NFZ.age.plots: At-age matrix plots

In rcheshire/FishGraph: Visualizations for fishery stock-assessment.

At-age matrix plots

Description

The function NFZ.age.plots generates barplots of estimated abundance and mortality at age over time and bubble plots of number and biomass at age. Bubble areas are scaled to the largest value within each plot.

Usage

NFZ.age.plots(
  x,
  DataName = deparse(substitute(x)),
  draft = TRUE,
  start.drop = 0,
  graphics.type = NULL,
  use.color = TRUE,
  units.naa = x$info$units.naa,
  units.biomass = x$info$units.biomass,
  units.ssb = x$info$units.ssb,
  max.bub = 4,
  user.plots = NULL,
  plot.CLD = FALSE,
  drop.last.NB = FALSE
)

Arguments

x	an R list with output from the assessment models.
DataName	string used in plot titles. Defaults to argument x.
draft	modifies plots for use in a report. When FALSE main titles are omitted.
start.drop	Number of years at the start of the data to be omitted from plots, as when a model includes an initialization period.
graphics.type	a vector of graphics file types to which graphics are saved. When NULL, no plots are saved.
use.color	plots are made in grayscale when FALSE
units.naa	A text string (e.g. "million fish") used in labeling the plot of numbers at age.
units.biomass	A text string (e.g. "t") used in labeling the plot of biomass at age.
max.bub	A numerical scalar for the maximum bubble size (e.g. "4.0") in bubble plots of numbers at age and biomass at age.
user.plots	A vector of text strings with the names of additional matrix components of x to be plotted.
plot.CLD	When TRUE, each matrix in x$CLD.est.mats is plotted, in addition to the plots described here.
drop.last.NB	boolean for whether to drop the last year of the abundance and biomass at age, when TRUE doesn't plot the last year of abundance, default FALSE.

Value

Graphics

Author(s)

M Prager

E Williams

K Shertzer

R Cheshire

K Purcell

Examples

NFZ.age.plots(gag)

rcheshire/FishGraph documentation built on Feb. 23, 2024, 11:27 a.m.