tfojo1/jheem_analyses
Nov 2024 – Oct 2025
12 Months active
Languages Used
RJavaScriptCSVShellGit configurationText
Technical Skills
CalibrationConfiguration ManagementData AnalysisData ManagementData MappingData Wrangling
Todd Fojo
PROFILE
Todd Fojo
Over the past year, tfojo1 developed and maintained the tfojo1/jheem_analyses repository, delivering robust epidemiological modeling and data analysis pipelines for public health decision support. Their work spanned feature-rich simulation frameworks, calibration workflows, and intervention modeling, with a focus on HIV, CDC testing, and Ryan White program analyses. Using R and shell scripting, tfojo1 engineered scalable MCMC calibration, parallelized workflows, and advanced data visualization, while integrating new specifications for PrEP and cost modeling. The codebase demonstrated strong data management, reproducibility, and maintainability, with careful attention to parameterization, statistical modeling, and cross-environment operability, resulting in reliable, policy-relevant analytical outputs.
Overall Statistics
Feature vs Bugs
70%Features
Repository Contributions
212Total
Bugs
30
Commits
212
Features
70
Lines of code
45,138
Activity Months12
Your Network
29 people
Work History
October 2025
3 Commits • 3 Features
Oct 1, 2025October 2025 monthly summary for tfojo1/jheem_analyses: Delivered critical enhancements to parameter estimation, updated Ryan White cost modeling, and established an external funding data source. These changes improve estimation accuracy, cost transparency, and data provenance for simulations and policy analyses.
3 Commits • 3 Features
Oct 1, 2025October 2025 monthly summary for tfojo1/jheem_analyses: Delivered critical enhancements to parameter estimation, updated Ryan White cost modeling, and established an external funding data source. These changes improve estimation accuracy, cost transparency, and data provenance for simulations and policy analyses.
October 2025
September 2025
15 Commits • 2 Features
Sep 1, 2025Monthly summary for 2025-09 focusing on tfojo1/jheem_analyses. This month delivered substantial CDC testing and prep enhancements and Ryan White CD interventions with anchor-year simulations. I expanded state-level coverage for CDC-related tests and prep specifications, improved extraction results, and implemented cost data integration for RW interventions. The work also included extensive configuration and run-time tuning to align simulation timelines with CDC interventions and NANB interventions, improving reproducibility and policy scenario analysis. In addition, tooling and code quality improvements were achieved, including updates to the Ryan White code and the addition of an assemble helper. Data delivery and readiness were enhanced by pushing cost CSVs and expanding RW-related data outputs, supporting business decisions and research with higher fidelity results.
September 2025
15 Commits • 2 Features
Sep 1, 2025Monthly summary for 2025-09 focusing on tfojo1/jheem_analyses. This month delivered substantial CDC testing and prep enhancements and Ryan White CD interventions with anchor-year simulations. I expanded state-level coverage for CDC-related tests and prep specifications, improved extraction results, and implemented cost data integration for RW interventions. The work also included extensive configuration and run-time tuning to align simulation timelines with CDC interventions and NANB interventions, improving reproducibility and policy scenario analysis. In addition, tooling and code quality improvements were achieved, including updates to the Ryan White code and the addition of an assemble helper. Data delivery and readiness were enhanced by pushing cost CSVs and expanding RW-related data outputs, supporting business decisions and research with higher fidelity results.
August 2025
2 Commits • 1 Features
Aug 1, 2025Summary for 2025-08 (tfojo1/jheem_analyses): Delivered a new CDC PrEP Program Modeling and Data Exploration feature, introducing the CDCP.SPECIFICATION for modeling CDC prevention programs and accompanying data exploration assets to simulate PrEP uptake, testing, and diagnosis dynamics under funding and effectiveness scenarios. Includes integrated/cumulative outcome tracking and web-tool sub-versions to support scenario analysis and stakeholder demonstrations. The work is documented via two commits and enhances decision support for public-health planning by enabling rapid scenario evaluation and clearer communications with stakeholders. No major bugs reported in this cycle; primary focus was model specification, data tooling, and ensuring reproducibility. Technologies/skills demonstrated include modeling framework extension, data exploration tooling, version-controlled development, and cross-functional collaboration.
