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#'@name lagosne_compile
#'@title Compile LAGOSNE data
#'
#'@description Compile LAGOSNE data from component flat files. This function should rarely be called directly outside of manual updating of source data.
#'
#'@param version character LAGOSNE database version string
#'@param limno_folder file.path to limno export folder
#'@param geo_folder file.path to geo export folder
#'@param locus_folder file.path to locus export folder
#'@param dest_folder file.path optional will default to the location returned
#'by \code{\link[rappdirs]{user_data_dir}}
#'
#'@importFrom utils read.table
#'@importFrom rappdirs user_data_dir
#'@importFrom qs qsave
#'@export
#'
#'@examples \dontrun{
#' lagosne_compile("1.087.3",
#' limno_folder = "~/Downloads/LAGOS-NE-LIMNO-EXPORT",
#' geo_folder = "~/Downloads/LAGOS-NE-GEO-EXPORT",
#' locus_folder = "~/Downloads/LAGOS-NE-LOCUS-EXPORT",
#' dest_folder = lagos_path())
#' }
#'
lagosne_compile <- function(version,
limno_folder = NA, geo_folder = NA,
locus_folder = NA, dest_folder = NA){
if(is.na(dest_folder)){
stop("Set the dest_folder argument to a folder on your local machine. Recommended setting is lagos_path().")
}
ingest <- lagos_ingest(version = version, limno_folder = limno_folder,
geo_folder = geo_folder, locus_folder = locus_folder)
geo <- ingest$geo
limno <- ingest$limno
locus <- ingest$locus
dir.create(lagos_path(), recursive = TRUE, showWarnings = FALSE)
res <- list("geo" = geo,
"limno" = limno,
"locus" = list(locus))
res <- purrr::flatten(res)
outpath <- file.path(dest_folder, paste0("data_", version, ".qs"))
qs::qsave(res, outpath)
message(paste0("LAGOSNE compiled to ", outpath))
}
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