SSplotComparisons: plot model comparisons

In r4ss: R Code for Stock Synthesis

plot model comparisons

Description

Creates a user-chosen set of plots comparing model output from a summary of multiple models, where the collection was created using the SSsummarize function.

Usage

SSplotComparisons(
  summaryoutput,
  subplots = 1:20,
  plot = TRUE,
  print = FALSE,
  png = print,
  pdf = FALSE,
  models = "all",
  endyrvec = NULL,
  indexfleets = NULL,
  indexUncertainty = TRUE,
  indexQlabel = TRUE,
  indexQdigits = 4,
  indexSEvec = NULL,
  indexPlotEach = FALSE,
  labels = c("Year", "Spawning biomass (t)", "Fraction of unfished",
    "Age-0 recruits (1,000s)", "Recruitment deviations", "Index", "Log index",
    "SPR-related quantity", "Density", "Management target",
    "Minimum stock size threshold", "Spawning output", "Harvest rate"),
  col = NULL,
  shadecol = NULL,
  pch = NULL,
  lty = 1,
  lwd = 2,
  spacepoints = 10,
  staggerpoints = 1,
  initpoint = 0,
  tickEndYr = TRUE,
  shadeForecast = TRUE,
  xlim = NULL,
  ylimAdj = 1.05,
  xaxs = "i",
  yaxs = "i",
  type = "o",
  uncertainty = TRUE,
  shadealpha = 0.1,
  legend = TRUE,
  legendlabels = NULL,
  legendloc = "topright",
  legendorder = NULL,
  legendncol = 1,
  sprtarg = NULL,
  btarg = NULL,
  minbthresh = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  plotdir = NULL,
  filenameprefix = "",
  densitynames = c("SSB_Virgin", "R0"),
  densityxlabs = NULL,
  rescale = TRUE,
  densityscalex = 1,
  densityscaley = 1,
  densityadjust = 1,
  densitysymbols = TRUE,
  densitytails = TRUE,
  densitymiddle = FALSE,
  densitylwd = 1,
  fix0 = TRUE,
  new = TRUE,
  add = FALSE,
  par = list(mar = c(5, 4, 1, 1) + 0.1),
  verbose = TRUE,
  mcmcVec = FALSE,
  show_equilibrium = TRUE
)

