PlotOutputFn: Plot output

In nwfsc-assess/nwfscAgeingError: Source Code for Punt et al. (2008): Ageing Error and Imprecision

Plot output

Description

Plots age comparisons and results from the fitted model. Comparisons must be conditioned on a true age that is not observed. And, in place of a true age, the diagnostic plots generally condition on an estimated age, which is fixed as the mode of the conditional probability at age for each otolith.

Usage

PlotOutputFn(
  Data,
  MaxAge,
  SaveFile,
  PlotType = c("PNG", "PDF"),
  subplot = 1:3,
  ReaderNames = NULL,
  ...
)

Arguments

Data	This is the data set with the first column being an integer providing the number of otoliths that are included in the row and the subsequent columns are the reader or lab estimated ag,e where each reader/lab has a unique reading error and bias. The modeling framework allows for, at most, 15 readers, i.e., 16 columns. There should not be any identical rows in the data frame because otoliths that have the exact same read from every reader/lab should be combined into a single row with the count as the first column. If you failed to combine identical rows prior to running the model, you will be alerted with an error and the XXX.rep file will have a properly formatted data which can be' cut-pasted into a XXX.dat file for use. Missing reads from a given reader/lab should be entered as -999. Order your reader/lab columns such that similar readers/labs are located next to one another because columns to the right can mirror columns to their immediate left in terms of parameter estimates.
MaxAge	An integer, specifying the maximum possible "true" age.
SaveFile	Directory where agemat.exe is located and where all ADMB intermediate and output files should be located. If AdmbFile is specified then agemat.exe is copied from that directory to SaveFile.
PlotType	A string specifying the type of saved plots that you desire. The default is to save .png files via an argument of "PNG". The other option is to save .pdf files via "PDF".
subplot	Vector of integers specifying which plots to create. The default is to create three plots.
ReaderNames	Vector with names of each reader, defaults to "Reader 1", "Reader 2", etc.
...	Additional arguments passed to ageing_comparison().

Details

1. Error and bias by reader/lab: A panel graph is provided where each panel shows the expected and standard deviation in age reads for that reader/lab. This is displayed against a scatter plot of the read and estimated ages for each otolith that was read by that reader/lab.

2. Proportion-at-age histogram: The estimated proportion at age can be plotted as a histogram and is displayed against the observed distribution of read ages. This is useful to determine if hte estimated proportion at age is generally plausible, e.g., whether it has too many ages where the estimated proportion at age approaches zero, which is unlikely in a composite sample with moderate effective sample sizes. This plot can also be used as a diagnostic to confirm that AIC has selected reasonable values for the MinusAge and PlusAge parameters.

The function will read in XXX.rep and XXX.par files that are located in SaveFile.

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.

See Also

• RunFn()

• StepwiseFn()

nwfsc-assess/nwfscAgeingError documentation built on Sept. 24, 2023, 10:19 a.m.