plot.Stock: Plot Operating Model Object

In DLMtool/DLMtool: Data-Limited Methods Toolkit

Description

Generate HTML reports with plots of operating model components ("Stock", "Fleet", "Obs", and "Imp"), the historical simulations ("Hist"), or the complete OM ("OM").

The individual component plots of objects of class Stock and Fleet can also be generated by using the generic plot.pars function. See Examples below.

Usage

## S3 method for class 'pars'
plot(
  x,
  Object,
  Stock = NULL,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

## S3 method for class 'Stock'
plot(
  x,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

## S3 method for class 'Fleet'
plot(
  x,
  Stock = NULL,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

## S3 method for class 'Obs'
plot(
  x,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

## S3 method for class 'Imp'
plot(
  x,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

## S3 method for class 'Hist'
plot(
  x,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

## S3 method for class 'OM'
plot(
  x,
  nsamp = 3,
  nsim = 200,
  nyears = 50,
  proyears = 28,
  output_file = NULL,
  output_dir = getwd(),
  quiet = TRUE,
  tabs = TRUE,
  title = NULL,
  date = NULL,
  plotPars = NULL,
  open = TRUE,
  dev = FALSE,
  ...
)

Arguments

x	An object of class Stock, Fleet, Obs, Imp, Hist, or OM, OR one of the following character strings for Object of class Stock: "M", "Growth", "Maturity", "Recruitment", "Spatial", or "Depletion" and for Object of class Fleet: "Effort", "Catchability", "MPA", and "Selectivity".
Object	An object of class Stock or Fleet
Stock	An object of class Stock required for Fleet parameters
nsamp	The number of random samples to show in the plot
nsim	The number of simulations (only used for objects not of class OM)
nyears	The number of historical years (only used for objects not of class OM)
proyears	The number of projection years (only used for objects not of class OM)
output_file	Name of the output html file (without file extension)
output_dir	Output directory. Defaults to getwd()
quiet	An option to suppress printing of the pandoc command line
tabs	Include tabs in the HTML file?
title	Optional title for the markdown report
date	Optional date for the markdown report
plotPars	A named list with options for plots: breaks - numeric. Number of breaks in histograms. col - character. Color of histograms. axes - logical. Include axes in histogram? cex.main - numeric. Size of main title in plots. lwd - numeric. Line width for time-series plots.
open	Logical. Open the html file?
dev	Logical. For development use only.
...	Not used

Examples

## Not run: 
# Plot Stock Object:
Stock <- DLMtool::Albacore
plot(Stock)

# Individual plots:
plot("M", Stock)
plot("Growth", Stock)
plot("Maturity", Stock)
plot("Recruitment", Stock)
plot("Spatial", Stock)
plot("Depletion", Stock)

# Plot Fleet Object
Fleet <- DLMtool::Generic_DecE
plot(Fleet, Stock)

# Individual plots:
plot("Effort", Fleet, Stock)
plot("Catchability", Fleet, Stock)
plot("MPA", Fleet, Stock)
plot("Selectivity", Fleet, Stock)


# Plot Obs Object
Obs <- DLMtool::Imprecise_Unbiased
plot(Obs)

# Plot Imp Object
Imp <- DLMtool::Overages
plot(Imp)


# Plot Hist Object
OM <- DLMtool::testOM 
Hist <- runMSE(OM, Hist=TRUE)
plot(Hist)

# Plot OM Object
plot(OM)

## End(Not run)

DLMtool/DLMtool documentation built on June 20, 2021, 5:20 p.m.