2 Commits • 1 Features
Aug 1, 2025Summary for 2025-08 (tfojo1/jheem_analyses): Delivered a new CDC PrEP Program Modeling and Data Exploration feature, introducing the CDCP.SPECIFICATION for modeling CDC prevention programs and accompanying data exploration assets to simulate PrEP uptake, testing, and diagnosis dynamics under funding and effectiveness scenarios. Includes integrated/cumulative outcome tracking and web-tool sub-versions to support scenario analysis and stakeholder demonstrations. The work is documented via two commits and enhances decision support for public-health planning by enabling rapid scenario evaluation and clearer communications with stakeholders. No major bugs reported in this cycle; primary focus was model specification, data tooling, and ensuring reproducibility. Technologies/skills demonstrated include modeling framework extension, data exploration tooling, version-controlled development, and cross-functional collaboration.
August 2025
July 2025
11 Commits • 4 Features
Jul 1, 2025July 2025 — This month delivered measurable business value through feature-rich reporting, robust data processing enhancements, and a critical bug fix for the JHEEM analyses pipeline. The work improved policy-relevant insights, accuracy of mortality and testing outputs, and collaboration readiness across the team.
July 2025
11 Commits • 4 Features
Jul 1, 2025July 2025 — This month delivered measurable business value through feature-rich reporting, robust data processing enhancements, and a critical bug fix for the JHEEM analyses pipeline. The work improved policy-relevant insights, accuracy of mortality and testing outputs, and collaboration readiness across the team.
June 2025
16 Commits • 4 Features
Jun 1, 2025June 2025 accomplishments focused on strengthening forecasting fidelity, data integrity, and operational robustness across the JHEEM analyses stack. Delivered longer-horizon EHE calibration and incidence modeling with NA handling and tapering, enhanced Ryan White intervention modeling with updated data and conservative scenarios, expanded CDC testing calibration and multi-location execution, and reinforced model reliability through SHIELD parameter handling fixes; added NA resampling for disparities to preserve downstream analytics. These updates drive more accurate policy guidance and improved decision support for multi-site implementations.
16 Commits • 4 Features
Jun 1, 2025June 2025 accomplishments focused on strengthening forecasting fidelity, data integrity, and operational robustness across the JHEEM analyses stack. Delivered longer-horizon EHE calibration and incidence modeling with NA handling and tapering, enhanced Ryan White intervention modeling with updated data and conservative scenarios, expanded CDC testing calibration and multi-location execution, and reinforced model reliability through SHIELD parameter handling fixes; added NA resampling for disparities to preserve downstream analytics. These updates drive more accurate policy guidance and improved decision support for multi-site implementations.
June 2025
May 2025
21 Commits • 8 Features
May 1, 2025May 2025 performance summary for tfojo1/jheem_analyses: Delivered major EHE state calibration enhancements with race/sex dimensions, integrated Ryan White state-level results, modernized CDC testing workflow, and strengthened build/deploy pipelines. Also added backward-compatible parameterization, and completed stability fixes to ensure robust end-to-end state analyses.
May 2025
21 Commits • 8 Features
May 1, 2025May 2025 performance summary for tfojo1/jheem_analyses: Delivered major EHE state calibration enhancements with race/sex dimensions, integrated Ryan White state-level results, modernized CDC testing workflow, and strengthened build/deploy pipelines. Also added backward-compatible parameterization, and completed stability fixes to ensure robust end-to-end state analyses.
