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r4ss (version 1.15)

SSplotIndices: Plot indices of abundance and associated quantities.

Description

Plot indices of abundance and associated quantities.

Usage

SSplotIndices(replist,subplots=1:8,
  plot=TRUE,print=FALSE,
  fleets="all",fleetnames="default",
  smooth=TRUE,add=FALSE,datplot=FALSE,
  labels=c("Year",         
    "Index",               
    "Observed index",      
    "Expected index",      
    "Log index",           
    "Log observed index",  
    "Log expected index",  
    "Standardized index",  
    "Catchability (Q)",    
    "Time-varying catchability"),
  col1="default", col2="default", col3="blue", col4="red",
  pch1=1, pch2=16, cex=1,
  legend=TRUE, legendloc="topright", seasnames=NULL,
  pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
  plotdir="default", verbose=TRUE)

Arguments

replist
list created by SS_output
subplots
vector controlling which subplots to create
plot
plot to active plot device?
print
print to PNG files?
fleets
optional vector to subset fleets for which plots will be made
fleetnames
optional replacement for fleenames used in data file
smooth
add smoothed line to plots of observed vs. expected sample sizes
add
add to existing plot (not yet implemented)
datplot
make plot of data only?
labels
vector of labels for plots (titles and axis labels)
col1
vector of colors for points in each season for time series plot. Default is red for single season models and a rainbow using the rich.colors.short function for multiple seasons.
col2
vector of colors for points in each season for obs. vs. exp. plot. Default is blue for single season models and a rainbow using the rich.colors.short function for multiple seasons.
col3
color of line showing expected index in time series plot. Default is blue.
col4
color of smoother shown in obs. vs. exp. plots. Default is red.
pch1
single value or vector of plotting characters (pch parameter) for time-series plots of index fit. Default=1.
pch2
single value or vector of plotting characters (pch parameter) for sample size plots of index fit. Default=16.
cex
character expansion factor for points showing observed values. Default=1.
legend
add a legend to seasonal colors (only for seasonal models)
legendloc
add a legend to seasonal colors (default is "topright")
seasnames
optional vector of names for each season to replace defaults if a legend is used
pwidth
width of plot written to PNG file
pheight
height of plot written to PNG file
punits
units for PNG file
res
resolution for PNG file
ptsize
ptsize for PNG file
cex.main
character expansion for plot titles
plotdir
directory where PNG files will be written. by default it will be the directory where the model was run.
verbose
report progress to R GUI?

Value