Open kellijohnson-NOAA opened 1 year ago
I didn't realize that PacFIN.Utilities::checkLenAge()
existed because the example {PacFIN.Utilities} script that @chantelwetzel-noaa provided uses nwfscSurvey::est_growth()
to estimate von Bertalanffy growth curve and flag outliers (adapted for Petrale here: https://github.com/pfmc-assessments/petrale/blob/main/R/process_pacfin_bds.R#L149-L167).
Therefore, one potential solution would be to just remove PacFIN.Utilities::checkLenAge()
(or initially deprecate but not require {knitr}) and rely on the {nwfscSurvey} version instead, similar to the plan proposed in https://github.com/pfmc-assessments/nwfscSurvey/issues/110 for weight-length estimation.
Given that we are mid-assessment season, I worried about getting rid of the PacFIN.Utilities::checkLenAge()
could interrupt users workflow so opted to have duplication for the time being. However, if we wanted to clean things up we could call the nwfscSurvey::est_growth()
from within the PacFIN.Utilities::checkLenAge()
.
I will make sure to keep it ... and it already calls the same fit
function that nwfscSurvey::est_growth()
calls so basically the only differences are formatting of the output.
{knitr} is a suggests not an import and yet this table function in
checkLenAge()
uses {knitr}. I will try to find some other way to summarize the information.https://github.com/pfmc-assessments/PacFIN.Utilities/blob/a067169fbca82ca51abc668a58b748a51620eb0d/R/checkLenAge.R#L163