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