Comp.yearly.plots: Plots of age- and length-composition fits by year
In rcheshire/FishGraph: Visualizations for fishery stock-assessment.

Comp.yearly.plots

R Documentation

Plots of age- and length-composition fits by year

Description

The routine Comp.yearly.plots generates plots of age- and length-composition fits by year and data series. Optionally, the sample size N, effective sample size Neff, angular deviation can be printed on the plot surface. The background is shaded if the model does not fit to the composition (Neff < 0). Plots of the ratio Neff/N over time may be made. Plots are available in two formats: one plot per page, or a compact format with 21 plots per page.

Usage

Comp.yearly.plots(
  x,
  DataName = deparse(substitute(x)),
  draft = TRUE,
  graphics.type = NULL,
  use.color = TRUE,
  units = x$info$units.length,
  print.n = !compact,
  print.neff = !compact,
  plot.missing = FALSE,
  plot.pred = TRUE,
  plot.neff = FALSE,
  compute.neff = FALSE,
  print.year = compact,
  compact = TRUE,
  uniform = TRUE,
  connect.obsd = 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.
`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`	a character string (e.g. `"cm"`) for labeling the X-axis of length-composition plots.
`print.n`	When `TRUE`, N is printed in each plot.
`print.neff`	When `TRUE`, N_eff (rounded) is printed in each plot.
`plot.missing`	When `TRUE`, plots out all comps. Otherwise comps where `is.na(N)` are not printed.
`plot.pred`	when `TRUE`, plots the fit to the composition data, when `FALSE` only plots the observed compositions
`plot.neff`	When `TRUE`, a timeplot of N_eff is made for each data series
`compute.neff`	When `TRUE`, FishGraph computes N_eff internally, rather than using values stored by the user. The computations are based on the sample sizes and observed and estimated proportions.
`print.year`	When `TRUE`, the year is printed in each plot.
`compact`	When `TRUE`, plots are arranged by default in 5x3 matrix on each page.
`uniform`	When `TRUE`, all years of the same data series are scaled the same.
`connect.obsd`	When `TRUE`, observed points are connected by lines.