WIP: modeling #1
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- Small changes to adapt to POMP 2.0+ - Finished Parameter estimation script - Determininstic R0 fits
- Adding MPI packages - Adding Pomp, etc.
- Now pulling data from new CSV
- Added script for cluster run - Hopefully a fix for parallel issue
- R0 and k deterministic estimates from cluster - shell script was not correctly formatted
- Changing model to reflect 0.67 case fatality ratio
Some preliminary results from attempting to estimate R0
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Most of the code has been translated/updated.
R0, k estimation script tested working on Linux (FORK, MPI) and Win 10 (PSOCK). Seeming lack of scaling on MPI compared to FORK, but may be due to internal setup within the CDC HPC. |
StatusWas working on the forecasting end but that's been stalled for the time being. Finally found some regional denomonator data (thanks @cliu822). Now thinking of ways to extend this mass action model to include variable interaction between regions where reliable mixing rates are not known apriori. A good starting place might just be looking at queen neighbors and computing a naive weighted distance and construct a WAIFW matrix from there. 🤷♂ |
- Also updating shell script
- Now using util.R - Shell script with LF line endings to avoid UNIX issues, 48 core SMP pe
- Using R module
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What
Found some decent code from the West Africa Ebola outbreak which was use for simulations and parameter estimations that I could retool for the current DRC outbreak.
TODO