Arguments

summaryoutput	List created by SSsummarize
subplots	Vector of subplots to be created Numbering of subplots is as follows: 1 spawning biomass 2 spawning biomass with uncertainty intervals 3 biomass ratio (hopefully equal to fraction of unfished) 4 biomass ratio with uncertainty 5 SPR ratio 6 SPR ratio with uncertainty 7 F value 8 F value with uncertainty 9 recruits 10 recruits with uncertainty 11 recruit devs 12 recruit devs with uncertainty 13 index fits 14 index fits on a log scale 15 phase plot 16 densities 17 cumulative densities
plot	Plot to active plot device?
print	Send plots to PNG files in directory specified by plotdir?
png	Has same result as print, included for consistency with SS_plots.
pdf	Write output to PDF file? Can't be used in conjunction with png or print.
models	Optional subset of the models described in summaryoutput. Either "all" or a vector of numbers indicating columns in summary tables.
endyrvec	Optional single year or vector of years representing the final year of values to show for each model. By default it is set to the ending year specified in each model.
indexfleets	Fleet numbers for each model to compare indices of abundance. Can take different forms: NULL: (default) create a separate plot for each index as long as the fleet numbering is the same across all models. integer: create a single comparison plot for the chosen index vector of length equal to number of models: a single fleet number for each model to be compared in a single plot list: list of fleet numbers associated with indices within each model to be compared, where the list elements are each a vector of the same length but the names of the list elements don't matter and can be absent.
indexUncertainty	Show uncertainty intervals on index data? Default=FALSE because if models have any extra standard deviations added, these intervals may differ across models.
indexQlabel	Add catchability to legend in plot of index fits (TRUE/FALSE)?
indexQdigits	Number of significant digits for catchability in legend (if indexQlabel = TRUE)
indexSEvec	Optional replacement for the SE values in summaryoutput[["indices"]] to deal with the issue of differing uncertainty by models described above.
indexPlotEach	TRUE plots the observed index for each model with colors, or FALSE just plots observed once in black dots.
labels	Vector of labels for plots (titles and axis labels)
col	Optional vector of colors to be used for lines. Input NULL makes use of rich.colors.short function.
shadecol	Optional vector of colors to be used for shading uncertainty intervals. The default (NULL) is to use the same colors provided by col (either the default or a user-chosen input) and make them more transparent by applying the shadealpha input as an alpha transparency value (using the adjustcolor() function)
pch	Optional vector of plot character values
lty	Optional vector of line types
lwd	Optional vector of line widths
spacepoints	Number of years between points shown on top of lines (for long timeseries, points every year get mashed together)
staggerpoints	Number of years to stagger the first point (if spacepoints > 1) for each line (so that adjacent lines have points in different years)
initpoint	Year value for first point to be added to lines. Points added to plots are those that satisfy (Yr-initpoint)%%spacepoints == (staggerpoints*iline)%%spacepoints
tickEndYr	TRUE/FALSE switch to turn on/off extra axis mark at final year in timeseries plots.
shadeForecast	TRUE/FALSE switch to turn on off shading of years beyond the maximum ending year of the models
xlim	Optional x limits
ylimAdj	Multiplier for ylim parameter. Allows additional white space to fit legend if necessary. Default=1.05.
xaxs	Choice of xaxs parameter (see ?par for more info)
yaxs	Choice of yaxs parameter (see ?par for more info)
type	Type parameter passed to points (default 'o' overplots points on top of lines)
uncertainty	Show plots with uncertainty intervals? Either a single TRUE/FALSE value, or a vector of TRUE/FALSE values for each model, or a set of integers corresponding to the choice of models.
shadealpha	Transparency adjustment used to make default shadecol values (implemented as adjustcolor(col=col, alpha.f=shadealpha))
legend	Add a legend?
legendlabels	Optional vector of labels to include in legend. Default is 'model1','model2',etc.
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.
legendorder	Optional vector of model numbers that can be used to have the legend display the model names in an order that is different than that which is represented in the summary input object.
legendncol	Number of columns for the legend.
sprtarg	Target value for SPR-ratio where line is drawn in the SPR plots and phase plot.
btarg	Target biomass value at which to show a line (set to 0 to remove)
minbthresh	Minimum biomass threshold at which to show a line (set to 0 to remove)
pwidth	Default width of plots printed to files in units of punits. The default is pwidth=6.5.
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).
plotdir	Directory where PNG or PDF files will be written. By default it will be the directory where the model was run.
filenameprefix	Additional text to append to PNG or PDF file names. It will be separated from default name by an underscore.
densitynames	Vector of names (or subset of names) of parameters or derived quantities contained in summaryoutput[["pars"]][["Label"]] or summaryoutput[["quants"]][["Label"]] for which to make density plots
densityxlabs	Optional vector of x-axis labels to use in the density plots (must be equal in length to the printed vector of quantities that match the densitynames input)
rescale	TRUE/FALSE control of automatic rescaling of units into thousands, millions, or billions
densityscalex	Scalar for upper x-limit in density plots (values below 1 will cut off the right tail to provide better contrast among narrower distributions
densityscaley	Scalar for upper y-limit in density plots (values below 1 will cut off top of highest peaks to provide better contrast among broader distributions
densityadjust	Multiplier on bandwidth of kernel in density function used for smoothing MCMC posteriors. See 'adjust' in ?density for details.
densitysymbols	Add symbols along lines in density plots. Quantiles are c(0.025,0.1,0.25,0.5,0.75,0.9,0.975).
densitytails	Shade tails outside of 95% interval darker in density plots?
densitymiddle	Shade middle inside of 95% interval darker in density plots?
densitylwd	Line width for density plots
fix0	Always include 0 in the density plots?
new	Create new empty plot window
add	Allows single plot to be added to existing figure. This needs to be combined with specific 'subplots' input to make sure only one thing gets added.
par	list of graphics parameter values passed to the par function
verbose	Report progress to R GUI?
mcmcVec	Vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE
show_equilibrium	Whether to show the equilibrium values for SSB. For some model comparisons, these might not be comparable and thus useful to turn off. Defaults to TRUE.

Author(s)

Ian G. Taylor, John R. Wallace

See Also

SS_plots(), SSsummarize(), SS_output(), SSgetoutput()

Examples

## Not run: 
# directories where models were run need to be defined
dir1 <- "c:/SS/mod1"
dir2 <- "c:/SS/mod2"

# read two models
mod1 <- SS_output(dir = dir1)
mod2 <- SS_output(dir = dir2)

# create list summarizing model results
mod.sum <- SSsummarize(list(mod1, mod2))

# plot comparisons
SSplotComparisons(mod.sum, legendlabels = c("First model", "Second model"))

# Example showing comparison of MLE to MCMC results where the mcmc would have
# been run in the subdirectory 'c:/SS/mod1/mcmc'
mod1 <- SS_output(dir = "c:/SS/mod1", dir.mcmc = "mcmc")
# pass the same model twice to SSsummarize in order to plot it twice
mod.sum <- SSsummarize(list(mod1, mod1))
# compare MLE to MCMC
SSplotComparisons(mod.sum,
  legendlabels = c("MCMC", "MLE"),
  mcmcVec = c(TRUE, FALSE)
)

## End(Not run)

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