SSplotIndices: Plot indices of abundance and associated quantities.

In r4ss: R Code for Stock Synthesis

Plot indices of abundance and associated quantities.

Description

Plot indices of abundance with or without model fit as well as other diagnostic plots such as observed vs. expected index and plots related to time-varying catchability (if present).

Usage

SSplotIndices(
  replist,
  subplots = c(1:10, 12),
  plot = TRUE,
  print = FALSE,
  fleets = "all",
  fleetnames = "default",
  smooth = TRUE,
  add = FALSE,
  datplot = TRUE,
  labels = c("Year", "Index", "Observed index", "Expected index", "Log index",
    "Log observed index", "Log expected index", "Standardized index", "Catchability (Q)",
    "Time-varying catchability", "Vulnerable biomass",
    "Catchability vs. vulnerable biomass", "Residual", "Deviation"),
  fleetcols = NULL,
  col1 = "default",
  col2 = "default",
  col3 = "blue",
  col4 = "red",
  pch1 = 21,
  pch2 = 16,
  cex = 1,
  bg = "white",
  legend = TRUE,
  legendloc = "topright",
  seasnames = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  mainTitle = FALSE,
  plotdir = "default",
  minyr = NULL,
  maxyr = NULL,
  maximum_ymax_ratio = Inf,
  show_input_uncertainty = TRUE,
  verbose = TRUE,
  ...
)

Arguments

replist	A list object created by SS_output().
subplots	vector controlling which subplots to create Numbering of subplots is as follows, where subplot 9 (comparison of all indices) is provided first: 1 index data by fleet 2 index data with fit by fleet 3 observed vs expected index values with smoother 4 index data by fleet on a log scale (lognormal error only) 5 index data with fit by fleet on a log scale (lognormal error only) 6 log(observed) vs log(expected) with smoother (lognormal error only) 7 time series of time-varying catchability (only if actually time-varying) 8 catchability vs. vulnerable biomass (if catchability is not constant) 9 comparison of all indices 10 index residuals based on total uncertainty 11 index residuals based on input uncertainty (not currently provided) 12 index deviations (independent of index uncertainty)
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)
fleetcols	vector of colors for all fleets (including those with no index data)
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=21.
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.
bg	Background color for points with pch=21.
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
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
mainTitle	switch which allows the plot title to be left off
plotdir	directory where PNG files will be written. by default it will be the directory where the model was run.
minyr	First year to show in plot (for zooming in on a subset of values)
maxyr	Last year to show in plot (for zooming in on a subset of values)
maximum_ymax_ratio	Maximum allowed value for ymax (specified as ratio of y), which overrides any value of ymax that is greater (default = Inf)
show_input_uncertainty	Switch controlling whether to add thicker uncertainty interval lines indicating the input uncertainty relative to the total uncertainty which may result from estimating a parameter for extra standard deviations. This is only added for the plots with index fit included (the data-only plots only show the input uncertainty).
verbose	report progress to R GUI?
...	Extra arguments to pass to calls to plot

Author(s)

Ian Stewart, Ian Taylor, James Thorson

See Also

SS_plots(), SS_output()

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