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plot many quantities related to output from Stock Synthesis

Source: R/SS_plots.R
SS_plots.Rd

Creates a user-chosen set of plots, including biological quantities, time series, and fits to data. Plots are sent to R GUI, single PDF file, or multiple PNG files. This is now just a wrapper which calls on separate functions to make all the plots.

Usage

SS_plots(
  replist = NULL,
  plot = 1:26,
  pdf = FALSE,
  png = TRUE,
  html = png,
  printfolder = "plots",
  dir = "default",
  fleets = "all",
  areas = "all",
  fleetnames = "default",
  fleetcols = "default",
  fleetlty = 1,
  fleetpch = 1,
  lwd = 1,
  areacols = NULL,
  areanames = "default",
  verbose = TRUE,
  uncertainty = TRUE,
  forecastplot = FALSE,
  datplot = TRUE,
  Natageplot = TRUE,
  samplesizeplots = TRUE,
  compresidplots = TRUE,
  comp.yupper = 0.4,
  sprtarg = "default",
  btarg = "default",
  minbthresh = "default",
  pntscalar = NULL,
  bub.scale.pearson = 1.5,
  bub.scale.dat = 3,
  pntscalar.nums = 2.6,
  pntscalar.tags = 2.6,
  minnbubble = 8,
  aalyear = -1,
  aalbin = -1,
  aalresids = TRUE,
  maxneff = 5000,
  cohortlines = c(),
  smooth = TRUE,
  showsampsize = TRUE,
  showeffN = TRUE,
  sampsizeline = FALSE,
  effNline = FALSE,
  showlegend = TRUE,
  pwidth = 6.5,
  pheight = 4,
  pheight_tall = 6.5,
  punits = "in",
  ptsize = 10,
  res = 300,
  mainTitle = FALSE,
  cex.main = 1,
  selexlines = 1:6,
  rows = 1,
  cols = 1,
  maxrows = 6,
  maxcols = 4,
  maxrows2 = 4,
  maxcols2 = 4,
  andrerows = 4,
  tagrows = 3,
  tagcols = 3,
  parrows = 4,
  parcols = 2,
  fixdims = TRUE,
  new = TRUE,
  SSplotDatMargin = 8,
  filenotes = NULL,
  catchasnumbers = NULL,
  catchbars = TRUE,
  legendloc = "topleft",
  minyr = -Inf,
  maxyr = Inf,
  sexes = "all",
  scalebins = FALSE,
  scalebubbles = FALSE,
  tslabels = NULL,
  catlabels = NULL,
  maxsize = 1,
  showmle = TRUE,
  showpost = TRUE,
  showprior = TRUE,
  showinit = TRUE,
  showdev = FALSE,
  fitrange = FALSE,
  ...
)

Arguments

replist

A list object created by SS_output().

plot

Plot sets to be created, see list of plots below. Use to specify only those plot sets of interest, e.g., c(1,2,5,10). Plots for data not available in the model run will automatically be skipped, whether called or not. Current grouping of plots is as follows:

  1. Biology

  2. Selectivity and retention

  3. Timeseries

  4. Recruitment deviations

  5. Recruitment bias adjustment

  6. Spawner-recruit

  7. Catch

  8. SPR

  9. Discards

  10. Mean weight

  11. Indices

  12. Numbers at age

  13. Length comp data (and generalized size comp data)

  14. Age comp data

  15. Conditional age-at-length data

  16. Length comp fits (and generalized size comp fits)

  17. Age comp fits

  18. Conditional age-at-length fits

  19. Francis and Punt conditional age-at-length comp fits

  20. Mean length-at-age and mean weight-at-age

  21. Tags

  22. Yield

  23. Movement

  24. Data range

  25. Parameter distributions

  26. Diagnostic tables

pdf

Send plots to PDF file instead of R GUI?

png

Send plots to PNG files instead of R GUI?

html

Run SS_html() on completion? By default has same value as png.

