tfojo1/jheem_analyses
Nov 2024 – Mar 2026
11 Months active
Languages Used
RCSVPythonUnknown
Technical Skills
Data AnalysisData MappingData VisualizationEpidemiological ModelingEpidemiologyModel Calibration
mschnure
PROFILE
Mschnure
Over an 11-month period, contributed to the tfojo1/jheem_analyses repository by developing and refining epidemiological modeling tools for HIV analysis. Delivered features such as state-level prevalence scripts, calibration enhancements, and intervention modeling for policy evaluation, using R and Python for scripting, data analysis, and statistical modeling. Expanded model fidelity through robust calibration workflows, improved data visualization with custom palettes, and enhanced reproducibility via documentation and version control. Addressed complex data integration challenges, including multi-year and demographic analyses, while maintaining code clarity and traceability. The work enabled more accurate scenario analysis, policy simulation, and research reporting across diverse public health datasets.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
51Total
Bugs
0
Commits
51
Features
22
Lines of code
12,174
Activity Months11
Your Network
23 peopleSame Organization
@jhmi.edu1
alhillMember
Shared Repositories
22
Andrew ZalesakMember
A-ZalesakMember
azalesakMember
Lauren ZallaMember
Lucia CilloniMember
Melissa SchnureMember
nsizemo1Member
nsizemo1Member
pkasaieMember
Work History
March 2026
11 Commits • 2 Features
Mar 1, 2026March 2026 monthly summary for tfojo1/jheem_analyses focused on business value and technical execution. Delivered two primary features in the jheem_analyses pipeline and stabilized data operations to enable reliable policy analytics: (1) National income data analysis and distribution modeling enhancements enabling population income data generation and median income calculations, with multi-year processing, distribution fitting, and demographic analyses; (2) Biktarvy intervention analysis and infection-rate visualization with scenario modeling for cessation effects on viral suppression. In addition, data hygiene improvements and git-tracking refinements were completed to improve reproducibility and maintainability.
11 Commits • 2 Features
Mar 1, 2026March 2026 monthly summary for tfojo1/jheem_analyses focused on business value and technical execution. Delivered two primary features in the jheem_analyses pipeline and stabilized data operations to enable reliable policy analytics: (1) National income data analysis and distribution modeling enhancements enabling population income data generation and median income calculations, with multi-year processing, distribution fitting, and demographic analyses; (2) Biktarvy intervention analysis and infection-rate visualization with scenario modeling for cessation effects on viral suppression. In addition, data hygiene improvements and git-tracking refinements were completed to improve reproducibility and maintainability.
March 2026
October 2025
1 Commits • 1 Features
Oct 1, 2025October 2025 monthly summary focusing on the developer's work in tfojo1/jheem_analyses. Emphasizes feature delivery for Part B Ryan White cessation intervention modeling, major accomplishments, and value delivered to the business and research goals.
October 2025
1 Commits • 1 Features
Oct 1, 2025October 2025 monthly summary focusing on the developer's work in tfojo1/jheem_analyses. Emphasizes feature delivery for Part B Ryan White cessation intervention modeling, major accomplishments, and value delivered to the business and research goals.
September 2025
1 Commits • 1 Features
Sep 1, 2025September 2025: Delivered an observability enhancement in tfojo1/jheem_analyses by adding an informational print in rw_state_results.R to signal usage of urbanicity data from an external R script. This improves data provenance, debugging, and reproducibility for downstream analyses. The change is tracked in commit 61fb70b9c1f55e1bd93df652a162e05a3853ce1d and lays groundwork for future data-automation improvements.
1 Commits • 1 Features
Sep 1, 2025September 2025: Delivered an observability enhancement in tfojo1/jheem_analyses by adding an informational print in rw_state_results.R to signal usage of urbanicity data from an external R script. This improves data provenance, debugging, and reproducibility for downstream analyses. The change is tracked in commit 61fb70b9c1f55e1bd93df652a162e05a3853ce1d and lays groundwork for future data-automation improvements.
September 2025
July 2025
4 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary for tfojo1/jheem_analyses: Focused on visualization theming for shaded table outputs. Delivered expanded color palettes, updates to thresholds color palette, default palette options, and new color schemes for age analysis and generated tables. No major bugs reported this month. This work enhances data clarity, consistency across reports, and user customization, enabling better business decisions based on more readable visuals.