April 2025
40 Commits • 10 Features
Apr 1, 2025April 2025 monthly summary for tfojo1/jheem_analyses focused on delivering robust, scalable analyses and improved forecasting capabilities, while hardening data handling and maintenance practices. Key business value: faster, more reliable analyses; state-level model fit improvements; and a clearer path for future scenario planning. What was delivered (highlights): - Ryan White Analysis and MCMC Workflow Enhancements: parallelized MCMC, updates to main/manuscript analyses, improved data handling, revised figures, and web-tool simsets. This included parallelization work, data flow improvements, and adjustments to simulate sets for the web tool. Representative commits include updates to ryan white main/manuscript analyses and parallelizable MCMC work. - RW Transmute/Intervention Script Enhancements: new print capability to improve script usability and diagnostics. - Missing data handling improvements: introduced a backup option when state-level data are missing for metro deaths, ensuring graceful handling of gaps. - SHIELD emigration correctness fix: corrected usage of emigration within the SHIELD workflow to ensure consistency. - Future incidence likelihood addition: added forward-looking incidence likelihood calculations to forecasting components. - Maintenance and cleanup: removed debug scripts and updated gitignore (local testing), reducing noise and improving reproducibility. - EHE likelihoods and HIV/AIDS modeling improvements: expanded likelihood components, priors, and ramp settings to improve state-level fits and modeling realism. - Web-based simulation updates (Ryan White): updated web simulation sets used by the model; kept simulations aligned with current parameters. - CDC testing scaffolding: sketched scaffolding for a CDC testing framework and related specifications to guide future work. - Setup/install process improvements: refined first-time install flow and adjusted package installation order for smoother onboarding. - State trial registrations tweaks: adjustments to registrations and related data handling to improve consistency. - Total mortality dimension fix: corrected dimensions for total.mortality to ensure accurate computation. - IDU parameterization and transmission calibration enhancements: extended IDU sex parameter specification to remission, adjusted sex-based pairing proportions, and added idu.sex.assortativity.multiplier to transmission calibration. - Bug fixes in pairing manager and parameter handling: OE handling fix, small apply function bug fix, and removal of empty parameter aliases to prevent errors. - Likelihood and model updates (incidence and custom likelihoods): updated custom likelihoods for performance (fast accessors), refined 5-year change evaluation, and adjusted priors to emphasize higher incidence in MSM/het male IDU scenarios. - Bug fix to custom likelihood (sim.metadata): corrected missing sim.metadata reference in custom likelihood. Overall impact and accomplishments: - Increased analysis throughput and scalability through MCMC parallelization and optimized likelihood computations, enabling faster turnarounds for updates to RW analyses and forecasting scenarios. - Improved state-level model fit and realism through EHE/HIV modeling enhancements and updated priors, with better handling of data gaps via robust missing-data options. - Strengthened reliability, maintainability, and on-boarding with cleanup work, clearer setup/install steps, and scaffolding for future testing frameworks. - Reduced risk of data and parameter handling errors through targeted bug fixes in pairing, emulation of parameter flows, and sim-metadata references. Technologies/skills demonstrated: - Parallel computing and optimization (parallelized MCMC, optimized likelihood accessors) - Epidemiological modeling (EHE, HIV/AIDS, IDU, MSM, heterosexual male dynamics) and forecasting - Data handling and quality controls for missing data scenarios - Script development and tooling (RW transmute scripts, print statements, scaffolding for CDC testing) - Web-tool integration and simulation set maintenance - DevOps hygiene (repo cleanup, gitignore, setup flow)
40 Commits • 10 Features
