random_geo_range: Random geographic occurrences and preliminary conservation...

In mlammens/occUncertain: Functions For Addressing Occurence Point Uncertainty When Calculating Spatial Metrics

Random geographic occurrences and preliminary conservation status assessment following IUCN Criterion B. Species area of occupancy (AOO) and extent of occurrence (EOO), from latitude and longitude coordinates accounting uncertainty values

Description

random_geo_range Given georeferenced coordinates and associated uncertainty. This function generates random statistics values (Extent of Occurrence, Area of Occupancy, number of locations, number of subpopulations) and provide a preliminary conservation status following Criterion B of IUCN. A graphical map output is also available.

Usage

random_geo_range(
  n_length,
  occs_df,
  lat_col = "latitude",
  lon_col = "longitude",
  lat_uncertainty = "lat_uncertainty",
  lon_uncertainty = "lon_uncertainty",
  taxa_col = "species",
  country_map = NULL,
  exclude.area = TRUE,
  method.range = "convex.hull",
  export_shp = FALSE,
  write_shp = FALSE,
  map_pdf = FALSE,
  draw.poly.EOO = TRUE,
  Cell_size_AOO = 2,
  Cell_size_locations = 10,
  DrawMap = TRUE,
  add.legend = TRUE,
  write_results = FALSE,
  write_file_option = "excel"
)

Arguments

n_length	Number of iterations
occs_df	a dataframe georeferenced occurrence
lat_col	latitude values decimal degrees column
lon_col	longitude decimal degrees column
lat_uncertainty	latitude uncertainty decimal degrees column
lon_uncertainty	longitude uncertainty decimal degrees column
taxa_col	character or factor, taxa names
country_map	a SpatialPolygonsDataFrame or SpatialPolygons showing for example countries or continent borders. This shapefile will be used for cropping the SpatialPolygons used for EOO computation if exclude.area is TRUE. By default, it is land
exclude.area	a logical, if TRUE, areas outside of country_map are cropped of SpatialPolygons used for EOO computation. By default, it is TRUE
method.range	a character string, if "convex.hull", EOO is based on a convex hull. if "alpha.hull", EOO is based on alpha hull of alpha value. By default, it is "convex.hull"
export_shp	a logical, if TRUE, shapefiles of SpatialPolygons used for EOO computation are exported. By default, it is FALSE
write_shp	a logical, if TRUE, shapefiles of SpatialPolygons used for EOO computation are written as ESRI shapefiles in a sub-directory in the working directory. By default, it is FALSE
map_pdf	a logical, if TRUE, maps are exported in one pdf file. Otherwise, each species map is exported in png. By default, it is FALSE
draw.poly.EOO	a logical, if TRUE, the polygon used for estimating EOO is drawn. By default, it is TRUE
Cell_size_AOO	a numeric, value indicating the grid size in kilometers used for estimating Area of Occupancy. By default, equal to 2
Cell_size_locations	a numeric, value indicating the grid size in kilometers used for estimating the number of location. By default, equal to 10
DrawMap	a logical, if TRUE a map is produced for each species in png format, unless map_pdf is TRUE. By default, it is TRUE
add.legend	a logical, if TRUE a legend and a submap showing distribution in 'country_map' are displayed for each map. By default, it is TRUE
write_results	a logical, if TRUE, results are exported in a file which can csv or excel, see write_file_option. By default, it is FALSE
write_file_option	a character, if "excel", results are exported in excel file, if "csv", results are exported in csv. By default, it is "excel"

Details

Input as a dataframe should have the following structure:

[,1]	ddlat	numeric, latitude (in decimal degrees)
[,2]	ddlon	numeric, longitude (in decimal degrees)
[,3]	ddlat unc	numeric, longitude uncertainty (in decimal degrees)
[,4]	ddlon unc	numeric, longitude uncertainty (in decimal degrees)
[,5]	tax	character or factor, taxa names

It is mandatory to respect field positions, but field names do not matter Starting position of the raster used for estimating the Area Of Occupancy

Different starting position of the raster used for estimate the AOO may provide different number of occupied cells. Hence, by default, 4 different translations of the raster is done (fixed increment of 1/4 resolution north and east) and the minimum number of occupied cells is used for estimating AOO. It is also possible to define a given number of random starting position of the raster using the argument nbe.rep.rast.AOO

Estimating number of locations

Locations are estimated by overlaying a grid of a given resolution (see Cell_size_locations for specifying the resolution). The number of locations is simply the number of occupied locations. Note that the grid position is overlaid in order to minimize the number of locations (several translation of the grid are performed and the one providing the minimum number of occupied cells is provided).

Taking into account protected area for estimating the number of locations
A location is defined by the IUCN as a "geographically or ecologically distinct area in which a single threatening event can affect all individuals of the taxon". A simple way to include threat level is to rely on a map of protected areas and assume that populations within and

outside protected areas are under different threat level.

If a map of protected area is provided, this one is used for estimating the number of locations by the following procedure:
- if method_protected_area is "no_more_than_one", all occurrences within a given protected area will be considered as one location. Occurrences outside protected area will be used for estimating the number of locations using overlaying grid as described above. See the vignette for illustration.
- if method_protected_area is NOT "no_more_than_one", number of locations will be estimated by the overlaying grid as described above, but by considering differently occurrences outside and inside protected area.

The protected areas layers should be given as as SpatialPolygonsocc_randomFrame in protec.areas. The ID_shape_PA should also be given and should represent the unique ID of each protected area in the provided shapefile. This can be checked by the following code:

colnames(ProtectedAreas@data) Where ProtectedAreas is the name of your shapefile.

Limitation in the estimations of EOO

For a species whose occurrences span more than 180 degrees, EOO is not computed. This is the case for example for species whose distribution span the 180th meridian.

mlammens/occUncertain documentation built on May 6, 2024, 11:19 p.m.