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Timeline of data used in the model likelihoods

Source: R/7-plot_data.R
plot_data.Rd

Plots a timeline of presence/absence (and optionally relative quantity) of the data sources contributing to an Rceattle model's likelihood, by year and fleet. Modelled after Stock Synthesis's r4ss::SSplotData().

Usage

plot_data(
  Rceattle,
  file = NULL,
  subplots = 1:2,
  datatypes = "all",
  fleets = "all",
  species = "all",
  ghost = FALSE,
  fleetcol = "default",
  width = 7,
  height = 5,
  res = 200,
  ptsize = 10,
  margins = c(5.1, 2.1, 2.1, 10.1),
  cex = 2,
  lwd = 12,
  maxsize = 1,
  alphasize = 1,
  mainTitle = FALSE,
  cex.main = 1
)

Arguments

Rceattle

Either a single Rceattle model object exported from Rceattle::fit_mod(), or a raw data_list (e.g. one of the bundled datasets such as BS2017MS).

file

Path/prefix used to save the figure. If NULL (default) the plot is drawn to the active device only. When supplied, the figure is written to paste0(file, "_data_plot.png") (and _data_plot2.png for the bubble subplot).

subplots

Integer vector controlling which subplots are produced:

  • 1 — equal-size points showing presence/absence by year/fleet

  • 2 — points scaled to relative quantity / precision within each data type (catch tonnage, 1/SE for indices, sample size for comps)

datatypes

Either "all" or a subset of c("catch", "index", "agecomp", "lencomp", "caal", "diet").

fleets

Either "all" or an integer vector of Fleet_codes to include. Diet "fleets" are encoded after the regular fleets (one per predator species).

species

Either "all" or an integer vector of species indices to include.

ghost

Logical. If TRUE, also include rows excluded from the likelihood (Year < 0). Defaults to FALSE.

fleetcol

Either "default" or a vector of colors (one per fleet shown after subsetting). Diet entries get an additional color appended.

width, height

Figure dimensions in inches.

res

Resolution (dpi) for the saved PNG.

ptsize

Pointsize passed to png().

margins

par("mar") for the plot. Increase the right margin if long fleet names are clipped.

cex

Character expansion for points showing isolated years.

lwd

Line width for runs of consecutive years (subplot 1).

maxsize

Max bubble radius (in plot units) for subplot 2.

alphasize

Bubble fill transparency (0–1).

mainTitle

Logical; if TRUE add a default title.

cex.main

Title character expansion.

Value

Invisibly, a list with typetable — the long data frame underlying the plot (year, fleet, data type, relative size).

Details

Years with Year > 0 contribute to the likelihood; rows with Year < 0 (kept for fitting comparison only) are shown when ghost = TRUE. Diet data uses Year == 0 for the fixed reference stomach composition; those entries are plotted at the model endyr and labelled per predator species.