files_2data: Creates a data.frame of species' references from files in a...

In claununez/biosurvey: Tools for Biological Survey Planning

Creates a data.frame of species' references from files in a directory

Description

Creates a data.frame of species' references that contains longitude, latitude, and species name, from a character.

Usage

files_2data(path, format, spdf_grid = NULL, parallel = FALSE, n_cores = NULL)

Arguments

path	(character) full path name of directory containing raster, shapefiles or geopackage files representing species geographic ranges. Each file must be named as the species that it represents. All files must be in the same format. If files are raster layers, values in each layer must be 1 (presence, suitable) and 0 (absence, unsuitable).
format	(character) the format files found in path. Current available formats are: "shp", "gpkg", "GTiff", and "ascii".
spdf_grid	geographic grid for the region of interest (output of function grid_from_region). Used when format equals "shp" or "gpkg". Default = NULL.
parallel	(logical) whether to perform analyses in parallel. Default = FALSE.
n_cores	(numeric) number of cores to be used when parallel = TRUE. The default, NULL, uses available cores - 1.

Value

If files are in raster format, a data.frame of species geographic records derived from values of presence in each layer.

If files are not in raster format, a data.frame of species' found in distinct positions (defined with identifiers); includes two columns: "ID" and "Species".

Examples

# Data for examples
mx <- terra::vect(system.file("extdata/mx.gpkg", package = "biosurvey"))
species_data <- terra::vect(system.file("extdata/species_data.gpkg",
                                        package = "biosurvey"))

# Saving species data in a temporal directory
tdir <- file.path(tempdir(), "testbio")
dir.create(tdir)

namessp <- unique(species_data$Species)


for (i in 1:length(species_data)) {
  terra::writeVector(species_data[species_data$Species == namessp[i], ],
                     filename = paste0(tdir, "/", namessp[i], ".gpkg"))
}

# Preparing grid for analysis
grid_reg <- grid_from_region(region = mx, cell_size = 100)

# Running analysis with data from directory
sp_data <- files_2data(path = tdir, format = "gpkg", spdf_grid = grid_reg)

claununez/biosurvey documentation built on April 25, 2024, 12:24 a.m.