plot_rcm_data: Plotting functions of data used for OM conditioning

In pbs-assess/ggmse: Tools for Working with openMSE (Including DLMtool, MSEtool, and SAMtool)

Plotting functions of data used for OM conditioning

Description

A set of functions that plots fits to data from a list of RCModel objects.

Usage

plot_rcm_index(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  i,
  index_names,
  color,
  MPD = FALSE
)

plot_rcm_age_comps(
  RCModel,
  scenario,
  french = FALSE,
  type = c("fleet", "index"),
  i = 1,
  color = "black",
  MPD = FALSE
)

plot_rcm_mean_age(
  rcm,
  scenario,
  type = c("fleet", "index"),
  i = 1,
  scales = "fixed",
  color = "black",
  alpha = 0.6,
  french = FALSE,
  MPD = FALSE
)

plot_rcm_length_comps(
  RCModel,
  scenario,
  french = FALSE,
  type = c("fleet", "index"),
  i = 1,
  color = "black",
  MPD = FALSE
)

plot_rcm_mean_length(
  rcm,
  scenario,
  type = c("fleet", "index"),
  i = 1,
  scales = "fixed",
  color = "black",
  alpha = 0.6,
  french = FALSE,
  MPD = FALSE
)

plot_rcm_biomass_age(
  RCModel,
  scenario,
  type = c("fleet", "index"),
  i = 1,
  color = "black",
  french = FALSE
)

Arguments

rcm	A list containing RCModel objects.
scenario	A character vector of names corresponding to rcm.
french	Logical, whether the axes are in French or not.
i	The corresponding index from the fleet or index of abundance.
index_names	Character vector of names for the indices of abundance.
color	Character vector of colors used for plotting.
MPD	Logical, whether to plot individual simulations (FALSE) or from the single fit (TRUE) in RCModel@mean_fit.
RCModel	An object of class RCModel
type	Whether the output is from a fishing fleet or index.
scales	The scales argument to facet_wrap.
alpha	The alpha parameter to control color transparency in the ggplots.

Functions

• plot_rcm_index(): Plot fits to index

• plot_rcm_age_comps(): Plot age comps from a fleet or index (single RCM only)

• plot_rcm_mean_age(): Plot mean age for a fleet or index of abundance

• plot_rcm_length_comps(): Plot length comps from a fleet or index (single RCM only)

• plot_rcm_mean_length(): Plot mean length for a fleet or index of abundance using the length compositions

• plot_rcm_biomass_age(): Plots the proportion of biomass vs. age from the predicted age composition of a fleet or index. Used as a diagnostic of whether a high residual in the plusgroup is problematic. Only plots years for which there are observed age data.

pbs-assess/ggmse documentation built on Nov. 21, 2023, 8:06 p.m.