mra (version 2.16.4)

plot.cjs: Plot CJS Model

Description

Plot the population size or survival estimates for a Cormack-Jolly-Seber model estimated by F.cjs.estim

Usage

"plot"(x, type="n", ci = TRUE, smooth = TRUE, occasions = -1, 
	animals = -1, smubass = 5, ...)

Arguments

x

An object of class 'cjs'. Objects of this class are estimated open population Cormack-Jolly-Seber models produced by F.cjs.estim.

type

Type of estimates to plot. type = "n" (the default) produces a plot of population size estimates versus capture occasion. type = "s" produces a plot of survival estimates versus capture occasion.

ci

Plot confidence intervals? If ci=TRUE, confidence intervals around population size or survival estimates are plotted (depending on 'type='), otherwise, only confidence intervals are not ploted.

smooth

Smooth estimates of population size? If type="n", smooth=TRUE will produce a smoothed (supsmu) line through plotted size estimates. Ignored for type="s".

occasions

Vector of occasion numbers to use in plot. If any(occasions

animals

Vector of individuals to plot. This parameter is used only when plotting survival estimates. For example, animals = c(1,2,10) plots the survival estimates of the 1st, 2nd, and 10th animals (rows 1, 2, and 10 of the survival estimate matrix).

smubass

Bass parameter for super-smoothed line, if called for by smooth=TRUE. Must be between 0 and 10. Larger numbers produce smoother lines.

...

Additional arguments to plot (for size estimates) or matplot (for survival estimates). Options such as ylim=, col=, cex.axis=, etc. may be useful.

Value

For type="s", the survival estimate matrix that was plotted is is invisibly returned. For type = "n", the smooth fit is invisibly returned if called for by smooth = TRUE, otherwise NA is invisibly returned if smooth = FALSE.

Details

Confidence intervals on survival estimates cannot be plotted with this routine. To plot confidence intervals surrounding survival estimates, call this routine with type="s", then compute confidence intervals for survival estimates, and use lines to add lines to the plot.

See Also

F.cjs.estim, matplot, lines, plot

Examples

data(dipper.histories)
xy <- F.cjs.covars( nrow(dipper.histories), ncol(dipper.histories) )
for(j in 1:ncol(dipper.histories)){ assign(paste("x",j,sep=""), xy$x[,,j]) }
dipper.cjs <- F.cjs.estim( ~x2+x3+x4+x5+x6, ~x1+x2+x3+x4+x5, dipper.histories )
plot(dipper.cjs)
print(dipper.cjs$s.hat)
plot(dipper.cjs, type="s", animals=1)