decline: Compute Declination and Explosion Probabilities

In Rramas: Matrix Population Models

Description

Compute declination (or explosion) probabilities for a stage-structured population. From a vector of initial stage abundances and a transition matrix, decline and explosion compute respectively the probability that the population size falls below or surpasses some abundance thresholds during a given time interval.

Usage

decline(rmas, bootsp = 1000)
explosion(rmas, bootsp = 1000)
## S3 method for class 'rmas.risk'
summary(object, q = c(0.025, 0.975),...)
## S3 method for class 'summary.rmas.risk'
plot(x, ylim = NULL, col = NULL, xlab = NULL, ylab = NULL, main = NULL, ...)

Arguments

rmas	An object of class rmas,i.e., resulting from projectn.
bootsp	number of botstraped samples.
object	An object of class rmas.rsik, i.e. resulting from declineor explosion.
x	An object of class summary.rmas.rsik.
q	vector of quantiles to compute bootstraped confidence intervals.
ylim	Vector with max and min values of the y (abundances) axis.
col	Color or vector of colors to draw the trajectories.
xlab	Label for the x-axis.
ylab	Label for the y-axis.
main	Text to appear as title.
...	Other parameters passed to plot and other methods.

Details

Both decline and explosion require that some stochastic simulations for a given time interval had been previously constructed (using projectn). Using those simulations decline computes the probability of falling bellow some population threshold (and explosion the probability of surpassing it) as the ratio between the number of times that these threshold has been attained and the number of replications. The set of abundances in each time interval (in all the simulations) are bootstraped (i.e. sampled with replacement) to build a confidence interval.

Value

Both decline and explosion return an object of class rmas.rsik, basically a list with the following elements

cf.obs	a data.frame with the evaluated thresholds and their probabilities.
cf.boot	a list of data.frames similar to cf.obs for each bootstraped sample.
abminbot	a list of bootstraped minimum (or maximum for explosion) abundances for each replica in the rmas object.
main	Text to appear as title when plotting the summary.

The methods summary and plot.summary summarize the results and print and plot probabilities and bootstraped confidence interval of attainning a particular population threshold.

Author(s)

Marcelino de la Cruz Rot

References

Akcakaya, H. R., Burgman, M. A. and Ginzburg L.R. 1999. Applied Population Ecology. Sinauer.

Caswell, H. 2003. Matrix Population Models: Construction, Analysis, and Interpretation . Sinauer.

Examples

  
     data(coryphanthaA)
     coryphanthaA <- as.tmatrix(coryphanthaA)
     #initial abundances:
     v0 <- c(100,0,0)
       
     # run 1000 simulations of 20 years with  demographic stochasticity:
     simu20.ds <- projectn(v0=v0, mat=coryphanthaA, time = 20, estdem=TRUE, nrep=1000)
     
     # compute declination probabilities
     simu20.ds.dec <- decline(simu20.ds)
     
     summary(simu20.ds.dec)
     
     

Rramas documentation built on May 2, 2019, 6:52 a.m.