ps_get_comm: Get 'phylospatial' community data

In phylospatial: Spatial Phylogenetic Analysis

Get phylospatial community data

Description

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)

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

phylospatial documentation built on April 4, 2026, 1:07 a.m.