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Adapt get predict table, renamed present/future climate to observed/projected climate #86

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148d587
Renamed two functions, according to discussions in the group.
merretbuurman Jan 30, 2025
dcadfa3
Renamed documentation item for more consistency.
merretbuurman Jan 30, 2025
1191ce2
Modified NAMESPACE to keep it in alphabetical order.
merretbuurman Jan 30, 2025
544c8cc
Updated the accepted variables in get_predict_table.
merretbuurman Jan 30, 2025
d198eba
get_predict_table: Moved slow check further down.
merretbuurman Jan 30, 2025
27e2343
get_predict_table: Improved variable name check by telling user which…
merretbuurman Jan 30, 2025
5d45c03
Cosmetics: Some error messages.
merretbuurman Jan 30, 2025
8dbf30e
get_predict_table: Allow passing tempdir.
merretbuurman Jan 30, 2025
2cd29bc
Unit tests for check_tiles_filesize can now be run without downloadin…
merretbuurman Jan 30, 2025
54842d8
Unit tests for check_tiles_filesize can now be run with or without do…
merretbuurman Jan 30, 2025
88c53f8
get_predict_table: Updated documentation and some log messages.
merretbuurman Jan 31, 2025
89a5475
get_predict_table: Added check for input table, as otherwise it fails…
merretbuurman Jan 31, 2025
1274de3
get_predict_table: Displaying bash script output if quiet is FALSE.
merretbuurman Jan 31, 2025
38bf17b
get_predict_table: Adding bash output.
merretbuurman Jan 31, 2025
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4 changes: 2 additions & 2 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@
export(crop_to_extent)
export(download_cgiar_tables)
export(download_flo1k_tables)
export(download_future_climate_tables)
export(download_hydrography90m_tables)
export(download_landcover_tables)
export(download_merit_dem_tables)
export(download_present_climate_tables)
export(download_observed_climate_tables)
export(download_projected_climate_tables)
export(download_soil_tables)
export(download_test_data)
export(download_tiles)
Expand Down
119 changes: 59 additions & 60 deletions R/download_env90m_tables.R
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Original file line number Diff line number Diff line change
Expand Up @@ -104,12 +104,12 @@
#' sub-catchment scale for freshwater biodiversity modeling, in prep.
#' Please contact the authors for more up-to-date citation info.
#'
#' @name download-env90m-tables
#' @name download_env90m_tables
NULL



#' @describeIn download-env90m-tables Download SOILGRIDS tables
#' @describeIn download_env90m_tables Download SOILGRIDS tables
#' (soilgrids250m_v2_0)
#' @examples
#'
Expand Down Expand Up @@ -166,7 +166,7 @@ download_soil_tables <- function(subset = NULL,



#' @describeIn download-env90m-tables Download flow tables (flo1k_v1_0)
#' @describeIn download_env90m_tables Download flow tables (flo1k_v1_0)
#' @examples
#'
#' ### Flow (mean): flo1k_v1_0 ###
Expand Down Expand Up @@ -225,7 +225,7 @@ download_flo1k_tables <- function(subset = NULL,



#' @describeIn download-env90m-tables Download CGIAR-CSI tables (cgiar_csi_v3)
#' @describeIn download_env90m_tables Download CGIAR-CSI tables (cgiar_csi_v3)
#' @examples
#'
#' ### CGIAR CSI dataset: cgiar_csi_v3 ###
Expand Down Expand Up @@ -280,7 +280,7 @@ download_cgiar_tables <- function(subset = NULL,
}


#' @describeIn download-env90m-tables Download MERIT-DEM tables
#' @describeIn download_env90m_tables Download MERIT-DEM tables
#' (Multi-Error-Removed Improved-Terrain Digital Elevation Model,
#' merit_dem_v1_0_3)
#' @examples
Expand Down Expand Up @@ -333,15 +333,15 @@ download_merit_dem_tables <- function(subset = NULL,

return(download_simple_tables(
"merit_dem_v1_0_3",
"env90m_merit_dem_paths_file_sizes.txt",
"env90m_meritdem_paths_file_sizes.txt",
subset, tile_ids, ignore_missing, download, download_dir,
file_format, delete_zips, tempdir, quiet
))
}



