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Survey catchability over time

Source: R/7-plot_diagnostics.R
plot_catchability.Rd

Plots the fitted survey catchability q by year, faceted by fleet. Every fleet holding index_data is drawn, a fishery with a CPUE series as much as a survey.

Usage

plot_catchability(
  Rceattle,
  file = NULL,
  model_names = NULL,
  species = NULL,
  spnames = NULL,
  mse = FALSE,
  minyr = NULL,
  maxyr = NULL,
  incl_mean = FALSE,
  log = FALSE,
  line_col = NULL,
  lwd = 3,
  lty = 1,
  width = 7,
  height = 6.5,
  right_adj = 0,
  top_adj = 0.05,
  single.plots = FALSE
)

Arguments

Rceattle

A single fit_mod() object or a list of them (overlaid).

file

Optional file stem; the figure is written to <file>_<suffix>.png if given.

model_names

Legend labels for the models.

species

Species to include, as indices (c(1, 3)), names, a logical mask, or "all". Default NULL plots every species. Species labels belong in spnames; a character species that matches no species name is read as labels for back-compatibility.

spnames

Species labels, length nspp. Default: the model's own.

mse

Is Rceattle an MSE object? Its operating models are drawn.

minyr, maxyr

First / last year to plot.

incl_mean

Add a horizontal line at the hindcast mean of each series.

log

Plot catchability on the log scale.

line_col

Line colours; names, hex, or base-graphics integers. NULL uses the colorblind-safe Okabe-Ito palette. Applied to whichever variable the figure separates by colour, in legend order. Too few colours are recycled, with a warning.

lwd

Line width on the base-graphics scale: the default 3 renders as a standard-weight ggplot line. A vector varies it across series.

lty

Line type. A vector varies it across the levels of whatever the figure separates by line type.

width, height

Saved figure size in inches.

right_adj

Ignored. Base-graphics leftover: the figure widened its right margin to fit the legend. Set margins on the returned ggplot instead.

top_adj

Ignored. Base-graphics leftover; see right_adj.

single.plots

Ignored. Base-graphics leftover: one device per panel. The ggplot facets instead.

Value

A ggplot object.

Details

The value plotted is the realized catchability the model scaled the survey by, whichever route produced it: an estimated or fixed mean, annual deviations under Time_varying_q, an environmental regression (Catchability = "Environmental"), a q linkage such as rw(1 | Year) or ar1(1 | Year), or the closed-form value under "Analytical" / "AnalyticalArith". A fleet with a time-invariant catchability draws a flat line, which is the honest picture of a constant q rather than an empty panel.

Hindcast years only. The model applies catchability over the hindcast and does not project it, so the series stops at endyr regardless of the projection horizon. There is no incl_proj.

line_col and lty separate the models, so overlaying several fits compares their catchability series panel by panel.

Examples

# \donttest{
data(BS2017SS)
fit <- Rceattle::fit_mod(data_list = BS2017SS, msmMode = 0)
#> `age_trans_matrix` data does not span range of age for species 1 will fill with 0s
#> Step 1: Parameter build complete
#> Step 2: Map build complete
#> Step 3: Parameter bounds complete
#> Step 4: Data rearrange complete
#> Step 5: Hindcast build complete
#> Step 6: Hindcast optimization complete
plot_catchability(fit)

plot_catchability(fit, log = TRUE)

# }