printfolder

The sub-directory under 'dir' (see below) in which the PNG files will be located. The default sub-directory is "plots". The directory will be created if it doesn\'t exist. If 'printfolder' is set to "", it is ignored and the PNG files will be located in the directory specified by 'dir'.

dir

The directory in which a PDF file (if requested) will be created and within which the printfolder sub-directory (see above) will be created if png=TRUE. By default it will be the same directory that the report file was read from by the SS_output function. Alternatives to the default can be either relative (to the working directory) or absolute paths. The function will attempt to create the directory it doesn't exist, but it does not do so recursively.

fleets

Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.

areas

Either the string "all", or a vector of numerical values, like c(1,3), listing areas for which plots should be made in a multi-area model. By default, plots will be made for all areas (excepting cases where the function has not yet been updated for multi-area models). Default="all".

fleetnames

Optional replacement for fleetnames used in data file.

fleetcols

Either the string "default", or a vector of colors to use for each fleet. Default="default".

fleetlty

Vector of line types used for each fleet in some plots. Default=1.

fleetpch

Vector of point types used for each fleet in some plots. Default=1.

lwd

Line width for plot elements.

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

Optional vector of names for each area used in titles. Default="default".

verbose

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

uncertainty

Include values in plots showing estimates of uncertainty (requires positive definite hessian in model? Default=TRUE.

forecastplot

Include forecast years in the timeseries plots and plots of time-varying quantities?

datplot

Plot the data by itself? This is useful in document preparation, but doesn't change across alternative model runs with the same data, so can be committed to save time once the plots have been created once. Setting datplot=FALSE is equivalent to leaving off plots 15 and 16. Default=TRUE.

Natageplot

Plot the expected numbers at age bubble plots and mean-age time series? Default=TRUE.

samplesizeplots

Show sample size plots? Default=TRUE.

compresidplots

Show residuals for composition plots?

comp.yupper

Upper limit on ymax for polygon/histogram composition plots. This avoids scaling all plots to have max=1 if there is a vector with only a single observed fish in it. Default=0.4.

sprtarg

Specify the F/SPR proxy target. Default=0.4.

btarg

Target %unfished to be used in plots showing %unfished. May be omitted by setting to NA.

minbthresh

Threshold depletion to be used in plots showing depletion. May be omitted by setting to NA.

pntscalar

This scalar defines the maximum bubble size for bubble plots. This option is still available but a better choice is to use bub.scale.pearson and bub.scale.dat, which are allow the same scaling throughout all plots.

bub.scale.pearson

Character expansion (cex) value for a proportion of 1.0 in bubble plot of Pearson residuals. Default=1.5.

bub.scale.dat

Character expansion (cex) value for a proportion of 1.0 in bubble plot of composition data. Default=3.

pntscalar.nums

This scalar defines the maximum bubble size for numbers-at-age and numbers-at-length plots.

pntscalar.tags

This scalar defines the maximum bubble size for tagging plots.

minnbubble

This defines the minimum number of years below which blank years will be added to bubble plots to avoid cropping. Default=8.

aalyear

Years to plot multi-panel conditional age-at-length fits for all length bins; must be in a "c(YYYY,YYYY)" format. Useful for checking the fit of a dominant year class, critical time period, etc. Default=-1.

aalbin

The length bin for which multi-panel plots of the fit to conditional age-at-length data will be produced for all years. Useful to see if growth curves are ok, or to see the information on year classes move through the conditional data. Default=-1.

aalresids

Plot the full set of conditional age-at-length Pearson residuals? Turn to FALSE if plots are taking too long and you don't want them.

maxneff

The maximum value to include on plots of input and effective sample size. Occasionally a calculation of effective N blows up to very large numbers, rendering it impossible to observe the relationship for other data. Default=5000.

cohortlines

Optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots. Default=c().

smooth

Add loess smoother to observed vs. expected index plots and input vs. effective sample size? Default=TRUE.

showsampsize

Display sample sizes on composition plots? Default=TRUE.

showeffN

Display effective sample sizes on composition plots? Default=TRUE.

sampsizeline

show line for input sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)

effNline

show line for effective sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)

showlegend

Display legends in various plots?

