sim.occ: Simulated Species Occurrence data
In fossil: Palaeoecological and Palaeogeographical Analysis Tools

Description Usage Arguments Details Value Author(s) See Also Examples

A function to simulate a species occurrence data set

1	sim.occ(total.species = 100, endemics = 0.1, regions = 3, locs = 30, avg.abund = 1)

`total.species`	The total number of species in the region (i.e. the number of rows in the result matrix)
`endemics`	The proportion of endemic species for the entire region
`regions`	The number of areas of endemicity
`locs`	The number of samples/locatlities per region of endemicity
`avg.abund`	The 'average' abundance of a species for any given sample

The function creates a matrix of $c$ rows of species (given by total.species) with $n$ number of sample columns (where $n$ equals $regions*locs$). The given abundance of any species at a given sample is determined by a log normal distribution, with each species being randomly assigned a value from rnorm(). The number of endemics for any given region is equal to $total.species*endemics/regions$. An endemic is conseidered to only occur within a given region, and all other non-ndemic species are considered to be 'cosmopolitan' and can occur in any region. The avg.abund value affects how many species are recovered at a given site, and for any given run there are typically species that are not present in the sample but are present in the region.

Returns a matrix of simulated species abundances per locality.

Matthew Vavrek

ecol.dist