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README2-branch_tag_descriptions.txt
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README2-branch_tag_descriptions.txt
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---------------------------------------------------------
MODEL BRANCHES:
---------------------------------------------------------
master
- Setting: KwaZulu-Natal, South Africa
- Base model
- Was updated to include CC treatment and symptomatic detection to be able to do CEAs
DRIVE_versionBeforeCCTreatment
- Setting: KwaZulu-Natal, South Africa
- This was the version of the model that Cara worked on. It is still being used for the CISNET
comparative analysis
- Does not contain CC treatment or symptomatic detection
Kenya_treatment
- Branched from nonVaxInfections_Kenya_national
- Being used for the Kenya single dose CEA, contains CC treatment and symptomatic detection
nonVaxInfections_DoArt
-Setting: KwaZulu-Natal, South Africa
-Used for DO ART CEA analysis, status quo clinic ART scenario
-DoArtOutputs directory includes model outputs for DO ART analysis
nonVaxInfections_DoArt_diagHiv
-Setting: KwaZulu-Natal, South Africa
-Used for DO ART CEA analysis, scenarios with 1x/5years home HTC
-Includes wrapper equations to calculate percent of PLWHIV diagnosed/undiagnosed
-vaxCEA_plotSaveDoArt_071720.m includes code to plot/save DO ART analysis outputs
nonVaxInfections_Kenya
-Setting: Kenya
-CISNET Kenya model
-Calibrating with ABC-SMC algorithm (in progress)
-See Issue #107 for key differences with nonVaxInfections_Kenya_national
nonVaxInfections_Kenya_national
-Setting: Kenya
-Gui Liu dissertation model
-Hand-calibrated
-Assumes HPV affects HIV natural history
nonVaxInfections_Nyanza
-Setting: Nyanza, Kenya
-Derived from Gui Liu dissertation model
-Hand-calibrated to HIV (HPV/CIN/cervical cancer calibration unfinished)
-Includes basic PrEP functionality
PAF_HIV
-Setting: KwaZulu-Natal, South Africa
-Used for Darcy Rao's IPVC 2020 PAF analysis
(follow-up paper uses master branch)
OptScrnAge
-Setting: KwaZulu-Natal, South Africa
-Used for Darcy Rao's IPVC 2020 optimal screening age analysis
---------------------------------------------------------
MODEL TAGS:
---------------------------------------------------------
KwaZulu-Natal model, multiple-HPV-types calibration:
Phase 2
091520_backup_22Apr20Ph2V11calib
083120_backup_22Apr20Ph2V10calib
082520_backup_22Apr20Ph2V9calib
082420_backup_22Apr20Ph2V8calib
082120_backup_22Apr20Ph2V7calib
080620_backup_22Apr20Ph2V6calib
080320_backup_22Apr20Ph2V5calib
072820_backup_22Apr20Ph2V4calib
072120_backup_22Apr20Ph2V3calib
071820_backup_22Apr20Ph2V2calib
062520_backup_22Apr20Ph2calib
Phase 1
010821_backup_22Apr20Ph1calib
Phase 0
041620_backup_handCalibFrom24Feb20calib
Trial calibration attempt
030420_backup_24Feb20calib
022420_backup_21Feb20calib
022120_backup_10Feb20calib
Calibration of kSymp
Round 1: kSymp_ParamSets.xlsx
Round 2: kSymp_ParamSets_recalib_round2.xlsx
Final parameter sets: kSympParams.xlsx
KwaZulu-Natal model outputs (presentation, abstract, result set, etc.):
062521_output_WHOcompareModelPaper (also used for IPVC2021 abstract)
100720_output_whoCompare
062320_output_IPVC2020
101819_output_5yearAgeGroups-whoReport
091019_output_uncertaintyAbstract
090519_output_whoMeetingWupdates
062719_output_whoMeeting
053119_output_whoReportP1VaxScreen
052019_output_cisnetMeetingHivSubgroup
040919_output_whoReportArtCCexplore
021919_output_whoReportHpv1910
020619_output_whoReport
Intermediate KwaZulu-Natal model versions:
Main model predecessor with HPV modeled as single infection
(prior to HPV infection split into 9v and non-9v types, several other model revisions, and re-calibration)
120319_backup_5yearAgeGroups
Version with single HPV infection, single age groups
071619_backup_singleAgeVax
Version testing all differential equations solved per timestep
100419_backup_allFuncsPerTimestep
Additional model backups, mostly before major merges or model additions/fixes
040621_backup_nonVaxInfections-b4mergeWmaster
040621_backup_master-b4caughtUpToNonVaxInfections
012720_backup_b4ARTlims
121719_backup_nonVaxInfections-retryMergeWnewHIVcd4vlStates
121319_backup_nonVaxInfections-b4mergeWnewHIVcd4vlStates
081919_backup_beforeMergeWautoCalibrate
081619_backup_singleAgeGroups-b4MasterAutoCalMerge
KwaZulu-Natal model version left by programmer Nicholas Tan:
010219_backup_afterNicholasTan
Version with some changes used for discarded CISNET comparative modeling analysis with Erasmus:
051420_backup_after_nicholas_Tan_Erasmus_05102020
Stale branches left by programmer Nicholas Tan:
120118_backup_4v
120118_backup_omniHPV
120118_backup_newLambda
120118_backup_fastMix
120118_backup_HPV_Smooth
120118_backup_ART_fix
Intermediate Kenya model versions:
090120_backup_KenyaWNyanza
073120_backup_KenyaHandCalib
031120_backup_Kenya
Stale branches left by programmer Christine Hathaway:
ccTreatment - this was the branch where I worked on updating the model with symptomatic detection
and CC treatment