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.

pheight_tall

Height of tall plots printed to png files in units of punits, where the tall plots are a subset of the plots which typically work best in a taller format.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

res

Resolution of plots printed to files. The default is res = 300.

mainTitle

Logical indicating if a title should be included at the top (not yet implemented for all plots).

cex.main

Character expansion for plot titles. The default is cex.main=1.

selexlines

Vector controlling which lines should be shown on selectivity plots if the model includes retention. Default=1:5.

rows

Number of rows to use for single panel plots. Default=1.

cols

Number of columns to use for single panel plots. Default=1.

maxrows

Maximum number of rows to for multi-panel plots.

maxcols

Maximum number of columns for multi-panel plots.

maxrows2

Maximum number of rows for conditional age-at-length multi-panel plots.

maxcols2

Maximum number of rows for conditional age-at-length multi-panel plots.

andrerows

Number of rows of Andre's conditional age-at-length plots within each page.

tagrows

Number of rows for tagging-related plots.

tagcols

Number of columns for tagging-related plots.

parrows

Number of rows for parameter distribution plots.

parcols

Number of columns for parameter distribution plots.

fixdims

Control whether multi-panel plots all have dimensions equal to maxrows by maxcols, or resized within those limits to fit number of plots. Default=TRUE.

new

Open a new window or add to existing plot windows. Default=TRUE.

SSplotDatMargin

Size of right-hand margin in data plot (may be too small if fleet names are long)

filenotes

Optional vector of character strings to be added to intro HTML page (if created) with notes about the model.

catchasnumbers

Is catch input in numbers instead of biomass? Default=F.

catchbars

show catch by fleet as barplot instead of stacked polygons (default=TRUE)

legendloc

Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See help("legend") for more info on the string options.

minyr

First year to show in time-series and time-varying plots

maxyr

Last year to show in time-series and time-varying plots. This can either be an alternative to, or redundant with, the forecastplot input.

sexes

Which sexes to show in composition plots. Default="all".

scalebins

Rescale expected and observed proportions in composition plots by dividing by bin width for models where bins have different widths? Caution!: May not work correctly in all cases.

scalebubbles

scale data-only bubbles by sample size, not just proportion within sample? Default=FALSE.

tslabels

Either NULL to have default labels for timeseries plots or a vector of appropriate length with labels for each figure

catlabels

Either NULL to have default labels for catch plots or a vector of appropriate length with labels for each figure

maxsize

The size of the largest bubble in the datasize plot. Default is 1.0.

showmle

Show MLE estimate and asymptotic variance estimate with blue lines in the parameter distribution plots?

showpost

Show posterior distribution as bar graph in parameter distribution plots (requires MCMC results to be available in replist)?

showprior

Show prior distribution as black line in the parameter distribution plots?

showinit

Show initial value as red triangle in the parameter distribution plots?

showdev

Include devs in the parameter distribution plots?

fitrange

Fit range in parameter distribution plots tightly around MLE and posterior distributions instead of full parameter range?

...

Additional arguments that will be passed to some subfunctions.

References

Walters, Hilborn, and Christensen, 2008, Surplus production dynamics in declining and recovering fish populations. Can. J. Fish. Aquat. Sci. 65: 2536-2551.

See also

SS_output(), SSplotBiology(), SSplotCatch(), SSplotComps(), SSplotDiscard(), SSplotIndices(), SSplotMnwt(), SSplotNumbers(), SSplotRecdevs(), SSplotSelex(), SSplotSpawnrecruit(), SSplotSPR(), SSplotTags(), SSplotTimeseries(), SSplotYield()

Author

Ian Stewart, Ian Taylor