Open darcyrao opened 5 years ago
Changes to the scripts
mainCalibrated.m
slurm_mainCalibrated.sbatch
In simVaxCEA2.m:
slurm_simVaxCEA2.sbatch
echo "${AGESCRN}"
export AGESCRN
echo "${SCRNALG}"
export SCRNALG
Make a new script called OptAge.sh (type vi OptAge.sh)
echo "Running simulations"
for AGESCRN in $(seq 21 5 51); do # to loop through ages 20 - 50 in 5yr increments
for SCRNALG in $(seq 1 1 2); do #to loop through pap and HPV testing
export AGESCRN
export SCRNALG
sbatch -p csde -A scde slurm_simVaxCEA2.sbatch
done
done
Then in command line just type sh OptAge.sh
and it will run all scenarios
To export results:
scp dpwhite@mox.hyak.uw.edu:/gscratch/csde/dpwhite/HHCoM/HHCoM_Results/Folder/*.mat .
But replace "Folder" with the relevant folder. REVISED CHANGES WITHOUT THE FUNCTION (IT WAS CAUSING SOME ISSUES)
The changes to mainCalibrated are as indicated above. For SimVaxCEA2:
pathModifier = ['090519__scrnscenario' ;
and change the if ~exist([.... part to create a folder in '/HHCoM_Results/OptimalAge'
baseline.screenAge = AgeScrn;
Then, each time I run it for the different scenario, change the pathModifier, the screenAlgorithm, and/or the AgeScrn and submit the job (wait until it starts running to make changes and submit the next one)
Skip the step about creating .sh file.
Follow the same instructions to export the results.
REVISED SCENARIOS AND SCRIPT CHANGE INSTRUCTIONS
Historical (up to 2020):
Intervention scenarios:
Outcomes:
Changes to the code, if editing a master branch. Otherwise, see below to make scenario-specific modifications, run analyses, and process outcomes using the OptScrnAge branch
git checkout [master]
then run git checkout -b OptScrnAge
screenAlgorithm = 3':
ScrnAges = [ #]and
ScrnAgeMults = [0.2];. Then, around line 137, above where the code defines
% HIV-positive screening ages`, past the below code:
% Screening ages
cyt0.screenAge = ScrnAges;
cytgen.screenAge = ScrnAges;
hpvgen.screenAge = ScrnAges;
cyt0.screenAgeMults = ScrnAgeMults; cytgen.screenAgeMults = ScrnAgeMults; hpvgen.screenAgeMults = ScrnAgeMults;
- Make changes to the slurm scripts to use my username and email address.
**To run the scenarios**
- Run historicalSim.m and change the filepath to where and what I want to save the file as.
- Run the futureSim.m file with the following changes:
- Update the pathmodifier for the historical sim
- Define a new file name for the relevant scenario
- In the screening section, set the screenAlgorithm to 3 if running cytology or 5 for HPV screening. Set the ScrnAges to a number 5-14 for age groups 20-24 through 65-69. Make sure hivPosScreen = 0.
- If running the no screening scenario, set the screenAlgorithm to 2 (cyt0) and ScrnAges to [1] (this will screen 0-4 year-olds, as a safeguard in case the coverage set in the cyt0 algorithm doesn't work...)
- In the vaccination scenario, set to 57% ages 9-14 (age groups 2,3). For comparator, could do 90%. Make sure vaxCU etc are all set to 0.
- Submit the jobs through mox as indicated in issue #55
- Export and process results as indicated in issue #55. A key difference with the export results script in Matlab is that we will not be saving HIV prevalence, and for this analysis we are defining crude incidence and mortality rates for ages 3 : age. We also don't need to save CC counts so ignore that. Change the directory names and filepaths to store results in the OptimalAge folder.
Historical (up to 2020):
Intervention scenarios:
Outcomes: