plotstand: plotstand plot optimum model from standLM vs Geometric mean

In haddonm/rforcpue: Functions to Assist With The Analysis of CPUE Data

plotstand plot optimum model from standLM vs Geometric mean

Description

plot optimum model from standLM vs Geometric mean. Has options that allow for log-normls P period's parameter estimate. Also can rescale the graph to have an average the same as the geometric mean average of the original time series of data.

Usage

plotstand(stnd, bars = FALSE, geo = 0, P = 95, catch = NA, usefont = 7)

Arguments

stnd	is the list output from standLM
bars	is a logical T or F determining whether to put confidence bounds around each estimate; defaults to FALSE
geo	is an estimate of the original geometric mean catch rate across all years. If this is > 0.0 it is used to rescale the graph to the nominal scale, otherwise the mean of each time-series will be 1.0, which simplifies visual comparisons. geo defaults to 0.0.
P	is the percentile used for the log-normal confidence bounds, if they are plotted; defaults to 95.
catch	if it is desired to plot the catch as well as the CPUE then a vector of catches needs to be input here
usefont	enables the font used in the plot to be modified. Most publications appear to prefer usefont=1; defaults to 7 - Times bold

Value

a plot of the model with the smallest AIC (solid line) and the geometric mean (model 1, always = LnCE ~ Year, the dashed line). 'Year' could be some other time step.

Examples

## Not run: 
data(abeg)
splabel = "SpeciesName"
labelM <- c("year","diver","month")
ab1 <- makecategorical(labelM[1:3],abeg)
mods <- makemodels(labelM)
out <- standLM(mods,ab1,splabel)
plotprep()
plotstand(out, bars=TRUE, P=90,geo=100.0,usefont=1)
plotstand(out)

## End(Not run)

haddonm/rforcpue documentation built on Oct. 12, 2024, 11:55 p.m.