Plot shows graphical display of what data is being used in the model. Some data types may not yet be included. Note, this is based on output from the model, not the input data file.
SSplotData(
replist,
plot = TRUE,
print = FALSE,
plotdir = "default",
subplot = 1:2,
fleetcol = "default",
datatypes = "all",
fleets = "all",
fleetnames = "default",
ghost = FALSE,
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
margins = c(5.1, 2.1, 2.1, 8.1),
cex = 2,
lwd = 12,
maxsize = 1,
alphasize = 1,
mainTitle = FALSE,
verbose = TRUE
)A list object created by SS_output().
plot to active plot device?
print to PNG files?
directory where PNG files will be written. by default it will be the directory where the model was run.
vector controlling which subplots to create Currently there are only 2 subplots:
1 equal size points showing presence/absence of data type by year/fleet
2 points scaled to indicate quantity or precision of data
Either the string "default", or a vector of colors to use for each fleet. If tagging data is included, an additional color needs to be added for the tag releases which are not assigned to a fleet.
Either the string "all", or a vector including some subset of the following: "catch", "cpue", "lendbase", "sizedbase", "agedbase", "condbase", "ghostagedbase", "ghostcondbase", "ghostlendbase", "ladbase", "wadbase", "mnwgt", "discard", "tagrelease", and "tagdbase1".
Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.
A vector of alternative names to use in the plot. By default the parameter names in the data file are used.
TRUE/FALSE indicator for whether to show presence of composition data from ghost fleets (data for which the fit is shown, but is not included in the likelihood calculations).
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
margins of plot (passed to par() function), which may need to be increased if fleet names run off right-hand margin
Character expansion for points showing isolated years of data
Line width for lines showing ranges of years of data
The size (cex) of the largest bubble in the datasize plot. Default is 1.
The transparency of the bubbles in the datasize plot. Defaults to 1 (no transparency). Useful for models with lots of overlapping points.
TRUE/FALSE switch to turn on/off the title on the plot.
report progress to R GUI?