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Create a presence-absence matrix of species' geographic ranges within a user's grid shapefile (beta version)

Source: R/lets_presab_grid.R
lets.presab.grid.Rd

Convert species' ranges (in shapefile format) into a presence-absence matrix based on a grid in shapefile format.

Usage

lets.presab.grid(
  shapes,
  grid,
  sample.unit,
  remove.sp = TRUE,
  presence = NULL,
  origin = NULL,
  seasonal = NULL
)

Arguments

shapes

Object of class SpatVect or Spatial (see packages terra and sf to read these files) containing the distribution of one or more species. Species names should be stored in the object as BINOMIAL/binomial or SCINAME/sciname.

grid

Object of class shapefile representing the spatial grid (e.g. regular/irregular cells, political divisions, hexagonal grids, etc). The grid and the shapefiles must be in the same projection.

sample.unit

Object of class character with the name of the column (in the grid) representing the sample units of the presence absence matrix.

remove.sp

Logical, if TRUE the final matrix will not contain species that do not match any cell in the grid.

presence

A vector with the code numbers for the presence type to be considered in the process (for IUCN spatial data https://www.iucnredlist.org/resources/spatial-data-download, see metadata).

origin

A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).

seasonal

A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).

Value

The result is a list containing two objects:

(I) A matrix the species presence (1) and absence (0) values per sample unity.

(II) The original grid.

Details

This function is an alternative way to create a presence absence matrix when users already have their own grid.

See also

plot.PresenceAbsence

lets.presab.birds

lets.shFilter

Author

Bruno Vilela & Fabricio Villalobos

Examples

if (FALSE) {
# Species polygons
data("Phyllomedusa")
data("wrld_simpl")
# Grid 
sp.r <- terra::as.polygons(terra::rast(resol = 5, 
crs = terra::crs(Phyllomedusa),
xmin = -93, xmax = -29, ymin = -57, ymax = 15))
sp.r$ID <- 1:length(sp.r)
                         

# PAM
resu <- lets.presab.grid(Phyllomedusa, sp.r, "ID")

# Plot
rich_plus1 <- rowSums(resu$PAM[, -1]) + 1
colfunc <- colorRampPalette(c("#fff5f0", "#fb6a4a", "#67000d"))
colors <- c("white", colfunc(max(rich_plus1)))
plot(resu$grid, border = "gray40",
     col = colors[rich_plus1])
plot(sf::st_geometry(wrld_simpl), add = TRUE)
}