July 2025
4 Commits • 1 Features
Jul 1, 2025July 2025 monthly summary for tfojo1/jheem_analyses: Focused on visualization theming for shaded table outputs. Delivered expanded color palettes, updates to thresholds color palette, default palette options, and new color schemes for age analysis and generated tables. No major bugs reported this month. This work enhances data clarity, consistency across reports, and user customization, enabling better business decisions based on more readable visuals.
May 2025
1 Commits • 1 Features
May 1, 2025May 2025 performance summary for tfojo1/jheem_analyses: Delivered a configurable, state-level HIV prevalence analysis script (R) that computes total prevalence for a set of target states in 2021 and compares it to the national prevalence for the same year. The script loads a config file and defines the target states list to enable reproducible analyses and easy extension to additional states or years. Commit recorded: 4c592343684ca6e9c10f654a09e1679a605347b4 (state-level prevalence total).
1 Commits • 1 Features
May 1, 2025May 2025 performance summary for tfojo1/jheem_analyses: Delivered a configurable, state-level HIV prevalence analysis script (R) that computes total prevalence for a set of target states in 2021 and compares it to the national prevalence for the same year. The script loads a config file and defines the target states list to enable reproducible analyses and easy extension to additional states or years. Commit recorded: 4c592343684ca6e9c10f654a09e1679a605347b4 (state-level prevalence total).
May 2025
April 2025
2 Commits • 1 Features
Apr 1, 2025April 2025 monthly summary for tfojo1/jheem_analyses: Delivered extended state-level AIDS data through 2000 and calibration enhancements to support accurate state-level analyses. Updated likelihood instructions and full calibration models; calibration code enhancements added to support extended data and new scenarios. Commits underpinning the work: 0f2c03a2299ee5281dbb5f752b84f4f570099586; f32fcf53d7ea3db0a731049a7d0dd862468b6c5a.
April 2025
2 Commits • 1 Features
Apr 1, 2025April 2025 monthly summary for tfojo1/jheem_analyses: Delivered extended state-level AIDS data through 2000 and calibration enhancements to support accurate state-level analyses. Updated likelihood instructions and full calibration models; calibration code enhancements added to support extended data and new scenarios. Commits underpinning the work: 0f2c03a2299ee5281dbb5f752b84f4f570099586; f32fcf53d7ea3db0a731049a7d0dd862468b6c5a.
March 2025
2 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for tfojo1/jheem_analyses. Delivered a feature expansion to include all states in location-based likelihood calculations, broadening geographic scope to MSAs and state-level data. This enhances suppression, awareness, heroin, and cocaine likelihood models with more complete data coverage and improved accuracy across jurisdictions.
2 Commits • 1 Features
Mar 1, 2025March 2025 monthly summary for tfojo1/jheem_analyses. Delivered a feature expansion to include all states in location-based likelihood calculations, broadening geographic scope to MSAs and state-level data. This enhances suppression, awareness, heroin, and cocaine likelihood models with more complete data coverage and improved accuracy across jurisdictions.
March 2025
February 2025
4 Commits • 3 Features
Feb 1, 2025February 2025 monthly summary for tfojo1/jheem_analyses: Delivered documentation expansion, model robustness, and code readability improvements that enhance onboarding, model reliability, and maintainability. Key outcomes include expanded reference materials, enforcement of minimum error standard deviation across EHE model likelihoods to prevent overly precise estimates, and clarifying input matrix orientation for pairing_input_manager to reduce misconfiguration risk. All changes are tracked via commits in the repo.
February 2025
4 Commits • 3 Features
Feb 1, 2025February 2025 monthly summary for tfojo1/jheem_analyses: Delivered documentation expansion, model robustness, and code readability improvements that enhance onboarding, model reliability, and maintainability. Key outcomes include expanded reference materials, enforcement of minimum error standard deviation across EHE model likelihoods to prevent overly precise estimates, and clarifying input matrix orientation for pairing_input_manager to reduce misconfiguration risk. All changes are tracked via commits in the repo.
