plot_output: Plot output

In nwfsc-assess/nwfscAgeingError: Estimating ageing error with 'TMB' from double reads

Plot output

Description

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.

Author(s)

James T. Thorson, Ian G. Taylor

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.

nwfsc-assess/nwfscAgeingError documentation built on July 4, 2025, 9:49 a.m.