Apr 1, 2025April 2025 monthly summary for tfojo1/jheem_analyses focused on delivering robust, scalable analyses and improved forecasting capabilities, while hardening data handling and maintenance practices. Key business value: faster, more reliable analyses; state-level model fit improvements; and a clearer path for future scenario planning. What was delivered (highlights): - Ryan White Analysis and MCMC Workflow Enhancements: parallelized MCMC, updates to main/manuscript analyses, improved data handling, revised figures, and web-tool simsets. This included parallelization work, data flow improvements, and adjustments to simulate sets for the web tool. Representative commits include updates to ryan white main/manuscript analyses and parallelizable MCMC work. - RW Transmute/Intervention Script Enhancements: new print capability to improve script usability and diagnostics. - Missing data handling improvements: introduced a backup option when state-level data are missing for metro deaths, ensuring graceful handling of gaps. - SHIELD emigration correctness fix: corrected usage of emigration within the SHIELD workflow to ensure consistency. - Future incidence likelihood addition: added forward-looking incidence likelihood calculations to forecasting components. - Maintenance and cleanup: removed debug scripts and updated gitignore (local testing), reducing noise and improving reproducibility. - EHE likelihoods and HIV/AIDS modeling improvements: expanded likelihood components, priors, and ramp settings to improve state-level fits and modeling realism. - Web-based simulation updates (Ryan White): updated web simulation sets used by the model; kept simulations aligned with current parameters. - CDC testing scaffolding: sketched scaffolding for a CDC testing framework and related specifications to guide future work. - Setup/install process improvements: refined first-time install flow and adjusted package installation order for smoother onboarding. - State trial registrations tweaks: adjustments to registrations and related data handling to improve consistency. - Total mortality dimension fix: corrected dimensions for total.mortality to ensure accurate computation. - IDU parameterization and transmission calibration enhancements: extended IDU sex parameter specification to remission, adjusted sex-based pairing proportions, and added idu.sex.assortativity.multiplier to transmission calibration. - Bug fixes in pairing manager and parameter handling: OE handling fix, small apply function bug fix, and removal of empty parameter aliases to prevent errors. - Likelihood and model updates (incidence and custom likelihoods): updated custom likelihoods for performance (fast accessors), refined 5-year change evaluation, and adjusted priors to emphasize higher incidence in MSM/het male IDU scenarios. - Bug fix to custom likelihood (sim.metadata): corrected missing sim.metadata reference in custom likelihood. Overall impact and accomplishments: - Increased analysis throughput and scalability through MCMC parallelization and optimized likelihood computations, enabling faster turnarounds for updates to RW analyses and forecasting scenarios. - Improved state-level model fit and realism through EHE/HIV modeling enhancements and updated priors, with better handling of data gaps via robust missing-data options. - Strengthened reliability, maintainability, and on-boarding with cleanup work, clearer setup/install steps, and scaffolding for future testing frameworks. - Reduced risk of data and parameter handling errors through targeted bug fixes in pairing, emulation of parameter flows, and sim-metadata references. Technologies/skills demonstrated: - Parallel computing and optimization (parallelized MCMC, optimized likelihood accessors) - Epidemiological modeling (EHE, HIV/AIDS, IDU, MSM, heterosexual male dynamics) and forecasting - Data handling and quality controls for missing data scenarios - Script development and tooling (RW transmute scripts, print statements, scaffolding for CDC testing) - Web-tool integration and simulation set maintenance - DevOps hygiene (repo cleanup, gitignore, setup flow)
April 2025
March 2025
44 Commits • 12 Features
Mar 1, 2025March 2025 highlights for tfojo1/jheem_analyses: Delivered major RW/EHE capabilities, bug fixes, and data enhancements across RW interventions and modeling pipelines. Key features include the RW Interventions Core and Processing workflow with survey integration and automated results processing; enhancements to RW Likelihoods, MCMC specification and cross-city results with deterministic seeding; and expanded RW data handling/visualization. Critical fixes stabilized the pipeline: SHIELD dimnames bug fix; IDU mortality migration fix; rolled back IDU incidence by sex in parameter mapping; and setup/run script reliability improvements. Additional updates cover COVID specification adjustments and EHE parameter mapping enhancements that improve calibration and mortality modeling. Overall impact includes improved model accuracy, reproducibility, city-wide coverage, and clearer data visualization, translating to higher confidence decisions and faster insight delivery.