January 2025
8 Commits • 3 Features
Jan 1, 2025January 2025 — Key deliverables for tfojo1/jheem_analyses focused on model stability, research support, and reproducibility. Key features delivered include Enhanced EHE Error Terms and Likelihood Modeling with multiple error variance types and parameter resets; MSM symptomatic disease proportion documentation; and a Simulation Data Preprocessing Script for burning and persisting multiple sim sets for consistent analysis. Major fixes stabilized EHE computations using LHD data, reset weights and default year-to-year correlation, and updated related parameters. Overall impact: more accurate risk estimates, robust scenario analysis, and improved reproducibility for research reporting. Technologies demonstrated: advanced modeling refinements, data processing scripts, documentation practices, and version control discipline.
8 Commits • 3 Features
Jan 1, 2025January 2025 — Key deliverables for tfojo1/jheem_analyses focused on model stability, research support, and reproducibility. Key features delivered include Enhanced EHE Error Terms and Likelihood Modeling with multiple error variance types and parameter resets; MSM symptomatic disease proportion documentation; and a Simulation Data Preprocessing Script for burning and persisting multiple sim sets for consistent analysis. Major fixes stabilized EHE computations using LHD data, reset weights and default year-to-year correlation, and updated related parameters. Overall impact: more accurate risk estimates, robust scenario analysis, and improved reproducibility for research reporting. Technologies demonstrated: advanced modeling refinements, data processing scripts, documentation practices, and version control discipline.
January 2025
December 2024
2 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for tfojo1/jheem_analyses: Delivered calibration tooling enhancements and a new review workflow to improve model weighting, scenario analysis, and reproducibility. Implemented TOTAL.WEIGHT = 0.5 across all likelihoods and migrated calibration code from full.with.aids to full.with.aids2, enabling more balanced calibration outcomes. Introduced a calibration review script suite that sets up the JHEEM engine, runs simulations with adjusted parameters, and generates plots (diagnosed prevalence, new diagnoses, AIDS diagnoses) across key dimensions and time horizons. Completed repository maintenance by archiving legacy configurations to simplify future experiments. No critical bugs fixed this month; primary focus was on robust calibration tooling, reproducibility, and maintainability.
December 2024
2 Commits • 1 Features
Dec 1, 2024December 2024 monthly summary for tfojo1/jheem_analyses: Delivered calibration tooling enhancements and a new review workflow to improve model weighting, scenario analysis, and reproducibility. Implemented TOTAL.WEIGHT = 0.5 across all likelihoods and migrated calibration code from full.with.aids to full.with.aids2, enabling more balanced calibration outcomes. Introduced a calibration review script suite that sets up the JHEEM engine, runs simulations with adjusted parameters, and generates plots (diagnosed prevalence, new diagnoses, AIDS diagnoses) across key dimensions and time horizons. Completed repository maintenance by archiving legacy configurations to simplify future experiments. No critical bugs fixed this month; primary focus was on robust calibration tooling, reproducibility, and maintainability.
November 2024
15 Commits • 7 Features
Nov 1, 2024November 2024 performance summary for tfojo1/jheem_analyses focused on strengthening model fidelity, calibration robustness, and maintainability. Delivered end-to-end calibration enhancements, expanded behavior parameterization for key risk groups, and improved visualization to support decision-making. All work was tracked in a single repo with explicit commits to facilitate traceability and future audits.
15 Commits • 7 Features
Nov 1, 2024November 2024 performance summary for tfojo1/jheem_analyses focused on strengthening model fidelity, calibration robustness, and maintainability. Delivered end-to-end calibration enhancements, expanded behavior parameterization for key risk groups, and improved visualization to support decision-making. All work was tracked in a single repo with explicit commits to facilitate traceability and future audits.
November 2024
Activity
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Quality Metrics
Correctness85.2%
Maintainability85.2%
Architecture81.2%
Performance75.6%
AI Usage20.4%
Skills & Technologies
Programming Languages
CSVPythonRUnknown
Technical Skills
Code DocumentationData AnalysisData MappingData ProcessingData VisualizationDocumentationEpidemiological ModelingEpidemiologyModel CalibrationOntology EngineeringPython scriptingR ProgrammingR ScriptingR programmingRepository Management
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