#' @describeIn download-env90m-tables Download Hydrography90m tables
#' @describeIn download_env90m_tables Download Hydrography90m tables
#' (hydrography90m_v1_0)
#' @examples
#'
Expand Down Expand Up @@ -397,27 +397,26 @@ download_hydrography90m_tables <- function(subset = NULL,
}


#' @describeIn download-env90m-tables Download CHELSA bioclimatic variables tables,
#' except for future simulations (Climatologies at high resolution for the
#' @describeIn download_env90m_tables Download CHELSA bioclimatic variables
#' tables, except for projections (Climatologies at high resolution for the
#' earth’s land surface areas, chelsa_bioclim_v2_1)
#'
#' @examples
#'
#' ### Bioclimatic Variables: chelsa_bioclim_v2_1 ###
#' ### (excluding future simulations) ###
#'
#' ### (excluding projections) ###
#' # Show all available bioclim variable names
#' # (excluding future simulations):
#' download_present_climate_tables()
#' # (excluding projections):
#' download_observed_climate_tables()
#'
#' # Compute download size of all bioclim variables, for one tile:
#' download_present_climate_tables(
#' download_observed_climate_tables(
#' subset = "ALL",
#' tile_ids = c("h00v04"),
#' download = FALSE)
#'
#' # Download one bioclim variable (Annual mean temperature), for two tiles:
#' \dontrun{
#' download_present_climate_tables(
#' download_observed_climate_tables(
#' subset = c("bio1"),
#' tile_ids = c("h00v04", "h10v04"),
#' download = TRUE,
Expand All @@ -428,7 +427,7 @@ download_hydrography90m_tables <- function(subset = NULL,
#' # Download one bioclim variable (Annual mean temperature), for one tile,
#' # unzip, and delete the zips:
#' \dontrun{
#' download_present_climate_tables(
#' download_observed_climate_tables(
#' subset = c("bio1"),
#' tile_ids = c("h00v04"),
#' download = TRUE,
Expand All @@ -438,71 +437,71 @@ download_hydrography90m_tables <- function(subset = NULL,
#' }
#'
#' @export
download_present_climate_tables <- function(subset = NULL,
tile_ids = NULL,
download = FALSE,
download_dir = ".",
file_format = "txt",
delete_zips = TRUE,
ignore_missing = FALSE,
tempdir = NULL,
quiet = FALSE) {
download_observed_climate_tables <- function(subset = NULL,
tile_ids = NULL,
download = FALSE,
download_dir = ".",
file_format = "txt",
delete_zips = TRUE,
ignore_missing = FALSE,
tempdir = NULL,
quiet = FALSE) {

return(download_simple_tables(
"chelsa_bioclim_v2_1",
"env90m_presentclimate_paths_file_sizes.txt",
"env90m_observedclimate_paths_file_sizes.txt",
subset, tile_ids, ignore_missing, download, download_dir,
file_format, delete_zips, tempdir, quiet
))
}


