simdata: Species abundance data simulator

In MDM: Multinomial Diversity Model

Description

Simulates species abundance data along a one-dimensional gradient

Usage

simdata(d, p = 10, n = 100, strip0 = TRUE, extreme = 0,
ret = TRUE, k.rand = FALSE, d.rand = TRUE, mu.rand = TRUE,
s = rep((4:8)/10, length = p), amp = c(sample(1:5), rep = TRUE,
length = p), skew = 1, ampfun, lst = FALSE, err = 1,
err.type = c("p", "n")[1], as.df = TRUE, plotit = TRUE,
ptype = "l", plty = 1, pcols = rainbow(p), add.rug = FALSE, ...)

Arguments

d	the (optional) locations of the species along the 1-D gradient. If d is given then it will define both the number of species and also the locations on the gradient e.g. d = rep(1:10,each=3) will generate species at locations 1,1,1,2,2,2,...,10,10,10. If d is not specified then d.rand = TRUE will randomly allocate the species modes along a gradient on [0, 1], but if d.rand = FALSE will uniformly distribute the species modes along a gradient.
p	number of species.
n	number of sites.
strip0	if TRUE the sites with zero total abundance are omitted.
extreme	number typically in the range -1 to +1 with larger numbers reducing the range of species.
ret	if TRUE the generated data are returned
k.rand	should the be random (TRUE) or fixed
d.rand	should the be random (TRUE) or fixed
mu.rand	should the be random (TRUE) or fixed
s	the spans of the species response curves; s is the standard deviation of the spread
amp	the amplitudes of the species response curves
skew	the skewness of the distribution; range (>0 to 5), 1 = symmetric.
ampfun	any function to modify the amplitude
lst	if lst == TRUE then both the systematic and random values are returned
err	if err == 0 then the values are systematic with no random variation
err.type	type of error; p = poison, g = gaussian
as.df	if return returns a data frame, otherwise a matrix
plotit	if TRUE then the data are plotted
ptype	species plot types e.g. "l" gives lines
plty	species plot line types
pcols	species plot colours
add.rug	should a rug be added?
...	other arguments passed to plot.

Value

if lst == FALSE then a data frame with variables "Locations", "Taxa.1" – "Taxa.N" where N is number of species. if lst == TRUE then two data frames "x" and "xs" with variables "Locations", "Taxa.1" – "Taxa.N" and additionally, components "sigma", "amp" and "mu" that represent the spans, amplitudes and locations of the N species along the 1-D gradient.

Examples

mydata <- simdata()
summary(mydata)
mydata <- simdata(p=5, n=50, amp=1, err=0, d.rand=FALSE,
mu.rand=FALSE, plotit = TRUE)
summary(mydata)

MDM documentation built on May 30, 2017, 4:58 a.m.