monographaR (version 1.3.1)

mapTable: Generates a presence/absence matrix of species on grids or countries

Description

This function will generate a presence/absence matrix based on a grid (if type="grid") or on countries (if type="countries").

Usage

mapTable(data, type = "grid", resolution = 1, pres.abs = TRUE, 
write.output = FALSE, layer = NULL)

Value

list, with a matrix and grid (if type="grid), or a matrix (if type="countries").

Arguments

data

data.frame

type

"grid", "countries" or "user"

resolution

numeric (degrees)

pres.abs

logical

write.output

logical

layer

Spatial DataFrame object

Author

Marcelo Reginato

Details

It requires a data.frame with three columns, ordered as: species, longitude and latitude. The resolution of the grid can be changed by the argument "resolution" (in degrees). If type = "user", a layer to intersect the points and create the matrix should be supplied (a Spatial DataFrame object). It uses functions of the package raster, sf and terra. If pres.abs = F the returned matrix will have "x" instead of 0 and 1.

See Also

raster

Examples

## loading the example data

data(monographaR_examples)
monographaR_examples$map_data -> data
head(data)

## running the function with grid

map.table <- mapTable(data, type="grid", resolution=3, 
write.output=FALSE)
  
map.table$table
t(map.table$table)

map.table$grid -> grid

### load world map
library(rnaturalearth)
library(sf)
library(sp)
ne_countries(type="countries", returnclass = "sv") -> wrld_simpl
st_as_sf(wrld_simpl) -> wrld_simpl
as_Spatial(wrld_simpl) -> wrld_simpl

### plot
plot(grid, border="white")
plot(wrld_simpl, add=TRUE)
plot(grid, add=TRUE)
raster::text(grid, grid@data$layer, cex=1)