6', 'MPI-ESM1-2-HR', 'MPI-ESM1-2-LR', 'MRI-ESM2-0', 'UKESM1-0-LL')
.c6url <- "https://geodata.ucdavis.edu/cmip6/"
.check_cmip6 <- function(res, var, ssp, model, time) {
stopifnot(ssp %in% c("126", "245", "370", "585"))
stopifnot(res %in% c("0.5", "2.5", "5", "10"))
stopifnot(var %in% c("tmin", "tmax", "prec", "bioc"))
if (!(model %in% .cmods)) {
stop(paste("not a valid model, use of of:\n", paste(.cmods, collapse=", ")))
}
stopifnot(time %in% c("2021-2040", "2041-2060", "2061-2080", "2081-2100"))
# some combinations do not exist. Catch these here.
#find 30s -type f -printf "%f\n" | cut -c11-100 > files.txt
tmpfile <- file.path(tempdir(), "cmip6_files.txt")
if (!file.exists(tmpfile)) {
suppressWarnings(try(utils::download.file(paste0(.c6url, "files.txt"), tmpfile, quiet=TRUE), silent=TRUE))
}
if (file.exists(tmpfile)) {
ff <- utils::read.table(tmpfile, sep="_")
if (nrow(ff) > 1000) {
i <- ff[,1] == var & ff[,2] == model & ff[,3] == paste0("ssp", ssp) & ff[,4] == paste0(time, ".tif")
if (sum(i) != 1) {
stop("This dataset is not available")
}
}
}
}
cmip6_world <- function(model, ssp, time, var, res, path, ...) {
res <- as.character(res)
fres <- ifelse(res==0.5, "30s", paste0(res, "m"))
ssp <- as.character(ssp)
if (var == "bio") var <- "bioc"
try(.check_cmip6(res, var, ssp, model, time), silent=TRUE)
path <- .get_path(path, "climate")
path <- file.path(path, paste0("wc2.1_", fres, "/"))
dir.create(path, showWarnings=FALSE)
outf <- paste0("wc2.1_", fres, "_", var, "_", model, "_ssp", ssp, "_", time, ".tif")
poutf <- file.path(path, outf)
if (!file.exists(poutf)) {
if (!file.exists(outf)) {
durl <- paste0(.c6url, fres, "/", model, "/ssp", ssp, "/", outf)
durl <- .data_url(durl=durl)
if (is.null(durl)) return(NULL)
if (!.downloadDirect(durl, poutf, ...)) return(NULL)
}
#fz <- try(utils::unzip(pzip, exdir=path, junkpaths=TRUE), silent=TRUE)
#try(file.remove(pzip), silent=TRUE)
#if (inherits(fz, "try-error")) { stop("unzip failed") }
}
rast(poutf)
}
cmip6_tile <- function(lon, lat, model, ssp, time, var, path, ...) {
ssp <- as.character(ssp)
if (var == "bio") var <- "bioc"
.check_cmip6(0.5, var, ssp, model, time)
path <- .get_path(path, "climate")
path <- file.path(path, paste0("wc2.1_30s/"))
dir.create(path, showWarnings=FALSE)
r <- rast(res=30)
ids <- cellFromXY(r, cbind(lon, lat))
if (any(is.na(ids))) stop("invalid coordinates (lon/lat reversed?)")
pth <- file.path(path, "wc2.1_tiles")
dir.create(pth, showWarnings=FALSE)
fname <- paste0("wc2.1_30s_", var, "_", model, "_ssp", ssp, "_", time, "_tile-", ids, ".tif")
outfname <- file.path(path, fname)
for (i in 1:length(outfname)) {
if (!file.exists(outfname[i])) {
turl <- paste0(.c6url, "tiles/", model, "/ssp", ssp, "/", fname[i])
turl <- .data_url(durl=turl)
if (!.downloadDirect(turl, outfname[i], ...)) return(NULL)
}
}
if (length(outfname) == 1) {
rast(outfname)
} else {
vrt(outfname)
}
}
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Defines functions cmip6_tile cmip6_world .check_cmip6 .cmip6_world_old worldclim_global worldclim_country worldclim_tile .wcerad21 .wcerad .get_id .wccruts
Documented in cmip6_tile cmip6_world worldclim_country worldclim_global worldclim_tile
.wccruts <- function(lon, lat, path, ...) {
}
.get_id <- function(lon, lat) {
r <- rast(res=5)
id <- unique(cellFromXY(r, cbind(lon,lat)))
if (any(is.na(id))) stop("invalid coordinates (lon/lat reversed?)")
path <- system.file(package="geodata")
tiles <- readRDS(file.path(path, "ex/tiles.rds"))
if (!(id %in% tiles)) {
stop("there is no weather data for this location (not on land?)")
