Shared plotting arguments

A common vocabulary, documented here once and inherited by the plotters that take it: plot_timeseries() and its wrappers (plot_biomass(), plot_ssb(), plot_recruitment(), the depletions, plot_exploitable_biomass(), plot_f()), the predation plotters (plot_b_eaten(), plot_b_eaten_prop(), plot_m_at_age(), plot_m2_at_age_prop(), plot_ration()), and plot_selectivity(). Each argument means the same thing wherever it appears, but not every plotter takes every one, incl_mean is on the predation plotters, add_ci only where the quantity holds standard errors, and alpha only where the figure has a ribbon or a fan. The remaining plot_*() functions still take their own arguments; see each one's help.

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.

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.

alpha

Transparency of confidence ribbons and shaded areas, between 0 and 1.

add_ci

Add a 95% confidence interval. Only available where the plotted quantity holds standard errors; warns and draws none otherwise.

minyr, maxyr

First / last year to plot.

incl_proj

Include the projection years, with a dashed divider at the last hindcast year.

incl_mean

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

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.

mod_cex

Ignored. Base-graphics leftover: legend text size. Use p + ggplot2::theme(legend.text = ggplot2::element_text(size = ...)).

legend.pos

Ignored. Base-graphics leftover: legend placement. Use p + ggplot2::theme(legend.position = "right").

single.plots

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

theta

Ignored. Base-graphics leftover: viewing angle of a persp surface, which is no longer drawn.

ymax

Ignored. Base-graphics leftover: y-axis maximum. Use p + ggplot2::coord_cartesian(ylim = c(0, ymax)).

cex

Ignored. Base-graphics leftover: point expansion.

Value

A ggplot object.

How line_col and lty are applied

They supply values for whichever discrete variable the plot already encodes with that aesthetic, matched in level order, which is not always the model. Each function's help says what its own figure separates.

Where colour encodes a continuous variable, the year fan in plot_selectivity(), line_col supplies the ramp anchors instead: one colour draws the fan in that colour, several interpolate between them.