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Merge pull request #17 from InstituteforDiseaseModeling/rtd
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Updated scenarios to break apart disease-specific sims from transmission-layer sims, version 2.20
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@lmgeorge
lmgeorge authored Sep 10, 2020
2 parents 2b78d7e + d7ddc34 commit 7a20f0f
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Showing 450 changed files with 1,507 additions and 1,901 deletions.
0 ...Typhoid/EnvironmentalDiagnostic/README.md → ...nmental/EnvironmentalDiagnostic/README.md
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0 ...oid/EnvironmentalDiagnostic/campaign.json → ...tal/EnvironmentalDiagnostic/campaign.json
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1 change: 0 additions & 1 deletion ...phoid/EnvironmentalDiagnostic/config.json → ...ental/EnvironmentalDiagnostic/config.json
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"Enable_Default_Shedding_Function": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Initial": 1,
"Enable_Demographics_Other": 0,
"Enable_Demographics_Reporting": 1,
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2 changes: 1 addition & 1 deletion ...hoid/EnvironmentalDiagnostic/invalid.json → ...ntal/EnvironmentalDiagnostic/invalid.json
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"Metadata": {
"DateCreated": "Sun Sep 25 23:19:55 2011",
"Tool": "convertdemog.py",
"Author": "IDM",
"Author": "jsteinkraus",
"IdReference": "Gridded world grump2.5arcmin",
"NodeCount": 1,
"Resolution": 150
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4 changes: 4 additions & 0 deletions Scenarios/Environmental/EnvironmentalDiagnostic/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "EnvironmentalDiagnostic"
@ENDLOCAL
5 changes: 5 additions & 0 deletions Scenarios/Environmental/EnvironmentalDiagnostic/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotPropertyReport.py output\PropertyReportEnvironmental.json
@ENDLOCAL

2 changes: 2 additions & 0 deletions Scenarios/Environmental/EnvironmentalDiagnostic/runEmod.bat
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
0 ...ute_HINT/A_Baseline_MR-HINT/campaign.json → ...te_HINT/A_Baseline_ MR-HINT/campaign.json
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1 change: 0 additions & 1 deletion ...Route_HINT/A_Baseline_MR-HINT/config.json → ...oute_HINT/A_Baseline_ MR-HINT/config.json
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"Enable_Default_Shedding_Function": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Initial": 1,
"Enable_Demographics_Other": 0,
"Enable_Demographics_Reporting": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Environmental/Multi-Route_HINT/A_Baseline_ MR-HINT/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "Multi-Route HINT"
@ENDLOCAL
5 changes: 5 additions & 0 deletions Scenarios/Environmental/Multi-Route_HINT/A_Baseline_ MR-HINT/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotPropertyReport.py output\PropertyReportEnvironmental.json
@ENDLOCAL

2 changes: 2 additions & 0 deletions Scenarios/Environmental/Multi-Route_HINT/A_Baseline_ MR-HINT/runEmod.bat
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..\..\..\..\Eradication.exe --config config.json --input-path ..\..\..\..\Demographics_Files
@pause
0 ...HINT/B_DownTheRiver_MR-HINT/campaign.json → ...HINT/B_DownTheRiver_MR-HINT/campaign.json
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1 change: 0 additions & 1 deletion ...e_HINT/B_DownTheRiver_MR-HINT/config.json → ...e_HINT/B_DownTheRiver_MR-HINT/config.json
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"Enable_Default_Shedding_Function": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Initial": 1,
"Enable_Demographics_Other": 0,
"Enable_Demographics_Reporting": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Environmental/Multi-Route_HINT/B_DownTheRiver_MR-HINT/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "Down The River MR-HINT"
@ENDLOCAL
5 changes: 5 additions & 0 deletions Scenarios/Environmental/Multi-Route_HINT/B_DownTheRiver_MR-HINT/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotPropertyReport.py output\PropertyReportEnvironmental.json
@ENDLOCAL

2 changes: 2 additions & 0 deletions Scenarios/Environmental/Multi-Route_HINT/B_DownTheRiver_MR-HINT/runEmod.bat
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..\..\..\..\Eradication.exe --config config.json --input-path ..\..\..\..\Demographics_Files
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0 Scenarios/Typhoid/Multi-Route_HINT/README.md → .../Environmental/Multi-Route_HINT/README.md
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0 Scenarios/Typhoid/Seasonality/README.md → ...arios/Environmental/Seasonality/README.md
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0 Scenarios/Typhoid/Seasonality/campaign.json → ...s/Environmental/Seasonality/campaign.json
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1 change: 0 additions & 1 deletion Scenarios/Typhoid/Seasonality/config.json → ...ios/Environmental/Seasonality/config.json
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"Enable_Default_Shedding_Function": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Initial": 1,
"Enable_Demographics_Other": 0,
"Enable_Demographics_Reporting": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Environmental/Seasonality/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "Seasonality"
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Environmental/Seasonality/runEmod.bat
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/DensityScaling/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/DensityScaling/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "Density Scaling"
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/DensityScaling/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c I -t "Density Scaling" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/DensityScaling/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 0,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "HINT - Baseline Outbreak"
@ENDLOCAL
5 changes: 5 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotPropertyReport.py output\PropertyReport.json
@ENDLOCAL

