Description Usage Arguments Author(s) See Also
View source: R/SSplotIndices.R
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 timevarying catchability (if present).
1 2 3 4 5 6 7 8 9 10 11 12 13 14  SSplotIndices(replist, subplots = c(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)",
"Timevarying 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, mainTitle = TRUE, plotdir = "default",
minyr = NULL, maxyr = NULL, maximum_ymax_ratio = Inf,
show_input_uncertainty = TRUE, verbose = TRUE, ...)

replist 
list created by 
subplots 
vector controlling which subplots to create Numbering of subplots is as follows:

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 timeseries 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 
mainTitle 
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 
Ian Stewart, Ian Taylor, James Thorson
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