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),
  x_lim = c(NA, NA),
  surv_point_type = 17,
  reg_point_type = 19,
  cohorts = NULL,
  color_offset = 0
)

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.
`x_lim`	A vector to specify x limits, default is to span what is being plotted.
`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
`cohorts`	A vector of years so as to plot only those cohorts if available (useful for talks). If `NULL` (the default) plots all available cohorts.
`color_offset`	A value to offset the colors to compared to the ten retrospective years. This may be used when comparing model where only five retrospective years were run with those that have ten.