Plot a stratified abundance or biomass index

Plots the output of calc_stratified_index() as a time-series. When the index contains multiple length groups (from a matrix HaulN), all groups are drawn in the same panel as separate coloured lines with a legend. An optional panel_var can split the plot into panels (e.g. by survey).

Usage

plot_stratified_index(
  x,
  x_var = NULL,
  panel_var = NULL,
  ci = TRUE,
  ci_alpha = 0.2,
  log_scale = FALSE,
  fixed_ylim = TRUE,
  col = NULL,
  lwd = 2,
  pch = 16,
  legend = TRUE,
  legend_pos = "topright",
  layout = TRUE,
  xlim = NULL,
  ylim = NULL,
  main = NULL,
  xlab = NULL,
  ylab = NULL
)

Arguments

x

Data frame returned by calc_stratified_index().

x_var

Name of the column to use as the x-axis. Defaults to "Year" if present, otherwise the first non-result column.

panel_var

Optional column name used to split the plot into panels (e.g. "Survey"). Default NULL (single panel).

ci

Logical; draw per-group confidence-interval ribbons. Default TRUE.

ci_alpha

Transparency of the CI ribbons (0-1). Default 0.2.

log_scale

Logical; log-transform the y-axis. Default FALSE.

fixed_ylim

Logical; share a common y-axis range across panels. Default TRUE.

col

Character vector of colours, one per unique group value. Defaults to the DATRASextra discrete palette.

lwd

Line width. Default 2.

pch

Point symbol. Default 16.

legend

Logical; draw a legend for the group colours. Default TRUE; suppressed automatically when there is only one group.

legend_pos

Legend position string passed to graphics::legend(). Default "topright".

layout

Logical; when TRUE (default) and the plot has multiple panels, the function sets par(mfrow) automatically and restores it on exit. Set to FALSE to draw panels sequentially into the caller's current layout – useful when combining with other plots via par(mfrow = ...).

xlim, ylim

Optional axis limits.

main

Optional plot title.

xlab, ylab

Axis labels. Auto-generated from cpue_method if NULL.

Value

Invisibly returns x.

See also

calc_stratified_index()

Examples

if (FALSE) { # \dontrun{
data(dab)
dab <- add_swept_area(dab)
dab <- add_total_numbers_by_haul(dab, length_cuts = c(15, 25))
res <- calc_stratified_index(dab, by = "Year")
plot_index(res)
} # }