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Plots age comparisons and results from the fitted Ageing Error model

Usage

plot_output(
  Data,
  IDataSet,
  MaxAge,
  Report,
  subplot = 1:3,
  Nparameters = 0,
  LogLike = 0,
  ReaderNames = NULL,
  Species = "AgeingError",
  SaveDir = getwd(),
  verbose = FALSE,
  ...
)

Arguments

Data

Input data matrix

IDataSet

Index of the data set used in creating the filename

MaxAge

Maximum estimated age

Report

Results from fitting the model

subplot

Vector of which plots to create.

Nparameters

Number of parameters

LogLike

Negative log likelihood from fitting the model

ReaderNames

Vector with names of each reader, defaults to 'Reader1', 'Reader2', etc. if left at the default argument of NULL. If you pass a vector of strings, the vector must be the same length as NCOL(Data) - 1.

Species

String used at beginning of the output files

SaveDir

Directory for fitted model

verbose

Report messages as function runs.

...

Additional arguments passed to ageing_comparison().

Value

Returns AIC, AICc, and BIC for fitted model.

References

Punt, A.E., Smith, D.C., KrusicGolub, K., and Robertson, S. 2008. Quantifying age-reading error for use in fisheries stock assessments, with application to species in Australias southern and eastern scalefish and shark fishery. Can. J. Fish. Aquat. Sci. 65: 1991-2005.

Author

James T. Thorson, Ian G. Taylor