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Plot indices of abundance and associated quantities.

Source: R/SSplotIndices.R
SSplotIndices.Rd

Plot indices of abundance with or without model fit as well as other diagnostic plots such as observed vs. expected index and plots related to time-varying catchability (if present).

Usage

SSplotIndices(
  replist,
  subplots = c(1:10, 12),
  plot = TRUE,
  print = FALSE,
  fleets = "all",
  fleetnames = "default",
  smooth = TRUE,
  add = FALSE,
  datplot = TRUE,
  labels = c("Year", "Index", "Observed index", "Expected index", "Log index",
    "Log observed index", "Log expected index", "Standardized index", "Catchability (Q)",
    "Time-varying catchability", "Vulnerable biomass",
    "Catchability vs. vulnerable biomass", "Residual", "Deviation"),
  fleetcols = NULL,
  col1 = "default",
  col2 = "default",
  col3 = "blue",
  col4 = "red",
  pch1 = 21,
  pch2 = 16,
  cex = 1,
  bg = "white",
  legend = TRUE,
  legendloc = "topright",
  seasnames = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  mainTitle = FALSE,
  plotdir = "default",
  minyr = NULL,
  maxyr = NULL,
  maximum_ymax_ratio = Inf,
  show_input_uncertainty = TRUE,
  verbose = TRUE,
  ...
)

Arguments

replist

A list object created by SS_output().

subplots

vector controlling which subplots to create Numbering of subplots is as follows, where subplot 9 (comparison of all indices) is provided first:

  • 1 index data by fleet

  • 2 index data with fit by fleet

  • 3 observed vs expected index values with smoother

  • 4 index data by fleet on a log scale (lognormal error only)

  • 5 index data with fit by fleet on a log scale (lognormal error only)

  • 6 log(observed) vs log(expected) with smoother (lognormal error only)

  • 7 time series of time-varying catchability (only if actually time-varying)

  • 8 catchability vs. vulnerable biomass (if catchability is not constant)

  • 9 comparison of all indices

  • 10 index residuals based on total uncertainty

  • 11 index residuals based on input uncertainty (not currently provided)

  • 12 index deviations (independent of index uncertainty)

plot

Plot to active plot device?

print

Print to PNG files?

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.

fleetnames

Optional replacement for fleetnames used in data file.

smooth

add smoothed line to plots of observed vs. expected sample sizes

add

add to existing plot (not yet implemented)

datplot

make plot of data only?

labels

Vector of labels for plots (titles and axis labels).

fleetcols

vector of colors for all fleets (including those with no index data)

col1

vector of colors for points in each season for time series plot. Default is red for single season models and a rainbow using the rich.colors.short function for multiple seasons.

col2

vector of colors for points in each season for obs. vs. exp. plot. Default is blue for single season models and a rainbow using the rich.colors.short function for multiple seasons.

col3

color of line showing expected index in time series plot. Default is blue.

col4

color of smoother shown in obs. vs. exp. plots. Default is red.

pch1

single value or vector of plotting characters (pch parameter) for time-series plots of index fit. Default=21.

pch2

single value or vector of plotting characters (pch parameter) for sample size plots of index fit. Default=16.

cex

character expansion factor for points showing observed values. Default=1.

bg

Background color for points with pch=21.

legend

add a legend to seasonal colors (only for seasonal models)

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.

seasnames

optional vector of names for each season to replace defaults if a legend is used

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).

plotdir

Directory where PNG files will be written.

minyr

First year to show in plot (for zooming in on a subset of values)

maxyr

Last year to show in plot (for zooming in on a subset of values)

maximum_ymax_ratio

Maximum allowed value for ymax (specified as ratio of y), which overrides any value of ymax that is greater (default = Inf)

show_input_uncertainty

Switch controlling whether to add thicker uncertainty interval lines indicating the input uncertainty relative to the total uncertainty which may result from estimating a parameter for extra standard deviations. This is only added for the plots with index fit included (the data-only plots only show the input uncertainty).

verbose

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

...

Extra arguments to pass to calls to plot

See also

SS_plots(), SS_output()

Author

Ian Stewart, Ian Taylor, James Thorson