ADD fishing mortality process, plus improvements 202207 #400
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MVE: the report execute for kInitialisation from model.cpp to the initialisation manger so we can print reports after each initialsation phase. CHG: child method from Execute -> DoExecute. This allowed me to pass the model pointer to the Execute(class) so that the manager could use the model to execute the reports. ADD: a check if we have scaled the partition for B0 models. For multiple initialisation phases we were re-scaling each phase which was an error.
ADD: check for logistic transformation if value at bounds
UPD: user-manual
ADD: log info for iterative initialisation when converged
…ion file will enter the objective function. If it isn't flagged it will report 0
…rmations This will stop or warn users if they try and do multiple uses with the same parameters. It is unknown what would happen if a user tryies to transform a parameter and time-vary it at the same time. We want to prevent this.
UPD: timevary report to have a standard label for the dataframe. Makes accessing it in R a lot easier.
…ld rather than Reset
.sh scripts need to be updated so it can be on linux
CHG: category loop for calculating catch at age values was poorly written. DEL: m pointer from the fishery struct.
accidently added to previous commit
ADD: MortalityHybrid process UPD: manual
…_process Now we have multiple mortality processes this will generalise the mortality specific observation classes rather than being bespoke for only instantaneous_mortality. ADD: MortalityHybrid test model
UPD: TwoSexHybrid test model assert
Craig44
changed the title
UPD: manual for mortality hybrid
…from Samik Datta and Vidette McGregor
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ADD:
initialisation_mortality_baranovprocess with unittestADD:
mortality_hybridprocess (#250) that follows the recommended option in stock synthesis.ADD: Mortality class in the process hierarchy. This was done to generalise mortality specific observations. Previously we had to dynamic cast specific mortality processes. By adding an in-between class we can have an mortality observation access multiple mortality process types.
CHG: report execute during intialisation from Model.cpp to InitialisationPhases/Manager.cpp. This will allow us to report quantities in between initialisation phases.
FIX: profiling with multiple same parameters
Solve issue #389
DEL: TestModel output from repository add to gitignore so they are not included in future commits.
FIX: AdressableTransformations (parameter transformations) when addressable is a vector. indexing starts at 1 (R-style) but was defaulting to C++ causing an misspecifed index.
UPD: usermanual
ADD: Test Case for SCI #399 using simulated data