Plot biology related quantities.

Description

Plot biology related quantities from Stock Synthesis model output, including mean weight, maturity, fecundity, and spawning output.

Usage

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SSplotBiology(replist,
 plot=TRUE,print=FALSE,add=FALSE,subplots=1:10,seas=1,
 col1="red",col2="blue",
 legendloc="topleft",
 plotdir="default",
 labels=c("Length (cm)",               
   "Age (yr)",                         
   "Maturity",                         
   "Mean weight (kg) in last year",    
   "Spawning output",                  
   "Length (cm, middle of the year)",  
   "Natural mortality",                
   "Female weight (kg)",               
   "Female length (cm)",               
   "Fecundity",                        
   "Default fecundity label"),         
 pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
 verbose=TRUE)

Arguments

replist

List created by SS_output

plot

Plot to active plot device?

print

Print to PNG files?

add

add to existing plot

subplots

vector controlling which subplots to create

seas

which season to plot (obviously only works in seasonal models, but maybe not fully implemented even then)

col1

color of some points/lines

col2

color of other points/lines

legendloc

Location of legend (see ?legend for more info)

plotdir

Directory where PNG files will be written. by default it will be the directory where the model was run.

labels

Vector of labels for plots (titles and axis labels)

pwidth

Width of plot written to PNG file

pheight

Height of plot written to PNG file

punits

Units for PNG file

res

Resolution for PNG file

ptsize

Point size for PNG file

cex.main

Character expansion for plot titles

verbose

Return updates of function progress to the R GUI?

Author(s)

Ian Stewart, Ian Taylor

See Also

SS_plots, SS_output

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