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

Description Usage Arguments Author(s) See Also

View source: R/SSplotData.R

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

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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

list 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 for PNG file

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 Oct. 30, 2019, 11:25 a.m.