Provide guidance on the formatting and structure of the dat file

[chantelwetzel-noaa]

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:

1. The labeling of Range_of_ages and Data_set_ are used to read the data file, so the text labeling needs is exact.
2. What is the difference between the 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.
3. The matrix of data with the counts and the age read by reader needs to be described clearly for the 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.

[iantaylor-NOAA]

@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

• range of ages: The minimum and maximum possible "true" age.
• minus group: The minimum age for which an age-specific age-composition is estimated. Ages below MinusAge have "true" proportion-at-age estimated as \deqn{P_a = 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.
• plus group: Identical to MinusAge except defining the age above with age-specific age composition is not estimated.
• reference age: an arbitrarily chosen age from which "true" age-composition fixed-effects are calculated as an offset. This has no effect on the answer but could potentially impact the estimation speed.