Topic: Demographic shifts

Topic Description:

Programs for fitting a distribution of population growth rates, and for modeling shifts in growth and mortality rates through time. Data required for fitting the population growth are N1 (initial population size), N2 (final population), and S (number of N1 still alive at final census) for all species in a community, coming from separate mortality and abundance tables as created by standard demography functions (and having matching rows).The mortality update and likelihood functions comes from mortality.fit.CTFS.r; the functions mu.mortGibbs, sd.mortGibbs, and spmean.mortGibbsare not duplicated here. Modeling shifts in growth and mortality require the standard R Analytical Tables, plus the functions lmer and lmerGibbs, the latter part of the CTFS R Package.



File: demogchange/abund.fit.CTFS.r

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Function: find.xaxis.hist

Function Description: find.xaxis.hist

Given an abundance fit and x axis range and divisions, return a sequence of x values for drawing the histogram. Used as a subroutine inside graph.abundmodel.

Function Arguments:

ArgumentDefault Value
fit
tinydiv.001
xrange

Function Source:

find.xaxis.hist=function(fit,tinydiv=.001,xrange)
{
if(is.null(xrange)) xrange=range(fit$demog$fitr)
xneg=seq(min(xrange),fit$means['hyperR'],by=tinydiv)
xpos=seq(fit$means['hyperR'],max(xrange),by=tinydiv)
return(c(xneg,xpos))
}