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

Source: R/SSplotData.R
SSplotData.Rd

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",
  subplots = 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,
  subplot = lifecycle::deprecated()
)

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.

subplots

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", "tagdbase1", and "morphcompdbase".

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

Optional replacement for fleetnames used in data file.

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

Default width of plots printed to files in units of punits.

pheight

Height of plots printed to png files in units of punits. Default is designed to allow two plots per page, with pheight_tall used for plots that work best with a taller format and a single plot per page.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".

res

Resolution of plots printed to files. The default is res = 300.

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

cex.main

Character expansion for plot titles. The default is cex.main=1.

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 plot elements.

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

Logical indicating if a title should be included at the top (not yet implemented for all plots).

verbose

A logical value specifying if output should be printed to the screen.

subplot

Deprecated. Use subplots instead.

See also

SS_plots(), SS_output(), SS_readdat()

Author

Ian Taylor, Chantel Wetzel, Cole Monnahan