Plot biology related quantities from Stock Synthesis model output, including mean weight, maturity, fecundity, and spawning output.
SSplotBiology(replist, plot = TRUE, print = FALSE, add = FALSE,
subplots = 1:14, seas = 1, colvec = c("red", "blue", "grey20"),
shadealpha = 0.1, legendloc = "topleft", plotdir = "default",
labels = c("Length (cm)", "Age (yr)", "Maturity",
"Mean weight (kg) in last year", "Spawning output",
"Length (cm, beginning of the year)", "Natural mortality",
"Female weight (kg)", "Female length (cm)", "Fecundity",
"Default fecundity label", "Year"), pwidth = 6.5, pheight = 5,
punits = "in", res = 300, ptsize = 10, cex.main = 1, verbose = TRUE)List created by SS_output
Plot to active plot device?
Print to PNG files?
add to existing plot
vector controlling which subplots to create
which season to plot (obviously only works in seasonal models, but maybe not fully implemented even then)
vector of length 3 with colors for various points/lines
Transparency parameter used to make default shadecol values (see ?rgb for more info)
Location of legend (see ?legend for more info)
Directory where PNG files will be written. by default it will be the directory where the model was run.
Vector of labels for plots (titles and axis labels)
Width of plot
Height of plot
Units for PNG file
Resolution for PNG file
Point size for PNG file
Character expansion for plot titles
Return updates of function progress to the R GUI?