generateAbundances: Generate Abundance Vector

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Generate Abundance Vector

Description

Generate a vector of taxon abundances.

Usage

generateAbundances(N, count = 1000, mode = 1, k = 0.5,
  probabs = FALSE)

Arguments

N	number of species
count	total number of individuals (ignored in mode 2, 4 and 7)
mode	1=each species receives round(count/N) counts, 2=sampled from uniform distribution with 0 as lower and count as upper bound, 3=dominant species takes 95 percent of the counts and all others split the remaining counts equally, 4=counts are sampled from a Poisson distribution with lambda set to count/N, 5=using bstick function from vegan, 6=using geometric series with parameter k, 7=sample from the exponential distribution and scale with count/N
k	evenness parameter of geometric series (the smaller, the more even is the abundance vector)
probabs	if true, return probabilities instead of abundances

Details

The taxon abundance vector can be used as initial abundance vector in models. Note: The geometric series (a niche apportionment model) is for instance described in "Comments about some species abundance patterns: classic, neutral, and niche partitioning models" by Ferreira and Petrere-Jr., Braz. J. Biol. 2008

Value

species abundances

See Also

simCountMat

Examples

  x <- round(generateAbundances(10, mode=6))

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.