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Plot marlin Simulation Results

Source: R/plot_marlin.R
plot_marlin.Rd

Generates time series, spatial, length composition, or age composition plots from one or more process_marlin outputs. Multiple scenarios can be overlaid by passing them as named arguments.

Usage

plot_marlin(
  ...,
  steps_to_plot = NA,
  plot_var = "ssb",
  plot_type = "time",
  fauna = NULL,
  drop_recruits = TRUE,
  plots = "fauna",
  max_scale = TRUE
)

Arguments

...

One or more named process_marlin outputs. Names appear in the plot legend. If unnamed, letters a, b, c, ... are used. Each argument should be the full list returned by process_marlin (i.e. with $fauna and $fleets elements).

steps_to_plot

Numeric or character vector. Which steps to include. Default NA uses all available steps.

plot_var

Character. Quantity to plot. One of:

"ssb"

Spawning stock biomass (default)

"b"

Total biomass

"c"

Catch in numbers

"n"

Abundance in numbers

plot_type

Character. Type of plot. One of "time" (default), "space", "length", or "age".

fauna

A fauna list from create_critter. Required only when plot_type = "length" (used to access the length-at-age key).

drop_recruits

Logical. If TRUE (default), drops the youngest 10\ length classes that can dominate the axis scale.

plots

Character. One of "fauna" (default; plots population state from $fauna) or "fleets" (plots fleet outcomes from $fleets).

max_scale

Logical. If TRUE (default for "time" and "space"), normalises each series by its maximum so that values are expressed as a proportion of the maximum observed value.

Value

A ggplot2 object. Print it to render the plot, or save with ggplot2::ggsave().

Details

Plot types

"time"

Line chart of the chosen plot_var summed across patches and ages over time, faceted by species. When max_scale = TRUE, each series is normalised by its own maximum so that all fits share a [0, 1] scale and cross-species comparisons are straightforward.

"space"

Tile map of plot_var at the last step in steps_to_plot, summed across ages, faceted by species and fit.

"length"

Density plot of length composition at specified steps, derived by projecting age-specific abundances through the critter's length-at-age key. Requires fauna. A maximum of 10 steps can be plotted simultaneously.

"age"

Density plot of age composition at the last step in steps_to_plot.

See also

process_marlin, simmar, theme_marlin

Examples

if (FALSE) { # \dontrun{
# Compare two scenarios
proc_base <- process_marlin(sim_base)
proc_mpa  <- process_marlin(sim_mpa)

# Time series of SSB
plot_marlin(`No MPA` = proc_base, `With MPA` = proc_mpa,
            plot_var = "ssb", plot_type = "time")

# Spatial biomass map at final time step
plot_marlin(proc_mpa, plot_var = "b", plot_type = "space")

# Length composition (requires fauna)
plot_marlin(proc_base, plot_type = "length", fauna = fauna)
} # }