This Repository documents changes made to the Age-structured Model for Alaska herring stocks, VERSION 0.1, Jan 2015. The authors of the assessment are Sherri Dressel, Sara Miller, and Kray Van Kirk. The code in VERSION 0.1 was developed by Peter Hulson pete.hulson@noaa.gov .
You can obtain the source code via cloning this project using Git, or you may also download a zip file with the latest code.
Go to the Github code repository for Ham, and click on the Clone or download button.
I would recommend using Git and Github, as they serve as valuable tools for version control, and tracking code changes over time. Its perfectly fine to just download the zip file; however, using Git is far more efficient for incorporating code changes and working in groups.
The R-scripts directory has two important files: 1. modelList.txt 2. R4HAM.R
The modelList.txt file is a list of models that R4HAM.R will read into R.
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Improve Numerical Stability:
- Parameter transformations to log-space
- Design matrix for estimated parameters (ival, lb, ub, phz, bayes)
- Develop option to condition the model on F and fit to catch.
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Code reorganization:
- HEAD::initializeModelParameters
- BIOL::initializeAgeSchedule
- BIOL::getNaturalMortality
- OBSM::getSelex
- BIOL::initializeStateVariables
- BIOL::updateStateVariables
- BIOL::calcSpawningStockRecruitment
- OBSM::calcAgeCompResiduals
- OBSM::calcEggMiledaySurveyResiduals
- OBSM::catchObservationModel
- STAT::calcObjectiveFunction
- STAT::penaltyFunctions
- STAT::negativeLogLikelihoods
- STAT::constraintFunctions
- STAT::calculateDIC
- FORE::runForecast
- FORE::ghlCalc
- FORE::calcTAC
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Control file reorganization
- add design matrix to control parameter bounds and phases.
- add contrls for time varying maturity
- add contrls for time varying natural mortality rate deviations.
- add design matrix for selectivity parameter controls.
- add Miscellaneous controls for appending.
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Simulation model:
- Add command line argument to turn on simulation model.
- Add FUNCTION runSimulationModel
- Get and use True Parameter values
- Generate random variables | random number seed.
- Population dynamics conditioned on catch & S-R curve.
- Cache observation model results into data variables.
- Add observation errors.
- Allow Alaska Herring Assessment to continue with parameter estimation.
Last updated: June 2020
setting value
version R version 3.5.3 (2019-03-11)
os Windows >= 8 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Anchorage
date 2020-06-11
- Packages -------------------------------------------------------------------------------------------
package * version date lib source
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[1] C:/Users/jysullivan/Documents/R/win-library/3.5
[2] C:/Users/jysullivan/Documents/R/R-3.5.3/library