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#' @title xfer_userExtent: user provided extent of transfer
#' @description This function generates an area of transfer according to a user
#' provided polygon and buffer.
#'
#' @details
#' This function is used in the transfer component. Here, the user provides
#' either a shapefile or a csv with vertex coordinates with the desired shape
#' for the extent of transfer, the user may include a buffer to the given
#' polygon. The function returns a SpatialPolygons object of the desired
#' extent (+ buffer).
#'
#' @param bgShp_path path to the user provided shapefile or csv with
#' vertex coordinates.
#' @param bgShp_name name of the user provided shapefile or csv with
#' vertex coordinates.
#' @param userBgBuf numeric. Buffer to be used in creating the background
#' extent must be >= 0.
#' @param logger Stores all notification messages to be displayed in the Log
#' Window of Wallace GUI. Insert the logger reactive list here for running
#' in shiny, otherwise leave the default NULL.
#' @param spN data frame of cleaned occurrences obtained from component
#' occs: Obtain occurrence data. Used to obtain species name for logger
#' messages.
#' @examples
#' pathShp <- list.files(system.file("extdata/shp", package = "wallace"),
#' full.names = TRUE)
#' nameShp <- list.files(system.file("extdata/shp", package = "wallace"),
#' full.names = FALSE)
#' xferUser <- xfer_userExtent(bgShp_path = pathShp, bgShp_name = nameShp,
#' userBgBuf = 1)
#' @return This function returns a SpatialPolygons object with the user
#' provided shape (+ a buffer is userBgBuf >0).
#' @author Jamie Kass <jamie.m.kass@@gmail.com>
#' @author Gonzalo E. Pinilla-Buitrago <gepinillab@@gmail.com>
#' @author Andrea Paz <paz.andreita@@gmail.com>
#' @seealso \code{\link{penvs_drawBgExtent}}, \code{\link{penvs_bgExtent}},
#' \code{\link{penvs_bgMask}} , \code{\link{penvs_bgSample}}
#' @export
xfer_userExtent <- function(bgShp_path, bgShp_name, userBgBuf,
logger = NULL, spN = NULL) {
pathdir <- dirname(bgShp_path)
pathfile <- basename(bgShp_path)
# get extensions of all input files
exts <- sapply(strsplit(bgShp_name, '\\.'), FUN = function(x) x[2])
if (length(exts) == 1 & exts[1] == 'csv') {
f <- utils::read.csv(bgShp_path, header = TRUE)
bgExt <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(f)), 1)))
} else if ('shp' %in% exts) {
if (length(exts) < 3) {
logger %>%
writeLog(type = 'error',
paste0('If entering a shapefile, please select all the ',
'following files: .shp, .shx, .dbf.'))
return()
}
# get index of .shp
i <- which(exts == 'shp')
if (!file.exists(file.path(pathdir, bgShp_name)[i])) {
file.rename(bgShp_path, file.path(pathdir, bgShp_name))
}
# read in shapefile and extract coords
bgExt <- sf::st_read(file.path(pathdir, bgShp_name)[i])
bgExt <- sf::as_Spatial(bgExt)
} else {
logger %>%
writeLog(type = 'error',
paste0('Please enter either a CSV file of vertex coordinates ',
'or shapefile (.shp, .shx, .dbf).'))
return()
}
if (userBgBuf > 0) {
bgExt <- sf::st_as_sf(bgExt)
bgExt <- sf::st_buffer(bgExt, dist = userBgBuf)
bgExt <- sf::as_Spatial(bgExt)
logger %>% writeLog(
hlSpp(spN),
'Transferring extent user-defined polygon buffered by ',
userBgBuf, ' degrees.')
} else if (userBgBuf < 0) {
logger %>%
writeLog(type = 'error',
'Change buffer distance to a positive value.')
return()
} else {
logger %>% writeLog(
hlSpp(spN),
"Transferring extent: user-defined polygon.")
}
return(bgExt)
}
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