Plot fit to discard fraction from Stock Synthesis output file.
Usage
SSplotDiscard(
replist,
subplots = 1:2,
plot = TRUE,
print = FALSE,
plotdir = "default",
fleets = "all",
fleetnames = "default",
datplot = FALSE,
labels = c("Year", "Discard fraction", "Total discards", "for"),
yhi = 1,
ymax = NULL,
col1 = "blue",
col2 = "black",
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
verbose = TRUE
)
Arguments
- replist
A list object created by
SS_output()
.- subplots
Vector of which plots to make (1 = data only, 2 = with fit). If
plotdat = FALSE
then subplot 1 is not created, regardless of choice ofsubplots
.- plot
Plot to active plot device?
Print to PNG files?
- plotdir
Directory where PNG files will be written.
- 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.
- datplot
Make data-only plot of discards? This can override the choice of
subplots
.- labels
Vector of labels for plots (titles and axis labels).
- yhi
Maximum y-value which will always be included in the plot (all data included regardless). Default = 1 so that discard fractions are always plotted on a 0-1 range, but total discard amounts which are greater than this value will exceed it.
- ymax
Optional maximum y-value to include (useful if upper tails on discard amounts are very high)
- col1
First color to use in plot (for expected values)
- col2
Second color to use in plot (for observations and intervals)
- pwidth
Default width of plots printed to files in units of
punits
.- pheight
Height of plots printed to png files in units of
punits
. Default is designed to allow two plots per page, withpheight_tall
used for plots that work best with a taller format and a single plot per page.- punits
Units for
pwidth
andpheight
. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default ispunits="in"
.- res
Resolution of plots printed to files. The default is
res = 300
.- ptsize
Point size for plotted text in plots printed to files (see
help("png")
in R for details).- cex.main
Character expansion for plot titles. The default is
cex.main=1
.- verbose
A logical value specifying if output should be printed to the screen.