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Plot cumulative catch by cohort.

Source: R/SSplotCohortCatch.R
SSplotCohortCatch.Rd

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

SSplotCohortCatch(
  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

A list object 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 for plot elements.

plotdir

Directory where PNG files will be written.

xlab

x-label for all plots

labels

Vector of labels for plots (titles and axis labels).

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, with pheight_tall used for plots that work best with a taller format and a single plot per page.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="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.

See also

SS_plots(), SS_output()

Author

Ian Taylor