Length based model 202204 #386
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CHG: kLength::selectivities to use midpoints ADD: BH recruitment for length ADD: instantanesous mortality for length model
FIX: BH recruitment ADD: modelrunner test CHG: usermanual
ADD: Tagging length based process ADD: Category transition for length based UPD: user manual
Add unit test for Biomass-length based
…ING() is encountered
Users either choose to get Casal2 to sum proportions = 1 or keep them as is and Casal2 will flag a warning if they don't sum = 1
FIX: tag recapture and proportions mature obseravtions
FIX: reset call so growth gets updated
DEL: expand categories call should be done by config loader
Some model runners will get complex to get high precision objs across minimiser we willl require extensive estimation time. To avoid this set a lower tolerance and make sure minimisers get 'close' without taking a long time.
Some observation classes have different error tables or none at all.
These are depreciated and now handled by the r4Casal2 R package found here https://github.com/NIWAFisheriesModelling/Casal2_contrib/tree/main/r4Casal2
To replicate CASAL ratio qs penalty
Nuisance Q's need a prior. If a Q parameter is used in a ratio additional prior this caused an error. This accessor ignores additional prior types of ratio for the nuisance q class
CHG: disease mortality definition UPD: R package to read in selectivityby year report UPD: length based processes
ADD: compound selectivities
This needs to be done for age based methods as well. Sum to one needs to change the expected values.
ADD: growth verification MOVE: methods to be protected.
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ADD: length based functionality for Casal2 with observations, processes and unit tests.
CHG Manual from one to and Age and Length manual.