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).
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,
...
)A list object created by SS_output().
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 to active plot device?
print to PNG files?
optional vector to subset fleets for which plots will be made
optional replacement for fleenames used in data file
add smoothed line to plots of observed vs. expected sample sizes
add to existing plot (not yet implemented)
make plot of data only?
vector of labels for plots (titles and axis labels)
vector of colors for all fleets (including those with no index data)
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.
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.
color of line showing expected index in time series plot. Default is blue.
color of smoother shown in obs. vs. exp. plots. Default is red.
single value or vector of plotting characters (pch parameter) for time-series plots of index fit. Default=21.
single value or vector of plotting characters (pch parameter) for sample size plots of index fit. Default=16.
character expansion factor for points showing observed values. Default=1.
Background color for points with pch=21.
add a legend to seasonal colors (only for seasonal models)
add a legend to seasonal colors (default is "topright")
optional vector of names for each season to replace defaults if a legend is used
width of plot
height of plot
units for PNG file
Resolution of plots printed to files.
The default is res = 300.
point size for PNG file
character expansion for plot titles
switch which allows the plot title to be left off
directory where PNG files will be written. by default it will be the directory where the model was run.
First year to show in plot (for zooming in on a subset of values)
Last year to show in plot (for zooming in on a subset of values)
Maximum allowed value for ymax (specified as ratio of y), which overrides any value of ymax that is greater (default = Inf)
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).
report progress to R GUI?
Extra arguments to pass to calls to plot