Explore and process PacFIN bds

[chantelwetzel-noaa]

Data questions that should be explored for PacFIN bds data:

Pre-data cleaning:

• Examine the ageing methods in the data (AGE_METHOD1, AGE_METHOD2, ...) to determine what ageing methods should be removed from the data and retained.
• Examine the prevalence of ages where the age method is NA or blank. Early data looks flagged that a number of ages from Oregon were not present in the early years of the data. Compare the age-at-length of fish without an ageing method to those with to determine if these ages look fundamentally different.
• Are there a number of Oregon samples with SAMPLE_TYPE == "S"? These samples should be kept, if possible, and not removed when applying PacFIN.Utilities::cleanPacFIN().

Post-data cleaning:

• Double-check the removed samples to ensure that all the requested ageing methods and sample types were retained.
• Look at the distribution of length and age samples by gear type before grouping. The model will likely use either a trawl, hook-and-line, pot or trawl and fixed gear fleet structure.
• Examine the distribution of length and age samples by port to identify areas that may have unrepresentative sampling. An example from the 2021 Dover sole assessment: length samples and age samples by port.

Data processing:

• Start from the vignette provided in PacFIN.Utilities that is based on sablefish.