}
id
}
.wcerad <- function(lon, lat, path, ...) {
path <- .get_path(path, "climate")
ids <- .get_id(lon, lat)
#ids <- unique(cellFromXY(r, cbind(lon,lat)))
pth <- file.path(path, "wcdera")
for (id in ids) {
fname <- paste0("wcdera_", id, ".nc")
outfname <- file.path(pth, fname)
if (!file.exists(outfname)) {
dir.create(pth, showWarnings=FALSE)
turl <- .wc_url(paste0("day/nc/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
}
sds(outfname)
}
.wcerad21 <- function(lon, lat, path, ...) {
path <- .get_path(path, "climate")
id <- .get_id(lon, lat)
pth <- file.path(path, "wcdera")
fname <- paste0("wcdera_", id, ".nc")
outfname <- file.path(pth, gsub("_", "21_", fname))
if (!file.exists(outfname)) {
dir.create(pth, showWarnings=FALSE)
turl <- .wc_url(paste0("day/nc21/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
sds(outfname)
}
worldclim_tile <- function(var, lon, lat, path, version="2.1", ...) {
stopifnot(var %in% c("tavg", "tmin", "tmax", "prec", "bio", "bioc", "elev", "wind", "vapr", "srad"))
version <- as.character(version)
stopifnot(version %in% c("2.1"))
if (var == "bioc") var <- "bio"
path <- .get_path(path, "climate")
r <- rast(res=30)
id <- cellFromXY(r, cbind(lon,lat))
if (is.na(id)) stop("invalid coordinates (lon/lat reversed?)")
pth <- file.path(path, "wc2.1_tiles")
dir.create(pth, showWarnings=FALSE)
fname <- paste0("tile_", id, "_wc2.1_30s_", var, ".tif")
outfname <- file.path(pth, fname)
if (!file.exists(outfname)) {
turl <- .wc_url(paste0("tiles/tile/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
rast(outfname)
}
worldclim_country <- function(country, var, path, version="2.1", ...) {
stopifnot(var %in% c("tavg", "tmin", "tmax", "prec", "bio", "bioc", "elev", "wind", "vapr", "srad"))
version <- as.character(version)
stopifnot(version %in% c("2.1"))
if (var == "bioc") var <- "bio"
iso <- .getCountryISO(country)
path <- .get_path(path, "climate")
pth <- file.path(path, "wc2.1_country")
dir.create(pth, showWarnings=FALSE)
fname <- paste0(iso, "_wc2.1_30s_", var, ".tif")
outfname <- file.path(pth, fname)
if (!file.exists(outfname)) {
turl <- .wc_url(paste0("tiles/iso/", fname))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, outfname, ...)) return(NULL)
}
rast(outfname)
}
worldclim_global <- function(var, res, path, version="2.1", ...) {
res <- as.character(res)
version <- as.character(version)
stopifnot(res %in% c("2.5", "5", "10", "0.5"))
stopifnot(var %in% c("tavg", "tmin", "tmax", "prec", "bio", "bioc", "elev", "wind", "vapr", "srad"))
stopifnot(version %in% c("2.1"))
if (var == "bioc") var <- "bio"
path <- .get_path(path, "climate")
fres <- ifelse(res=="0.5", "30s", paste0(res, "m"))
path <- file.path(path, paste0("wc2.1_", fres, "/"))
dir.create(path, showWarnings=FALSE)
zip <- paste0("wc2.1_", fres, "_", var, ".zip")
if (var == "elev") {
ff <- paste0("wc2.1_", fres, "_elev.tif")
} else {
nf <- if (var == "bio") 1:19 else formatC(1:12, width=2, flag=0)
ff <- paste0("wc2.1_", fres, "_", var, "_", nf, ".tif")
}
pzip <- file.path(path, zip)
ff <- file.path(path, ff)
if (!all(file.exists(ff))) {
turl <- .wc_url(paste0("base/", zip))
if (is.null(turl)) return(NULL)
if (!.downloadDirect(turl, pzip, ...)) return(NULL)
fz <- try(utils::unzip(pzip, exdir=path), silent=TRUE)
try(file.remove(pzip), silent=TRUE)
if (inherits(fz, "try-error")) {
message("download failed")
return(NULL)
}
}
rast(ff)
}
.cmip6_world_old <- function(model, ssp, time, var, res, path, ...) {
res <- as.character(res)
stopifnot(res %in% c("2.5", "5", "10"))
stopifnot(var %in% c("tmin", "tmax", "prec", "bio", "bioc"))
ssp <- as.character(ssp)
stopifnot(ssp %in% c("126", "245", "370", "585"))
stopifnot(model %in% c("BCC-CSM2-MR", "CanESM5", "CNRM-CM6-1", "CNRM-ESM2-1", "GFDL-ESM4", "IPSL-CM6A-LR", "MIROC-ES2L", "MIROC6", "MRI-ESM2-0"))
stopifnot(time %in% c("2021-2040", "2041-2060", "2061-2080"))
