Plot cumulative catch by cohort.

Description

Cumulative catch contributions for each cohort are plotted based on estimated catch-at-age matrix and weight-at-age values by fleet. Curves are shown in units of both numbers and biomass.

Usage

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SSplotCohorts(replist, subplots = 1:2, add = FALSE, plot = TRUE,
  print = FALSE, cohortcols = "default", cohortfrac = 1,
  cohortvec = NULL, cohortlabfrac = 0.1, cohortlabvec = NULL, lwd = 3,
  plotdir = "default", xlab = "Year", labels = c("Age",
  "Cumulative catch by cohort (in numbers x1000)",
  "Cumulative catch by cohort (x1000 mt)"), pwidth = 6.5, pheight = 5,
  punits = "in", res = 300, ptsize = 10, cex.main = 1, verbose = TRUE)

Arguments

replist

List created by SS_output

subplots

Vector controlling which subplots to create

add

Add to existing plot? (not yet implemented)

plot

Plot to active plot device?

print

Print to PNG files?

cohortcols

Vector of colors to show for each cohort. Default is range of colors shade indicating time period.

cohortfrac

What fraction of the cohorts to include in plot. If value < 1 is used, then cohorts are filtered to only include those with the highest maximum cumulative catch. Value will be overridden by cohortvec.

cohortvec

Optional vector of birth years for cohorts to include in plot. Value overrides cohortfrac.

cohortlabfrac

What fraction of the cohorts to label in plot. By default, top 10% of cohorts are labeled. Value will be overridden by cohortlabvec.

cohortlabvec

Optional vector of birth years for cohorts to label in plot. Value overrides cohortlabfrac.

lwd

Line width

plotdir

Directory where PNG or PDF files will be written. By default it will be the directory where the model was run.

xlab

x-label for all plots

labels

Vector of labels for plots (titles and axis labels)

pwidth

Width of plot

pheight

Height of plot

punits

Units for PNG file

res

Resolution for PNG file

ptsize

point size for PNG file

cex.main

Character expansion for plot titles (no titles in this function yet)

verbose

Report progress to R console?

Author(s)

Ian Taylor

See Also

SS_plots, SS_output

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