View source: R/SSplotIndices.R
SSplotIndices | R Documentation |
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,
...
)
replist |
A list object created by |
subplots |
vector controlling which subplots to create Numbering of subplots is as follows, where subplot 9 (comparison of all indices) is provided first:
|
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 |
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
|
pheight |
Height of plots printed to png files in units of |
punits |
Units for |
res |
Resolution of plots printed to files.
The default is |
ptsize |
Point size for plotted text in plots printed to files (see
|
cex.main |
Character expansion for plot titles.
The default is |
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 |
Ian Stewart, Ian Taylor, James Thorson
SS_plots()
, SS_output()
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