SSplotTimeseries: Plot timeseries data

In r4ss: R Code for Stock Synthesis

Plot timeseries data

Description

Plot timeseries data contained in TIME_SERIES output from Stock Synthesis report file. Some values have optional uncertainty intervals.

Usage

SSplotTimeseries(
  replist,
  subplot,
  add = FALSE,
  areas = "all",
  areacols = "default",
  areanames = "default",
  forecastplot = TRUE,
  uncertainty = TRUE,
  bioscale = 1,
  minyr = -Inf,
  maxyr = Inf,
  plot = TRUE,
  print = FALSE,
  plotdir = "default",
  verbose = TRUE,
  btarg = "default",
  minbthresh = "default",
  xlab = "Year",
  labels = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  mainTitle = FALSE,
  mar = NULL
)

Arguments

replist	A list object created by SS_output().
subplot	number controlling which subplot to create Numbering of subplots is as follows, where the spawning biomass plots (7 to 10) are provided first when this function is called by SS_plots(): 1 Total biomass (mt) with forecast 2 Total biomass by area (spatial models only) 3 Total biomass (mt) at beginning of spawning season with forecast 4 Summary biomass (mt) with forecast 5 Summary biomass (mt) by area (spatial models only) 6 Summary biomass (mt) at beginning of season 1 with forecast 7 Spawning output with forecast with ~95% asymptotic intervals 8 Spawning output by area (spatial models only) 9 Relative spawning output with forecast with ~95% asymptotic intervals 10 Relative spawning output by area (spatial models only) 11 Age-0 recruits (1,000s) with forecast with ~95% asymptotic intervals 12 Age-0 recruits by area (spatial models only) 13 Fraction of recruits by area (spatial models only) 14 Age-0 recruits (1,000s) by birth season with forecast 15 Fraction of total Age-0 recruits by birth season with forecast
add	add to existing plot? (not yet implemented)
areas	optional subset of areas to plot for spatial models
areacols	vector of colors by area. Default uses rich.colors by Arni Magnusson
areanames	names for areas. Default is to use Area1, Area2,...
forecastplot	add points from forecast years
uncertainty	add intervals around quantities for which uncertainty is available
bioscale	scaling for spawning biomass. Default = 1. Previously this was set to 0.5 for single-sex models, and 1.0 for all others, but now single-sex models are assumed to use the -1 option for Nsexes in the data file so the scaling is done automatically by SS.
minyr	optional input for minimum year to show in plots
maxyr	optional input for maximum year to show in plots
plot	plot to active plot device?
print	print to PNG files?
plotdir	directory where PNG or PDF files will be written. by default it will be the directory where the model was run.
verbose	report progress to R GUI?
btarg	Target depletion to be used in plots showing depletion. May be omitted by setting to 0. "default" chooses value based on modeloutput.
minbthresh	Threshold depletion to be used in plots showing depletion. May be omitted by setting to 0. "default" assumes 0.25 unless btarg in model output is 0.25 in which case minbthresh = 0.125 (U.S. west coast flatfish).
xlab	x axis label for all plots
labels	vector of labels for plots (titles and axis labels)
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	Logical indicating if a title should be included at the top (not yet implemented for all plots)
mar	Either NULL to allow the default (which depends on whether the main title is included or not) or a numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot, which is passed to par().

Author(s)

Ian Taylor, Ian Stewart

See Also

SS_plots(), SS_output()

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