plot.cjs: Plot CJS Model
In mra: Mark-Recapture Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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

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## S3 method for class 'cjs'
plot(x, type="n", ci = TRUE, smooth = TRUE, occasions = -1, 
	animals = -1, smubass = 5, ...)

`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.

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.

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.

Trent McDonald, WEST-INC, tmcdonald@west-inc.com

F.cjs.estim, matplot, lines, plot

 
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)