2 changes: 2 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/runEmod.cmd
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..\..\..\..\Eradication.exe --config config.json --input-path ..\..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 0,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "HINT - Age-Targeted Vaccine"
@ENDLOCAL
5 changes: 5 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotPropertyReport.py output\PropertyReport.json
@ENDLOCAL

2 changes: 2 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/runEmod.cmd
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..\..\..\..\Eradication.exe --config config.json --input-path ..\..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 0,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "HINT - Access-Targeted Vaccine"
@ENDLOCAL
5 changes: 5 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\..\Scripts\plotPropertyReport.py output\PropertyReport.json
@ENDLOCAL

2 changes: 2 additions & 0 deletions Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/runEmod.cmd
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..\..\..\..\Eradication.exe --config config.json --input-path ..\..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/HINT_SeattleCommuting/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 1,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/HINT_SeattleCommuting/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "HINT Seattle Commuting"
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/HINT_SeattleCommuting/plotPropertyReport.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotPropertyReport.py output\PropertyReport.json -m
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/HINT_SeattleCommuting/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
2 changes: 1 addition & 1 deletion Scenarios/Generic/HINT_SeattleCommuting/script/Seattle_30arcsec_demographics.json
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"Metadata": {
"DateCreated": "Mon Sep 26 09:59:35 2011",
"Tool": "convertdemog.py",
"Author": "IDM",
"Author": "jsteinkraus",
"IdReference": "Legacy",
"NodeCount": 124
},
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2 changes: 1 addition & 1 deletion Scenarios/Generic/HINT_SeattleCommuting/script/Seattle_template.json
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"Metadata": {
"DateCreated": "Mon Sep 26 09:59:35 2011",
"Tool": "convertdemog.py",
"Author": "IDM",
"Author": "jsteinkraus",
"IdReference": "Legacy",
"NodeCount": 1
},
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1 change: 0 additions & 1 deletion Scenarios/Generic/SEIR/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SEIR/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "Generic SEIR"
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SEIR/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SEIR -t "Generic SEIR" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SEIR/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
1 change: 0 additions & 1 deletion Scenarios/Generic/SEIRS/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 1,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SEIRS/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json SEIRS
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SEIRS/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SEIRW -t "SEIRS" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SEIRS/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/SEIR_VitalDynamics/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 1,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SEIR_VitalDynamics/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json Generic_SEIR_VItalDynamics
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SEIR_VitalDynamics/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SEIR -t "Generic SEIR with vital dynamics" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SEIR_VitalDynamics/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
1 change: 0 additions & 1 deletion Scenarios/Generic/SI/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SI/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json SI
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SI/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SI -t "SI" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SI/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
1 change: 0 additions & 1 deletion Scenarios/Generic/SIR/config.json
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"Enable_Aging": 1,
"Enable_Default_Reporting": 1,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SIR/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json "SIR"
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SIR/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SIR -t "SIR" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SIR/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
1 change: 0 additions & 1 deletion Scenarios/Generic/SIRS/config.json
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"Enable_Aging": 1,
"Enable_Default_Reporting": 1,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
"Enable_Heterogeneous_Intranode_Transmission": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SIRS/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json SIRS
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SIRS/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SIRW -t "SIRS" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SIRS/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
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1 change: 0 additions & 1 deletion Scenarios/Generic/SIS/config.json
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"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 0,
"Enable_Demographics_Reporting": 1,
"Enable_Demographics_Risk": 0,
"Enable_Disease_Mortality": 0,
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4 changes: 4 additions & 0 deletions Scenarios/Generic/SIS/plotAllCharts.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotAllCharts.py output\InsetChart.json SIS
@ENDLOCAL
4 changes: 4 additions & 0 deletions Scenarios/Generic/SIS/plotInsetChart.bat
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@SETLOCAL
@SET PATH=%PATH%;C:\Python36
python ..\..\..\Scripts\plotSIRChannels.py -c SI -t "SIS" output\InsetChart.json
@ENDLOCAL
2 changes: 2 additions & 0 deletions Scenarios/Generic/SIS/runEmod.cmd
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..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
@pause
1 change: 0 additions & 1 deletion Scenarios/Generic/Vaccinations/A_BaselineOutbreak/config.json
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Expand Up @@ -17,7 +17,6 @@
"Enable_Default_Reporting": 1,
"Enable_Demographics_Birth": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Gender": 1,
"Enable_Demographics_Other": 0,
"Enable_Demographics_Reporting": 1,
"Enable_Disease_Mortality": 0,
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