# some combinations do not exist. Catch these here.
if (var == "bio") var <- "bioc"
path <- .get_path(path, "climate")
fres <- ifelse(res==0.5, "30s", paste0(res, "m"))
path <- file.path(path, paste0("wc2.1_", fres, "/"))
dir.create(path, showWarnings=FALSE)
outf <- paste0("wc2.1_", fres, "_", var, "_", model, "_ssp", ssp, "_", time, ".tif")
poutf <- file.path(path, outf)
if (!file.exists(poutf)) {
if (!file.exists(outf)) {
url <- .wc_url(paste0("cmip6/", fres, "/", model, "/ssp", ssp, "/", outf))
if (is.null(url)) return(NULL)
if(!.downloadDirect(url, poutf, ...)) return(NULL)
}
}
rast(poutf)
}
.cmods <- c('ACCESS-CM2', 'ACCESS-ESM1-5', 'AWI-CM-1-1-MR', 'BCC-CSM2-MR', 'CanESM5', 'CanESM5-CanOE', 'CMCC-ESM2', 'CNRM-CM6-1', 'CNRM-CM6-1-HR', 'CNRM-ESM2-1', 'EC-Earth3-Veg', 'EC-Earth3-Veg-LR', 'FIO-ESM-2-0', 'GFDL-ESM4', 'GISS-E2-1-G', 'GISS-E2-1-H', 'HadGEM3-GC31-LL', 'INM-CM4-8', 'INM-CM5-0', 'IPSL-CM6A-LR', 'MIROC-ES2L', 'MIROC6', 'MPI-ESM1-2-HR', 'MPI-ESM1-2-LR', 'MRI-ESM2-0', 'UKESM1-0-LL')
.c6url <- "https://geodata.ucdavis.edu/cmip6/"
.check_cmip6 <- function(res, var, ssp, model, time) {
stopifnot(ssp %in% c("126", "245", "370", "585"))
stopifnot(res %in% c("0.5", "2.5", "5", "10"))
stopifnot(var %in% c("tmin", "tmax", "prec", "bioc"))
if (!(model %in% .cmods)) {
stop(paste("not a valid model, use of of:\n", paste(.cmods, collapse=", ")))
}
stopifnot(time %in% c("2021-2040", "2041-2060", "2061-2080", "2081-2100"))
# some combinations do not exist. Catch these here.
#find 30s -type f -printf "%f\n" | cut -c11-100 > files.txt
tmpfile <- file.path(tempdir(), "cmip6_files.txt")
if (!file.exists(tmpfile)) {
suppressWarnings(try(utils::download.file(paste0(.c6url, "files.txt"), tmpfile, quiet=TRUE), silent=TRUE))
}
if (file.exists(tmpfile)) {
ff <- utils::read.table(tmpfile, sep="_")
if (nrow(ff) > 1000) {
i <- ff[,1] == var & ff[,2] == model & ff[,3] == paste0("ssp", ssp) & ff[,4] == paste0(time, ".tif")
if (sum(i) != 1) {
stop("This dataset is not available")
}
}
}
}
cmip6_world <- function(model, ssp, time, var, res, path, ...) {
res <- as.character(res)
fres <- ifelse(res==0.5, "30s", paste0(res, "m"))
ssp <- as.character(ssp)
if (var == "bio") var <- "bioc"
try(.check_cmip6(res, var, ssp, model, time), silent=TRUE)
path <- .get_path(path, "climate")
path <- file.path(path, paste0("wc2.1_", fres, "/"))
dir.create(path, showWarnings=FALSE)
outf <- paste0("wc2.1_", fres, "_", var, "_", model, "_ssp", ssp, "_", time, ".tif")
poutf <- file.path(path, outf)
if (!file.exists(poutf)) {
if (!file.exists(outf)) {
durl <- paste0(.c6url, fres, "/", model, "/ssp", ssp, "/", outf)
durl <- .data_url(durl=durl)
if (is.null(durl)) return(NULL)
if (!.downloadDirect(durl, poutf, ...)) return(NULL)
}
#fz <- try(utils::unzip(pzip, exdir=path, junkpaths=TRUE), silent=TRUE)
#try(file.remove(pzip), silent=TRUE)
#if (inherits(fz, "try-error")) { stop("unzip failed") }
}
rast(poutf)
}
cmip6_tile <- function(lon, lat, model, ssp, time, var, path, ...) {
ssp <- as.character(ssp)
if (var == "bio") var <- "bioc"
.check_cmip6(0.5, var, ssp, model, time)
path <- .get_path(path, "climate")
path <- file.path(path, paste0("wc2.1_30s/"))
dir.create(path, showWarnings=FALSE)
r <- rast(res=30)
ids <- cellFromXY(r, cbind(lon, lat))
if (any(is.na(ids))) stop("invalid coordinates (lon/lat reversed?)")
pth <- file.path(path, "wc2.1_tiles")
dir.create(pth, showWarnings=FALSE)
fname <- paste0("wc2.1_30s_", var, "_", model, "_ssp", ssp, "_", time, "_tile-", ids, ".tif")
outfname <- file.path(path, fname)
for (i in 1:length(outfname)) {
if (!file.exists(outfname[i])) {
turl <- paste0(.c6url, "tiles/", model, "/ssp", ssp, "/", fname[i])
turl <- .data_url(durl=turl)
if (!.downloadDirect(turl, outfname[i], ...)) return(NULL)
}
}
if (length(outfname) == 1) {
rast(outfname)
} else {
vrt(outfname)
}
}
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