plot_TS: Plots the median and quantiles of a time-series

In openMSE: Easily Install and Load the 'openMSE' Packages

Plots the median and quantiles of a time-series

Description

Plots the median and quantiles of a time-series

Usage

plot_TS(
  x,
  xlab = "Year",
  ylab = "Spawning Biomass",
  title = "",
  quantiles = c(0.025, 0.975),
  scale = NULL,
  alpha = 0.1,
  lwd = 1,
  use_theme = NULL,
  colpalette = "Dark2",
  facet = TRUE,
  inc.Legend = !facet,
  inc.Hist = FALSE,
  print = TRUE,
  get_function = get_SSB,
  years = NULL,
  ...
)

plot_SSB(x, ...)

plot_Biomass(x, ylab = "Biomass", ...)

plot_Landings(x, ylab = "Landings", ...)

plot_Removals(x, ylab = "Removals", ...)

plot_Recruits(x, ylab = "Recruits", ...)

plot_F(x, ylab = "Fishing Mortality (F)", ...)

plot_LifeHistory(
  x,
  xlab = "Year",
  ylab = "Median (quantiles)",
  title = "",
  quantiles = c(0.025, 0.975),
  scale = NULL,
  alpha = 0.1,
  lwd = 1,
  use_theme = NULL,
  colpalette = "Dark2",
  facet = TRUE,
  inc.Legend = !facet,
  inc.Hist = FALSE,
  print = TRUE
)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
xlab	X-axis label (default 'Year')
ylab	Y-axes label
title	Optional title
quantiles	Lower and upper quantiles to calculate. Numeric vector of length 2.
scale	An optional function with a single numeric argument that returns transformed or scaled numeric values. See lb2kg and kg2lb for example. Can be a list of functions for list objects (NA for no transformation)
alpha	Transparency parameter
lwd	Line width
use_theme	Optional ggplot theme
colpalette	Color palette from RColorBrewer
facet	Logical. Facet the plot?
inc.Legend	Logical. Include legend?
inc.Hist	Logical. For MSE results, include the historical period?
print	Logical. Print the plot?
get_function	get_ function to extract time-series information from x
years	Optional numeric vector specifying the years to plot. Default is all years.
...	Named arguments passed to plot_TS

Value

A named list with:

p	The ggplot object
df	Data.frame with the summary statistics (median and quantiles)

Functions

• plot_SSB(): Plot the Spawning Biomass

• plot_Biomass(): Plot the Total Biomass

• plot_Landings(): Plot the Landings (biomass)

• plot_Removals(): Plot the Removals (biomass)

• plot_Recruits(): Plot the Recruits (numbers)

• plot_F(): Plot the Recruits (numbers)

• plot_LifeHistory(): Plot the Life-History parameters

openMSE documentation built on Sept. 30, 2024, 9:32 a.m.