plot.cjs {mra}

Plot CJS Model

Description

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

Usage

## S3 method for class 'cjs'
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 plotted.

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 <= 0), all occasions are plotted. Otherwise, plot the occasions specified. For example, if occasions = c(1,3,5), only estimates from the 1st, 3rd, and 5th capture occasion are plotted. If type = "n", occasion = 1 (1st occasion) cannot be plotted because it can't be estimated. If type = "s", occasion = ncol(y) (last occasion) cannot be plotted because no survival interval exist beyond the end of the study.

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.

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.

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.

Author(s)

Trent McDonald, WEST-INC, [e-mail]

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)