rangemap_enm generates a distributional range for a given species using a continuous raster layer produced using ecological niche modeling or species distribution modeling tools. This function binarizes the model in suitable and unsuitable areas using a user specified level of omission or a given threshold value. Optionally, representations of the species extent of occurrence (using convex hulls) and the area of occupancy according to the IUCN criteria can also be generated. Shapefiles can be saved in the working directory if it is needed.
rangemap_enm(model_output, occurrences = NULL, threshold_value = NULL, threshold_omission = NULL, min_polygon_area = 0, simplify = FALSE, simplify_level = 0, polygons = NULL, extent_of_occurrence = TRUE, area_of_occupancy = TRUE, final_projection = NULL, save_shp = FALSE, name, overwrite = FALSE, verbose = TRUE)
| model_output | a RasterLayer of suitability for the species of interest
generated using a ENM or SDM algorithm, that will be binarized using the a
user-defined |
|---|---|
| occurrences | a data.frame containing geographic coordinates of species
occurrences, columns must be: Species, Longitude, and Latitude. Geographic
coordinates must be in decimal degrees. |
| threshold_value | (numeric) value used for reclassifying the
|
| threshold_omission | (numeric) percentage of occurrence records to be
excluded from suitable areas considering their values of suitability in the
continuous model (e.g., 0, 5, or 10). Ignored if |
| min_polygon_area | (numeric) minimum area of polygons that will be kept as part of the species ranges after defining suitable areas and convert raster layer to polygon. Default = 0. A value of 0 will keep all polygons. |
| simplify | (logical) if |
| simplify_level | (numeric) tolerance to consider when simplifying polygons
created from suitable areas in |
| polygons | (optional) a SpatialPolygons* object to clip polygons and
adjust extent of occurrence to these limits. Projection must be WGS84
(EPSG:4326). If |
| extent_of_occurrence | (logical) whether to obtain the extent of occurrence
of the species based on a simple convex hull polygon; default = |
| area_of_occupancy | (logical) whether to obtain the area of occupancy
of the species based on a simple grid of 4 km^2 resolution;
default = |
| final_projection | (character) string of projection arguments for
resulting Spatial objects. Arguments must be as in the PROJ.4 documentation.
See |
| save_shp | (logical) if |
| name | (character) valid if |
| overwrite | (logical) whether or not to overwrite previous results with
the same name. Default = |
| verbose | (logical) whether or not to print messages about the process. Default = TRUE. |
If occurrences and threshold_omission are defined, a sp_range
object (S4) containing: (1) a data.frame with information about the species
range, and Spatial objects of (2) unique occurrences, (3) species range,
(4) extent of occurrence, and (5) area of occupancy.
If instead of occurrences and threshold_omission,
threshold_value is provided, the result will be a sp_range object
(S4) of two elements: (1) a data.frame with information about the species
range, and (2) a SpatialPolygons object of the species range.
If extent_of_occurrence and/or area_of_occupancy = FALSE,
the corresponding spatial objects in the resulting sp_range object will be
empty, an areas will have a value of 0.
All resulting Spatial objects in the list of results will be projected to the
final_projection. Areas are calculated in square kilometers using the
Lambert Azimuthal Equal Area projection, centered on the centroid of occurrence
points given as inputs or, if points are not provided, the resulting range.
# \donttest{ # parameters sp_mod <- raster::raster(list.files(system.file("extdata", package = "rangemap"), pattern = "sp_model", full.names = TRUE)) data("occ_train", package = "rangemap") thres <- 5 save <- TRUE name <- "test" enm_range <- rangemap_enm(model_output = sp_mod, occurrences = occ_train, threshold_omission = thres) summary(enm_range)#> #> Summary of sp_range_iucn object #> --------------------------------------------------------------------------- #> #> Species range derived from: ENM #> #> Species Unique_records Range_area Extent_of_occurrence #> Amblyomma_americanum 89 2824883 3535078 #> Area_of_occupancy #> 356 #> #> #> #> Other contents: #>#> Length Class Mode #> species_range 11 SpatialPolygonsDataFrame S4 #> species_unique_records 89 SpatialPointsDataFrame S4 #> extent_of_occurrence 1 SpatialPolygonsDataFrame S4 #> area_of_occupancy 89 SpatialPolygonsDataFrame S4# }