New age specific mortality files
After updating to the latest in the repository, anyone using Atlantis will now find some extra output files, specifically
- SpecificMort.txt - this reports the non-predation, predation and fishing mortality per age class per stock for each group through time. With the format of the column headers being
group-cohort-stock-mortality type
where
M1 = mortality due to mL, mQ etc
M2 = predation mortality
F = fishing mortality
This follows the US stock assessment convention regarding the definition of natural mortality types. Stock refers to genetic stock
- SpecificPredMort.txt - this reports the predation mortality per cohort, per stock per predator for each group through time. With the format of the column headers in this case being
group-cohort-stock-predator-M2
These files effectively replace MortPerPred (which will eventually be retired). That old file was indicative (and potentially confusing) while the new file is the actual mortality experienced.
These new files can be quite large (!!) and so will need to be post-processed in R. Asta has donated some scripts she uses for anyone who might like a start script to modify (you will obviously need to modify species codes etc). The scripts can be found here (check attachments if the link is broken)