covid19-bayes-model-run.sh

#!/bin/bash

# call form:
# sh run.sh <stan_model> \
#   <minimumDeaths> \
#   <nIterations> \
#   (-stateList | -batch) \
#   (<stateList> | <batchID>) \
#   [--validate]

# example calls:
## sh run.sh us_mobility 150 200 -stateList "Illinois,NewYork"
## sh run.sh us_mobility 150 200 -stateList "Illinois,NewYork" --validate
## sh run.sh us_mobility 150 200 -stateList "all"
## sh run.sh us_mobility 150 200 -batch 1

set -e

echo "\n--- running input ETL and model with these parameters ---"
echo 'stanModel = '         $1
echo 'minimumDeaths = '     $2
echo 'mcmcIterations = '    $3
echo 'countySelector = '    $4
echo 'selectorValue = '     $5
echo 'validationFlag = '    $6

# run the etl to generate all input tables
echo "\n- Input ETL -"
cd py
python3 etl.py

## MOBILITY DATA
echo "\n- Fetch Mobility Data  -"
cd ../modelInput/mobility/
wget -O Global_Mobility_Report.csv --no-verbose https://www.gstatic.com/covid19/mobility/Global_Mobility_Report.csv
cd ./visit-data/
sh get-visit-data.sh
cd ../../../r
Rscript mobility-regression.r

# run the model via R script
echo "\n- Model Run -"
# cd ../r
Rscript base.r $1 $2 $3 $4 $5 $6

cd ..

echo "\n- Routine Completed -\n"