plot_profile: Plot results from MCBE parameter profile analysis

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

Plot results from MCBE parameter profile analysis

Description

Plot results from MCBE parameter profile analysis

Usage

plot_profile(
  sim_summary,
  nm_par = "steep",
  nm_obj = c("parms", "parm.cons"),
  like_pattern = "^lk.",
  like_groups = c("L", "D", "U", "lenc", "agec", "SR"),
  like_shift = "min_par",
  like_exclude = c("lk.unwgt.data", "lk.Nage.init", "lk.fullF", "lk.Ftune", "lk.SRearly",
    "lk.SRend"),
  like_exclude_stacked = c("lk.total", "lk.unwgt.data"),
  like_plot_last = "lk.total",
  par_args = list(mfrow = c(2, 1), mar = c(3, 3, 0, 0), mgp = c(1, 0.3, 0), tck = -0.01),
  matplot_args_all = list(),
  matplot_args_group = list(),
  plot_profiles = TRUE,
  plot_stacked = TRUE,
  filter_info = list(gradient.max = c(0, 0.01)),
  par_val_ref = NULL,
  col_sub = c(total = rgb(0, 0, 0))
)

Arguments

sim_summary	Output object from summarize_MCBE
nm_par	Name of parameter to plot profile
nm_obj	Name of object where par should be found in sim_summary. By default, plot_profile will look in parms and parm.cons and use the first instance of nm_par it finds. It works with data frames in sim_summary like parms and is programmed to work with parm.cons as a special case, but may not work with other objects within sim_summary.
like_pattern	pattern to use to identify likelihood components from like object in sim_summary. Internally, the function uses grepl to identify names in like. The default "^lk." uses regular expression to identify all likelihood components.
like_groups	names of groups to use when plotting grouped likelihoods. The function adds "^lk." to the group names to find parameters to group in like.
like_shift	method to use to scale likelihood components for plotting: "min" shifts each likelihood component by the overall minimum, "min_par" shifts each likelihood component by its own minimum, "none" returns raw likelihoods
like_exclude	Names of columns in like to exclude from plotting profiles
like_exclude_stacked	Names of columns in like to exclude from plotting stacked barplot
like_plot_last	Name of the likelihood component to plot last so that it is on top in the plots.
par_args	arguments to pass to par
matplot_args_all	arguments to pass to matplot for plot of all likelihoods
matplot_args_group	arguments to pass to matplot for plot of grouped likelihoods
plot_profiles	logical. Plot likelihood profiles as lines, possibly shifted with like_shift.
plot_stacked	logical. Plot likelihood profiles as stacked areas (ggplot) columns not in like_prop_exclude.
filter_info	list of ranges used to filter out sim runs. set to NULL to retain all results.
par_val_ref	reference value to add to profile plots (e.g. parameter value from base model)
col_sub	Specify colors to substitute for colors in the ungrouped profile plot. named vector where the names match the names match the names in the plot legend.

nikolaifish/bamExtras documentation built on April 17, 2025, 9:44 p.m.