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Plot length samples

Source: R/plots_data.R
plot_lfd.Rd

  • type = "bars" (default): the classic length-frequency histogram, one panel per year (rows) and source (columns), see below.

  • type = "ridge": one length distribution per year, drawn as a ridge along the time axis (as FLRef's plot_lfd_ridgeline()), one panel per source; with cohorts = TRUE, von Bertalanffy lines follow each year class, so modes can be followed along them.

  • type = "bubble": one row per year, bubble area = proportion of the year's sample at each length. With cohorts = TRUE, von Bertalanffy growth lines follow each year class through the samples: real modes move along these lines; patterns that jump or vanish are sampling noise or selectivity, not dynamics.

  • type = "bars": the classic length-frequency histogram, one panel per year (rows) and source (columns), as proportions of each year's sample. With cohorts = TRUE, the mean length of each age class in that year is marked at the top, so modes can be matched to year classes.

Usage

plot_lfd(
  data,
  species = NULL,
  iter = 1,
  source = NULL,
  type = c("bars", "ridge", "bubble"),
  years = NULL,
  cohorts = FALSE,
  season = NULL,
  lfd = NULL,
  by_season = 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).

source

fleets / survey to show; default all.

type

"bars", "ridge" or "bubble".

years

years to show; default the last six for "bars", all for "ridge" and "bubble".

cohorts

add cohort growth lines (bubble) or age-class marks (bars).

season

seasons to include; default all.

lfd

optional length table to plot instead of data$lfd, e.g. from lfd_aggregate() (pooled over fleets or raised to the catch).

by_season

show the seasons separately instead of pooling them.

Value

a ggplot.

Details

Seasonal samples are pooled for the year (counts summed), unless by_season = TRUE: then each season is shown separately (histogram: a panel per year and season; ridge: one ridge per season within the year, coloured by season, as FLRef's plot_lfd_ridgeline() with seasonal data; bubble: seasons stacked within the year). Fish grow through the year, so modes move to the right from season to season; with imbalanced sampling (season_design()) some seasons have few or no samples.

Examples

# \donttest{
x <- simulate_fishery("lutjanus_bohar", nsim = 2, iters = 1)
plot_lfd(x$data, cohorts = TRUE)

plot_lfd(x$data, type = "bars", source = c("gillnet", "linefish"))

# }