SSplotData: Timeline of presence/absence of data by type, year, and fleet.

Description

Plot shows graphical display of what data is being used in the model. Some data types may not yet be included. Note, this is based on output from the model, not the input data file.

Usage

SSplotData(replist, plot=TRUE,print=FALSE,
  plotdir="default", fleetcol="default",
  datatypes="all",fleets="all",fleetnames="default",ghost=FALSE,
  pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
  margins = c(5.1,2.1,4.1,8.1), verbose=TRUE)

Arguments

replist

list created by SS_output

plot

plot to active plot device?

print to PNG files?

plotdir

directory where PNG files will be written. by default it will be the directory where the model was run.

fleetcol

Either the string "default", or a vector of colors to use for each fleet.

datatypes

Either the string "all", or a vector including some subset of the following: "catch", "cpue", "lendbase", "sizedbase", "agedbase", "condbase", "ghostagedbase", "ghostcondbase", "ghostlendbase", "ladbase", "wadbase", "mnwgt", "discard", "tag

fleets

Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.

fleetnames

A vector of alternative names to use in the plot. By default the parameter names in the data file are used.

ghost

TRUE/FALSE indicator for whether to show presence of composition data from ghost fleets (data for which the fit is shown, but is not included in the likelihood calculations).

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

margins

margins of plot (passed to par() function), which may need to be increased if fleet names run off right-hand margin

verbose

report progress to R GUI?

SSplotData: Timeline of presence/absence of data by type, year, and fleet.

Description

Usage

Arguments

Value

See Also