SSplotTimeseries {r4ss}

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()