simul.comm: Simulation of ecological data structured by single ecological...
In zdealveindy/theta: Co-occurrence based measure of species habitat specialization

Description Usage Arguments Value Author(s)

Simulation of ecological data structured by single ecological gradient

simul.comm(totS = 300, gr.length = 5000, niche.type = "random",
  max.niche.breath = gr.length, min.niche.breath = 10, amplitude = NULL,
  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, cv.no.ind = 0.01, k = 0.2, seed = NULL, pa = FALSE,
  based.on = "individuals", standardize.rowsums = TRUE)

## S3 method for class 'simcom'
plot(simcom, xlab = "Gradient", ylab = "Abundance", ...)

## S3 method for class 'samcom'
plot(samcom, xlab = "Gradient", ylab = "Abundance", ...)

`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`	Maximum niche breath along the gradient (default = `gr.length`)
`min.niche.breath`	Minimum niche breath along the gradient (default = `10`). Cannot be more than `max.niche.breath`.
`amplitude`	Amplitude of species response curve (height in its optimum). Default is to generate amplitude as random values from lognormal distribution (with meanlog = 2 and sdlog = 1). Can be vector of numeric values; if the vector is shorter than `totS`, the values are recycled. If all amplitudes should be equal, supply vector of the length one.
`spec.optima`	Distribution of species optima along simulated gradient. Either one of `'random'`, `'unimodal'` or `'skewed'`, or a 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 one.
`simul.comm`	Object created by `simul.comm` function with parameters of individual species response curves.
`Np`	Number of samples to be generated.
`sample.x`	Positions of sampling locations 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 sampled from the species pool (if `based.on = 'individuals'`).
`cv.no.ind`	Coefficient of variation of number of indiduals sampled from the species pool. Increasing it allows to create set of samples with various levels of undersampling.
`k`	Mean proportion of species from species pool to be drawn into local community (if `based.on = 'species'`). If only one number is given, in each sample given proportion of species will be sampled from species pool. If vector of two numbers (range of `k` valus) is given, random `k` in given range will be generated (with uniform distribution) for each sample; this allows to vary the degree of undersampling among generated samples.
`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`.
`simcom`	Object returned by the function `simul.comm`.
`xlab`	Label of the x-axis. Default to "Gradient".
`ylab`	Label of the y-axis. Default to "Abundance".
`...`	Other parameters passed into `plot`.
`samcom`	Object returned by the function `sample.comm`.

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

totS Total number of species in simulation.
gr.length Length of the gradient.
niche.type Shape of species response curves.
Ao Vector of species amplitudes for the simulated gradient (heights of species response curves, corresponding to maximum probability of species to be selected to community in species optima).
m Vector of species optima along the simulated gradient.
r Vector of generated species ranges along the simulated gradient (generated niche breaths).
range Vector of realised species ranges along the simulated gradient, considering the truncation of species response curves by gradient margins (these differ from r especially at the gradient margins, where the generated species niche may be wide, but since the margin cuts the species occurrences, realised species niche is narrower.)
a, g Vectors of shape parameters for curves (used in beta function to generate the shape of the species response curve)
A.all Matrix (dim = gradient length x number of species) with simulated probabilites of individual specie at individual location along the simulated gradient.

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:

a.mat Matrix (sample x species) of species abundances in samples.
p.mat Matrix (sample x species) of species occurrence probabilities in samples.
sample.x Vector with positions of samples along the simulated gradient (environmental variable).
sample.comm List of 7 items storing initial settings of arguments in sample.comm (namely arguments Np, based.on, no.ind, k, seed, pa and standardize.rowsums).
simul.comm List of 10 items returned by function simul.comm.

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