SSplotIndices: Plot indices of abundance and associated quantities.

Description Usage Arguments Author(s) See Also

View source: R/SSplotIndices.R

Description

Plot indices of abundance and associated quantities.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
SSplotIndices(replist, subplots = 1:9, plot = TRUE, print = FALSE,
  fleets = "all", fleetnames = "default", smooth = TRUE, add = FALSE,
  datplot = FALSE, 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"),
  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, addmain = TRUE,
  plotdir = "default", minyr = NULL, maxyr = NULL,
  maximum_ymax_ratio = Inf, show_input_uncertainty = TRUE, verbose = TRUE,
  ...)

Arguments

replist

list created by SS_output

subplots

vector controlling which subplots to create

plot

plot to active plot device?

print

print to PNG files?

fleets

optional vector to subset fleets for which plots will be made

fleetnames

optional replacement for fleenames 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)

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

add a legend to seasonal colors (default is "topright")

seasnames

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

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

addmain

switch which allows the plot title to be left off

plotdir

directory where PNG files will be written. by default it will be the directory where the model was run.

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

verbose

report progress to R GUI?

...

Extra arguments to pass to calls to plot

Author(s)

Ian Stewart, Ian Taylor, James Thorson

See Also

SS_plots, SS_output


r4ss documentation built on May 29, 2017, 2:24 p.m.