Open chantelwetzel-noaa opened 3 weeks ago
@paulburch has volunteered to expand the vignette to include more information about these things.
There is some documentation of the inputs in the old RunFn() which has not been updated to work with the TMB version: https://github.com/pfmc-assessments/AgeingError/blob/main/R/RunFn.R. In that function which applied to the ADMB version of the package, the quantities in the data file were documented as follows
MinusAge
have "true" proportion-at-age estimated as \deqn{Pa = P{MinusAge}exp^{(\beta(MinusAge - a))}}, where beta is an estimated log-linear trend in the "true" proportion-at-age. If MinusAge
= MinAge
, beta is not estimated.MinusAge
except defining the age above with age-specific age composition is not estimated.
I could not find instructions on how to format the needed data file for
CreateData()
. I found the attached package examples in the exdata file, but more guidance should be given to the user. For example:Range_of_ages
andData_set_
are used to read the data file, so the text labeling needs is exact.range_of_ages
and the minus and plus group? I have an idea since I have used previous versions of this package but this information is not included in the vignette for a new user.Additionally, the function description is insufficient for for
CreateData()
. It was unclear to me at first what this function was doing since the user needed to provide a formatted data file.