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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. Modeled 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").

subplots, res, ptsize, margins, cex, lwd, maxsize, mainTitle, cex.main

Deprecated base-graphics arguments, retained for back-compatibility and ignored. One faceted figure is drawn; size, resolution and titles come from the ggplot theme and from width/height.

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.

alphasize

Bubble fill transparency (0-1).

Value

Invisibly, a list with typetable, the long data frame underlying the plot (year, fleet, data type, relative size). Point area is scaled within each data type: catch in metric tons, 1/SE for indices, sample size for compositions.

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 labeled per predator species.