Plot timeseries data

Description

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

Usage

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SSplotTimeseries(replist, subplot, add = FALSE, areas = "all",
  areacols = "default", areanames = "default", forecastplot = TRUE,
  uncertainty = TRUE, bioscale = "default", minyr = NULL, maxyr = NULL,
  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)

Arguments

replist

list created by SS_output

subplot

number controlling which subplot to create

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 by default it will be set to 0.5 for single-sex models, and 1.0 for all others

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 for PNG file

ptsize

point size for PNG file

cex.main

character expansion for plot titles

Author(s)

Ian Taylor, Ian Stewart

See Also

SS_plots, SS_output

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