#' Estimates pest arrivals by returning residents
#'
#' Estimates arrival rate attributable to returning residents as a function of
#' population density.
#'
#' @param pop_density A `RasterLayer` or file path to a raster file
#' containing population density.
#' @param leakage_rate Numeric vector of 2 values, giving the lower and upper
#' bounds of a 95% CI for leakage rate (the number of pest leakage events in
#' a random year).
#' @param establishment_rate Numeric vector of 2 values, giving the lower and
#' upper bounds of a 95% CI for establishment rate (the rate of survival, to
#' establishment, for leakage events).
#' @param outfile Character. Output raster file path. If `probability` has
#' length > 1, the file type must support multiband rasters (e.g. GeoTiff). If
#' not provided, raster object will be returned to R.
#' @param return_rast Logical. Should the raster object be returned to R?
#' Ignored if `outfile` is not provided.
#' @param overwrite Logical. If `TRUE` and `outfile` is not missing,
#' it will be overwritten if the file specified by `outfile` already
#' exists.
#' @return If `outfile` is specified, the resulting raster (multiband if
#' `probability` has length > 1) is saved as a tiff at that path. If
#' `return_rast` is `TRUE` or `outfile` is not specified the
#' resulting raster object is returned, otherwise `NULL` is returned
#' invisibly.
#' @family functions estimating arrivals
#' @importFrom raster raster writeRaster stack
#' @export
arrivals_by_residents <- function(pop_density, leakage_rate, establishment_rate,
outfile, return_rast=FALSE, overwrite=FALSE) {
if(length(leakage_rate) != 2) {
stop('leakage_rate must be a vector of two values.')
}
if(length(establishment_rate) != 2) {
stop('establishment_rate must be a vector of two values.')
}
# Load raster
if(is.character(pop_density)) {
pop_density <- raster::raster(pop_density)
} else if(!is(pop_density, 'RasterLayer')) {
stop('pop_density must be a RasterLayer or a file path to a raster file.')
}
# Calculate proportion of population density
prop_pop <- calc_proportion(pop_density)
# Disperse passengers and calculate arrival rate
EE <- calc_EE(leakage_rate, establishment_rate)
out <- calc_pathway_pr(EE, prop_pop, return_rast=TRUE)
if(!missing(outfile)) {
# Create directory if it does not exist
if(!dir.exists(dirname(outfile))) {
dir.create(dirname(outfile), recursive = TRUE)
}
# write out raster
raster::writeRaster(out, outfile, overwrite = overwrite)
}
if(isTRUE(return_rast) || missing(outfile)) {
out
} else {
invisible(NULL)
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.