#' @describeIn download-env90m-tables Download CHELSA bioclimatic variables tables,
#' future simulations only (Climatologies at high resolution for the
#' @describeIn download_env90m_tables Download CHELSA bioclimatic variables,
#' tables, projections only (Climatologies at high resolution for the
#' earth’s land surface areas, chelsa_bioclim_v2_1)
#' @param base_vars (Only in `download_future_climate_tables()` and
#' @param base_vars (Only in `download_projected_climate_tables()` and
#' `download_landcover_tables()`) Vector of the desired base variables, e.g.
#' the landcover variable "c20_1992" can be expressed as base variable "c20"
#' and year "1992".
#' @param time_periods (Only in `download_future_climate_...`) Vector of the
#' @param time_periods (Only in `download_projected_climate_...`) Vector of the
#' desired time periods (leave `NULL` or specify `"ALL"` for all available
#' time periods).
#' @param models (Only in `download_future_climate_...`) Vector of the desired
#' @param models (Only in `download_projected_climate_...`) Vector of the desired
#' models (leave `NULL` or specify `"ALL"` for all available models).
#' @param scenarios (Only in `download_future_climate_...`) Vector of the
#' @param scenarios (Only in `download_projected_climate_...`) Vector of the
#' desired scenarios (leave `NULL` or specify `"ALL"` for all available
#' scenarios).
#' @param versions (Only in `download_future_climate_...`) Vector of the
#' @param versions (Only in `download_projected_climate_...`) Vector of the
#' desired versions (leave `NULL` or specify `"ALL"` for all available
#' versions). As of January 2025, the only available version is "V.2.1".
#'
#' @examples
#'
#' ### Bioclimatic Variables: chelsa_bioclim_v2_1 ###
#' ### (future simulations) ###
#' # Show all available future bioclim variable names
#' download_future_climate_tables()
#' ### (projections only) ###
#' # Show all available projected bioclim variable names
#' download_projected_climate_tables()
#'
#' # Compute download size of all variables, for one tile:
#' download_future_climate_tables(
#' download_projected_climate_tables(
#' subset = "ALL",
#' tile_ids = c("h00v04"),
#' download = FALSE)
#'
#' # Download one hy90m variable (Annual mean temperature), for two tiles:
#' # Download one variable (Annual mean temperature), for two tiles:
#' \dontrun{
#' download_future_climate_tables(
#' download_projected_climate_tables(
#' subset = c("bio1"),
#' tile_ids = c("h00v04", "h10v04"),
#' download = TRUE,
#' download_dir = ".",
#' file_format = "zip")
#' }
#'
#' # Download one hy90m variable (Annual mean temperature), for one tile,
#' # Download one variable (Annual mean temperature), for one tile,
#' # unzip, and delete the zips:
#' \dontrun{
#' download_future_climate_tables(
#' download_projected_climate_tables(
#' subset = c("bio1"),
#' tile_ids = c("h00v04"),
#' download = TRUE,
Expand All @@ -512,27 +511,27 @@ download_present_climate_tables <- function(subset = NULL,
#' }
#'
#' @export
download_future_climate_tables <- function(base_vars = NULL,
time_periods = NULL,
models = NULL,
scenarios = NULL,
versions = NULL,
subset = NULL,
tile_ids = NULL,
download = FALSE,
download_dir = ".",
file_format = "txt",
delete_zips = TRUE,
ignore_missing = FALSE,
tempdir = NULL,
quiet = FALSE) {
download_projected_climate_tables <- function(base_vars = NULL,
time_periods = NULL,
models = NULL,
scenarios = NULL,
versions = NULL,
subset = NULL,
tile_ids = NULL,
download = FALSE,
download_dir = ".",
file_format = "txt",
delete_zips = TRUE,
ignore_missing = FALSE,
tempdir = NULL,
quiet = FALSE) {

#########################################
### Extract info from file size table ###
#########################################

# Use file_size_table from tempdir or download it:
file_name <- "env90m_futureclimate_paths_file_sizes.txt"
file_name <- "env90m_projectedclimate_paths_file_sizes.txt"
file_size_table <- get_file_size_table(file_name, tempdir, quiet)

# Info:
Expand Down Expand Up @@ -858,7 +857,7 @@ download_future_climate_tables <- function(base_vars = NULL,
variables$tile_ids=tile_ids
}

# Download the future climate data if requested:
# Download the projected climate data if requested:
if (download) {
if (is.null(tile_ids)) {
msg <- "To download, please specify parameter 'tile_ids'."
Expand Down Expand Up @@ -889,10 +888,10 @@ download_future_climate_tables <- function(base_vars = NULL,
}


#' @describeIn download-env90m-tables Download ESA Land Cover tables
#' @describeIn download_env90m_tables Download ESA Land Cover tables
#' (esa_cci_landcover_v2_1_1)
#'
#' @param base_vars (Only in `download_future_climate_tables()` and
#' @param base_vars (Only in `download_projected_climate_tables()` and
#' `download_landcover_tables()`) Vector of the desired base variables, e.g.
#' the landcover variable "c20_1992" can be expressed as base variable "c20"
#' and year "1992".
Expand Down
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