MDM (version 1.3)

simdata: Species abundance data simulator

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)