March 2025
44 Commits • 12 Features
Mar 1, 2025March 2025 highlights for tfojo1/jheem_analyses: Delivered major RW/EHE capabilities, bug fixes, and data enhancements across RW interventions and modeling pipelines. Key features include the RW Interventions Core and Processing workflow with survey integration and automated results processing; enhancements to RW Likelihoods, MCMC specification and cross-city results with deterministic seeding; and expanded RW data handling/visualization. Critical fixes stabilized the pipeline: SHIELD dimnames bug fix; IDU mortality migration fix; rolled back IDU incidence by sex in parameter mapping; and setup/run script reliability improvements. Additional updates cover COVID specification adjustments and EHE parameter mapping enhancements that improve calibration and mortality modeling. Overall impact includes improved model accuracy, reproducibility, city-wide coverage, and clearer data visualization, translating to higher confidence decisions and faster insight delivery.
February 2025
35 Commits • 15 Features
Feb 1, 2025February 2025 focused on reliability, data modeling enhancements, and performance improvements across the JHEEM analyses suite. Key outcomes include feature deliveries in shield and Ryan White (RW) specifications, data-management cleanup, flexibility enhancements for package usage (jheem2), and caching-driven performance gains for RW workflows. Major bug fixes improved stability and robustness across data helpers and parameter handling, enabling more accurate, timely insights for decision-making.
35 Commits • 15 Features
Feb 1, 2025February 2025 focused on reliability, data modeling enhancements, and performance improvements across the JHEEM analyses suite. Key outcomes include feature deliveries in shield and Ryan White (RW) specifications, data-management cleanup, flexibility enhancements for package usage (jheem2), and caching-driven performance gains for RW workflows. Major bug fixes improved stability and robustness across data helpers and parameter handling, enabling more accurate, timely insights for decision-making.
February 2025
January 2025
4 Commits • 3 Features
Jan 1, 2025January 2025 monthly work summary for tfojo1/jheem_analyses focused on delivering more representative mobility insights and strengthening epidemiological modeling capabilities, while advancing SHIELD/HIV/EHE specification work. The work aligns with business value goals of more accurate data-driven decision support and robust modeling pipelines.
January 2025
4 Commits • 3 Features
Jan 1, 2025January 2025 monthly work summary for tfojo1/jheem_analyses focused on delivering more representative mobility insights and strengthening epidemiological modeling capabilities, while advancing SHIELD/HIV/EHE specification work. The work aligns with business value goals of more accurate data-driven decision support and robust modeling pipelines.
December 2024
3 Commits • 2 Features
Dec 1, 2024Concise monthly summary for 2024-12 focused on business value and technical achievements for the tfojo1/jheem_analyses repository. The period delivered cross-cutting improvements in weighting stability, long-running calibration workflows, and uncertainty modeling.
3 Commits • 2 Features
Dec 1, 2024Concise monthly summary for 2024-12 focused on business value and technical achievements for the tfojo1/jheem_analyses repository. The period delivered cross-cutting improvements in weighting stability, long-running calibration workflows, and uncertainty modeling.
December 2024
November 2024
18 Commits • 6 Features
Nov 1, 2024November 2024 performance for tfojo1/jheem_analyses focused on delivering data-aligned epidemiological modeling improvements, cross-environment operability, and robustness in parameterization and likelihood calculations. Key outcomes include ontology/data mapping refinements, environment-aware execution paths, and enhanced age susceptibility and CV-based likelihoods, supported by targeted bug fixes to improve stability and scalability.
November 2024
18 Commits • 6 Features
Nov 1, 2024November 2024 performance for tfojo1/jheem_analyses focused on delivering data-aligned epidemiological modeling improvements, cross-environment operability, and robustness in parameterization and likelihood calculations. Key outcomes include ontology/data mapping refinements, environment-aware execution paths, and enhanced age susceptibility and CV-based likelihoods, supported by targeted bug fixes to improve stability and scalability.
Activity
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Quality Metrics
Correctness82.4%
Maintainability82.4%
Architecture79.2%
Performance69.2%
AI Usage20.2%
Skills & Technologies
Programming Languages
CSVGit configurationJavaScriptRShellText
Technical Skills
Bayesian InferenceBug FixBug FixingCachingCalibrationCode DocumentationCode OrganizationCode refactoringConfiguration ManagementData AnalysisData CachingData CleaningData EngineeringData ManagementData Mapping
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