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Plot biological samples (observations only)

Source: R/plots_data.R
plot_bio.Rd

  • "age_length": length against observed age.

  • "length_weight": weight against length.

  • "maturity": observed proportion mature by length bin (point size = number of fish).

  • "alk": observed age-length key (counts; bubble area).

  • "length": length composition of the biological samples.

Usage

plot_bio(
  data,
  species = NULL,
  iter = 1,
  what = c("age_length", "length_weight", "maturity", "alk", "length"),
  source = NULL,
  by = c("fleet", "aggregate", "season"),
  truth = FALSE
)

Arguments

data

a floss_data (or read_dataset() list).

species

species name; default the first.

iter

iteration(s); several iterations are overlaid (lines) or shown in rows (length samples).

what

one of the options above.

source

sources to include; default all.

by

panels: "fleet" (one panel per fleet), "aggregate" (all fleets in one panel, as a naive analyst would pool them) or "season" (one panel per sampling season: fish grow through the year, so length at age rises from season to season).

truth

draw the true growth, length-weight and maturity curves.

Value

a ggplot.

Details

Points are always coloured by fleet (or survey); by sets the panels. With truth = TRUE the true relationship of the operating model is drawn over the observations: the von Bertalanffy growth curve (at the middle of the sampling season, or mid-year), the length-weight curve and the maturity ogive.