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Plot timeseries data

Source: R/SSplotTimeseries.R
SSplotTimeseries.Rd

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 = NULL,
  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

Optional vector of colors for each area if model has multiple areas. NULL value will be replaced by a default set of areas.

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 SS3.

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 files will be written.

verbose

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

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

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.

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().

See also

SS_plots(), SS_output()

Author

Ian Taylor, Ian Stewart