Simulation of species abundance distributions (SAD).

Description

Creates artificial communities following given SADs.

Usage

sim.sad(n, s, sad = "lognormal", sd = 1)

Arguments

Details

Species Abundance Distributions may take a number of forms. A lognormal SAD probably is the most supported by empirical data, but we include other common types useful for testing multiple algorithms including several of the functions in BAT.

Value

A matrix of species x abundance per species.

Examples

comm1 <- sim.sad(10000, 100)
comm2 <- sim.sad(10000, 100, sd = 2)
comm3 <- sim.sad(10000, 100, sad = "uniform")
par(mfrow=c(1,3))
hist(log(comm1$Freq))
hist(log(comm2$Freq))
hist(log(comm3$Freq))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(BAT)
Loading required package: nls2
Loading required package: proto
Loading required package: raster
Loading required package: sp
Loading required package: spatstat
Loading required package: nlme

Attaching package: 'nlme'

The following object is masked from 'package:raster':

    getData

Loading required package: rpart

spatstat 1.45-2       (nickname: 'Caretaker Mode') 
For an introduction to spatstat, type 'beginner' 


Attaching package: 'spatstat'

The following objects are masked from 'package:raster':

    area, rotate, shift

Loading required package: vegan
Loading required package: permute
Loading required package: lattice

Attaching package: 'lattice'

The following object is masked from 'package:spatstat':

    panel.histogram

This is vegan 2.4-0

Attaching package: 'BAT'

The following object is masked from 'package:base':

    beta

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BAT/sim.sad.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sim.sad
> ### Title: Simulation of species abundance distributions (SAD).
> ### Aliases: sim.sad
> 
> ### ** Examples
> 
> comm1 <- sim.sad(10000, 100)
> comm2 <- sim.sad(10000, 100, sd = 2)
> comm3 <- sim.sad(10000, 100, sad = "uniform")
> par(mfrow=c(1,3))
> hist(log(comm1$Freq))
> hist(log(comm2$Freq))
> hist(log(comm3$Freq))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>