Get phylospatial community data

Get phylospatial community data

Usage

ps_get_comm(ps, tips_only = TRUE, spatial = TRUE)

Arguments

ps

phylospatial object.

tips_only

Logical indicating whether only the terminal taxa (TRUE, the default) or all taxa (FALSE) should be returned.

spatial

Logical indicating whether a spatial (SpatRaster or sf) object should be returned. Default is TRUE; if FALSE, a matrix is returned.

Value

If spatial = TRUE, a SpatRaster or sf object with a layer/column for every taxon, with NA for unoccupied sites. If spatial = FALSE, a matrix containing only occupied sites (i.e., with nrow equal to the number of occupied sites, not the total number of grid cells). Use ps_expand() to expand an occupied-only matrix back to the full spatial extent if needed.

Examples

ps <- ps_simulate()

# the defaults return a spatial object of terminal taxa distributions:
ps_get_comm(ps)
#> class       : SpatRaster 
#> size        : 20, 20, 10  (nrow, ncol, nlyr)
#> resolution  : 1, 1  (x, y)
#> extent      : 0, 20, 0, 20  (xmin, xmax, ymin, ymax)
#> coord. ref. :  
#> source(s)   : memory
#> varnames    : t4 
#>               t8 
#>               t5 
#>               ...
#> names       :       t4,        t8,        t5,        t9,       t10,        t6, ... 
#> min values  : 0.000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, ... 
#> max values  : 0.667054, 0.8274968, 0.8483195, 0.1515441, 0.6230429, 0.4927548, ... 

# get distributions for all taxa, as a matrix
pcomm <- ps_get_comm(ps, tips_only = FALSE, spatial = FALSE)