plot_rcm: Plotting functions from OM conditioning

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

Plotting functions from OM conditioning

Description

A set of functions that plots output from a list of RCModel objects used to condition a set of operating models.

Usage

plot_rcm_SSB(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  scales = "fixed",
  ylim = NULL,
  MPD = FALSE
)

plot_rcm_SSBMSY(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  scales = "fixed",
  histogram = FALSE,
  bins = NULL,
  MPD = FALSE
)

plot_rcm_depletion(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  scales = "fixed",
  histogram = FALSE,
  bins = NULL,
  MPD = FALSE
)

plot_rcm_F(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  scales = "fixed",
  ylim = NULL,
  MPD = FALSE
)

plot_rcm_FMSY(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  scales = "fixed",
  ylim = NULL,
  MPD = FALSE
)

plot_rcm_recdev(
  rcm,
  scenario,
  french = FALSE,
  proj = FALSE,
  logspace = FALSE,
  scales = "fixed",
  ylim = NULL,
  MPD = FALSE
)

plot_rcm_rec(
  rcm,
  scenario,
  french = FALSE,
  scales = "fixed",
  ylim = NULL,
  MPD = FALSE
)

plot_rcm_bio_sel(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  french = FALSE,
  bio_type = c("LAA", "mat"),
  sel_type = c("fleet", "index"),
  sel_i = 1,
  sel_name = "Selectivity"
)

plot_rcm_sel(
  rcm,
  scenario,
  type = c("fleet", "index"),
  i = "all",
  color = "black",
  french = FALSE,
  MPD = FALSE
)

plot_rcm_sel_multi(
  rcm,
  scenario = paste("Scenario", 1:length(rcm)),
  fleet_i = 1,
  index_i = 1,
  fleet_names = paste("Fleet", fleet_i),
  index_names = paste("Index", index_i),
  french = FALSE,
  color
)

plot_rcm_corr(
  rcm,
  scenario,
  var = c("D", "M", "h", "R0"),
  status = TRUE,
  bins = NULL,
  do_corr = FALSE,
  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.
scales	The scales argument to facet_wrap.
ylim	Optional y-axes limits to figures.
MPD	Logical, whether to plot individual simulations (FALSE) or from the single fit (TRUE) in RCModel@mean_fit.
histogram	Logical, whether to show a histogram (TRUE) for the terminal year only. Otherwise, a time series plot.
bins	The number of bins for geom_histogram.
proj	Logical, whether to plot the recruitment deviates in the projection period
logspace	Logical, whether to plot the recruitment deviates in logspace or normal space
bio_type	Character vector to plot either length-at-age ("LAA") or maturity-at-age ("mat")
sel_type	Character to indicate whether to grab a fleet or index selectivity
sel_i	The index of the fleet or index for the selectivity
sel_name	The name for the selectivity
type	Whether the output is from a fishing fleet or index.
i	The corresponding index from the fleet or index of abundance.
color	Character vector of colors used for plotting.
fleet_i	Vectors of indices for the fleets, i.e., 1 is the first fleet, etc. Use NA if no fleets will be plotted.
index_i	Vectors of indices for the indices of abundance. Use NA if no indices will be plotted.
fleet_names	Character vector for the names of the fleets
index_names	Character vector for the names of the indices
var	Parameters to plot. Select up to two.
status	Logical, whether to identify estimated status with each point in scatter plot. Only used if two parameters are selected in var.
do_corr	Whether to report the correlation between parameters. Only used if two parameters are selected in var.

Functions

• plot_rcm_SSB(): Plot historical SSB

• plot_rcm_SSBMSY(): Plot SSB/SSBMSY

• plot_rcm_depletion(): Plot historical spawning depletion

• plot_rcm_F(): Plot historical apical F

• plot_rcm_FMSY(): Plot historical F/FMSY

• plot_rcm_recdev(): Plot recruitment deviates

• plot_rcm_rec(): Plot recruitment

• plot_rcm_bio_sel(): Compare maturity and length-at-age schedule vs. selectivity (of a single index or fleet)

• plot_rcm_sel(): Plot selectivity of a single index or fleet (all simulations)

• plot_rcm_sel_multi(): Plot selectivity of a multiple indices or fleets overlayed on top of each other

• plot_rcm_corr(): Plot histogram or scatter plot of operating model parameters

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