plot_squid: Make the retrospective recruitment deviations plot (squid...
In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

plot_squid

R Documentation

Make the retrospective recruitment deviations plot (squid plot)

Description

Make the retrospective recruitment deviations plot (squid plot)

Usage

plot_squid(
  model,
  relative = FALSE,
  show_ci = FALSE,
  ci_alpha = 0.2,
  ci_yrs = NULL,
  year_label_font_size = 4,
  y_lim = c(NA, NA),
  surv_point_type = 17,
  reg_point_type = 19
)

Arguments

`model`	Model with retrospectives
`relative`	Logical. If `TRUE`, plot the deviaitons relative to the most recent estimate for each cohort
`show_ci`	Logical. If `TRUE`, plot the credible interval ribbons around the median lines
`ci_alpha`	The a transparency value for the credible interval ribbon fill
`ci_yrs`	A vector of years to include credible intervals for. If `NULL`, all will be shown. Only used if `show_ci` is `TRUE`
`year_label_font_size`	Size of the font for the year labels
`y_lim`	A vector to specify y limits, default is to span what is being plotted. If `full` then automatically span all the credible intervals even when not showing them all (useful for showing sequential plots in a talk). Not tested with `relative = TRUE` and `show_ci = TRUE` as we do not currently use those.
`surv_point_type`	The point shape type for ages in age-1 index years
`reg_point_type`	The point shape type for ages in non-age-1-index years