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

In r4ss: R Code for Stock Synthesis

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",
  subplot = 1:2,
  fleetcol = "default",
  datatypes = "all",
  fleets = "all",
  fleetnames = "default",
  ghost = FALSE,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  margins = c(5.1, 2.1, 2.1, 8.1),
  cex = 2,
  lwd = 12,
  maxsize = 1,
  alphasize = 1,
  mainTitle = FALSE,
  verbose = TRUE
)

Arguments

replist	A list object created by SS_output().
plot	plot to active plot device?
print	print to PNG files?
plotdir	directory where PNG files will be written. by default it will be the directory where the model was run.
subplot	vector controlling which subplots to create Currently there are only 2 subplots: 1 equal size points showing presence/absence of data type by year/fleet 2 points scaled to indicate quantity or precision of data
fleetcol	Either the string "default", or a vector of colors to use for each fleet. If tagging data is included, an additional color needs to be added for the tag releases which are not assigned to a 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", "tagrelease", and "tagdbase1".
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
pheight	height of plot
punits	units for PNG file
res	Resolution of plots printed to files. The default is res = 300.
ptsize	point size 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
cex	Character expansion for points showing isolated years of data
lwd	Line width for lines showing ranges of years of data
maxsize	The size (cex) of the largest bubble in the datasize plot. Default is 1.
alphasize	The transparency of the bubbles in the datasize plot. Defaults to 1 (no transparency). Useful for models with lots of overlapping points.
mainTitle	TRUE/FALSE switch to turn on/off the title on the plot.
verbose	report progress to R GUI?

Author(s)

Ian Taylor, Chantel Wetzel, Cole Monnahan

See Also

SS_plots(), SS_output(), SS_readdat()

r4ss documentation built on May 28, 2022, 1:11 a.m.