Methods for Creating, Accessing and Assigning Kobe objects

The Kobe function is used both to create and modify an Kobe-class() object. and to access and assign Kobe for an object of class Slick-class(). See Details.

Usage

Kobe(
  Code = "",
  Label = "",
  Description = "",
  Time = numeric(),
  TimeLab = "Year",
  Value = array(),
  Preset = list(),
  Target = 1,
  Limit = NULL,
  Defaults = list(),
  TimeTerminal = numeric(),
  Misc = list()
)

Kobe(Slick) <- value

# S4 method for class 'missing'
Kobe()

# S4 method for class 'character'
Kobe(
  Code = "",
  Label = "",
  Description = "",
  Time = numeric(),
  TimeLab = "Year",
  Value = array(),
  Preset = list(),
  Target = 1,
  Limit = NULL,
  Defaults = list(),
  TimeTerminal = numeric(),
  Misc = list()
)

# S4 method for class 'list'
Kobe(
  Code = "",
  Label = "",
  Description = "",
  Time = numeric(),
  TimeLab = "Year",
  Value = array(),
  Preset = list(),
  Target = 1,
  Limit = NULL,
  Defaults = list(),
  TimeTerminal = numeric(),
  Misc = list()
)

# S4 method for class 'Slick'
Kobe(Code)

# S4 method for class 'Slick'
Kobe(Slick) <- value

Arguments

Code: A short code for the Performance Indicators for this object. A character string length nPI or a named list for multi-language support. See Details
Label: A short label for the Performance Indicators for this object. Used to label axes on charts. Can be longer than Code but recommended to keep short as possible so it shows clearly in plots and tables. A character string length nPI or a named list for multi-language support. See Details
Description: A description for the Performance Indicators for this object. Can include Markdown, see Examples. A character string length nPI or a named list for multi-language support. See Details
Time: A numeric vector with values for the projection time-steps. Must match length nTS in Value
TimeLab: Character string length 1. Name of the time step (e.g., 'Year'). Will be used as the label in the Kobe Time plot. Use a named list for multiple languages.
Value: A numeric array with the stochastic performance indicator values for each simulation (sim), operating model (OM), management procedure (MP), performance indicator (PI), and projection time-steps (nTS). Dimensions: c(nsim, nOM, nMP, nPI, nTS)
Preset: An optional named list for the preset buttons in the App(). The name of the list element will appear as a button in the App().
Target: Numeric vector length nPI with the target value for the PIs. Defines the color quadrants on the Kobe plot. Defaults to c(1,1).
Limit: Numeric vector length nPI with the limit value for the PIs. Shows as red line on Kobe plot. NULL to ignore.
Defaults: A list object with default selections for the Kobe See Kobe()
TimeTerminal: Optional. By default the Kobe plot shows the terminal projection year. TimeTerminal can be used to override this. Use a numeric value indicating the time (must match a value in Time) to use for the Kobe plot
Misc: A named list for additional miscellaneous information.
Slick: A Slick-class() object
value: A Kobe-class() object

Details

Objects of class Kobe are created with Kobe()

The Kobe plot typically shows B/BMSY (or something similar) on the x-axis, and F/FMSY (or something similar) on the y-axis.

Performance Indicators

The first PI will be on the x-axis (usually B/BMSY or something similar) and the second on the y-axis (e.g., F/FMSY)

Multi-Language Support

Text with multi-language supported can be provided as a named list. Available languages:

en: English (default)
es: Spanish
fr: French

Note

Character strings in Code, Label, and Description must all be same length as the number of performance indicators (nPIs) in Value

Functions

Kobe(missing): Create an empty Kobe object
Kobe(character): Create a populated Kobe object
Kobe(list): Create a populated Kobe object
Kobe(Slick): Return Kobe from a Slick-class() object
Kobe(Slick) <- value: Assign a Kobe-class() object to a Slick-class() object

Examples

# Generate dummy values
nsim <- 10
nOM <- 2
nMP <- 4
nPI <- 2
nTS <- 30

values <- array(NA, dim=c(nsim, nOM, nMP, nPI, nTS))

pi_means <- c(1,1)

for (om in 1:nOM) {
  for (mp in 1:nMP) {
    for (pi in 1:nPI) {
      values[,om, mp, pi,] <- pi_means[pi] *
        matrix(
        cumprod(c(rlnorm(nTS*nsim, 0, 0.05))),
        nrow=nsim)
    }
  }
}

# Create and populate Object
kobe <- Kobe(Code=c('B/BMSY', 'F/FMSY'),
             Label=c('B/BMSY',
                     'F/FMSY'),
             Description = c('This is the description for PI 1',
                             'This is the description for PI 2'),
             Value=values
)

# Add values for projection time steps
Time(kobe) <- seq(2025, by=1, length.out=nTS)

# Check
Check(kobe)
#> 
#> ── Checking: "Kobe" ──
#> 
#> ✔ Complete

# Add to `Slick` object
slick <- Slick()
Kobe(slick) <- kobe

# Plots
plotKobe(slick)
#> Error in plotKobe(slick): object 'nMP' not found

plotKobe(slick, Time=TRUE)
#> Error in plotKobe(slick, Time = TRUE): object 'nMP' not found

Methods for Creating, Accessing and Assigning `Kobe` objects