simul.comm: Simulation of ecological data structured by single ecological...

Description Usage Arguments Value Author(s)

Description

Simulation of ecological data structured by single ecological gradient

Usage

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simul.comm(totS = 300, gr.length = 5000, niche.type = "random",
  max.niche.breath = gr.length, min.niche.breath = 10,
  spec.optima = "random", prop.random.species = 0, seed = NULL,
  plotting = F, highlight.species = NULL)

sample.comm(simul.comm = NULL, Np = 300, sample.x = "random",
  no.ind = 100, k = 0.2, seed = NULL, pa = FALSE,
  based.on = "individuals", standardize.rowsums = TRUE)

Arguments

totS

total number of species in simulation

gr.length

length of the gradient in units

niche.type

shape of species response curves ('random', 'normal', 'skewed')

max.niche.breath

number, maximum niche breath along the gradient (default = gr.length)

min.niche.breath

number, minimum niche breath along the gradient (default = 10). Cannot be more than max.niche.breath.

spec.optima

distribution of species optima along simulated gradient. Either one of 'random', 'unimodal' or 'skewed', or the vector (of the length equal to totS) with numbers (ranging between 1 and gr.length). Default = 'random'.

prop.random.species

Proportion of random species, i.e. species which are not related to the gradient. Should be real number from [0,1]. These species are generated by randomizing occurrence of given proportion of species among samples. Default = 0.

seed

set random seed for reproducing always the same result

plotting

should the species response curves along simulated gradient be drawned? Default = FALSE.

highlight.species

vector of species numbers which should be highlighted by color in ploted diagram (if plotting = TRUE). Default = NULL, which means that if plot is drawned, two species will be highlighted - the most generalized and the most specialized ones.

simul.comm

result of simul.comm function with parameters of individual species response curves

Np

number of samples

sample.x

positions of sampling along the gradient. Default = "random", meaning that random locations are generated. Other options include "equal" with samples distributed in equal distances, "biased" with samples accumulated toward higher values of the gradient. Can be also vector of the same length as Np with exact positions of the samples.

no.ind

mean number of individuals to be drawn from the species pool (if based.on = 'individuals')

k

mean proportion of species from species pool to be drawn into local community (if based.on = 'species')

pa

result table will be generated in presence-absence form (default pa = FALSE)

based.on

should the sampling of species from species pool be based on 'individuals' or 'species'? (default = 'individuals')

standardize.rowsums

Standardizes the abundances of species in samples so as the sum of species abundances in sample is 100 (standardizes to rowsums equal to 100). Applies only if pa = FALSE. Default = TRUE.

Value

The function simul.comm returns list with 10 items, describing the set of parameters used to simulate community of species response curves:

The function sample.comm returns list of 5 items with parameters of generated community data; the last item contains also all items returned by simul.comm function:

Author(s)

David Zeleny (zeleny.david@gmail.com) - based on the scripts of Jason Fridley (Fridley et al. 2007, Appendix S2) and David Zeleny (Zeleny 2009, Appendix S1)


zdealveindy/genspe documentation built on May 4, 2019, 9:13 p.m.