tfojo1/jheem_analyses
Nov 2024 – Jul 2025
9 Months active
Languages Used
RShellSQLBashBatch
Technical Skills
CalibrationData AnalysisData CalibrationData ManagementData ModelingData Visualization
Parastu
PROFILE
Parastu
Over nine months, Payam Kasaie engineered and refined epidemiological modeling workflows in the tfojo1/jheem_analyses repository, focusing on syphilis and demographic simulation for public health analysis. He developed robust calibration pipelines, integrated Bayesian and MCMC methods, and implemented dynamic parameterization to improve model accuracy and reproducibility. Using R and Bash, Payam automated data ingestion, enhanced likelihood computation, and stabilized simulation runtimes across high-performance computing environments. His work included code refactoring, documentation scaffolding, and workflow automation, resulting in more reliable scenario analysis and streamlined collaboration. The depth of his contributions advanced both technical rigor and operational reliability for policy-driven modeling.
Overall Statistics
Feature vs Bugs
69%Features
Repository Contributions
205Total
Bugs
26
Commits
205
Features
59
Lines of code
26,342
Activity Months9
Your Network
34 people
Work History
July 2025
41 Commits • 14 Features
Jul 1, 2025July 2025 monthly performance summary for tfojo1/jheem_analyses focused on delivering robust modeling fidelity, scalable calibration workflows, and data governance to support policy-relevant scenario analysis. The month delivered a set of feature-driven advancements, calibration improvements, and targeted bug fixes that enhance reliability, throughput, and traceability of results.
41 Commits • 14 Features
Jul 1, 2025July 2025 monthly performance summary for tfojo1/jheem_analyses focused on delivering robust modeling fidelity, scalable calibration workflows, and data governance to support policy-relevant scenario analysis. The month delivered a set of feature-driven advancements, calibration improvements, and targeted bug fixes that enhance reliability, throughput, and traceability of results.
July 2025
June 2025
19 Commits • 2 Features
Jun 1, 2025June 2025 (2025-06) monthly summary for tfojo1/jheem_analyses: Key SHIELD model enhancements completed to improve realism, calibration, and stability. Implemented start-year alignment and data-driven seeding for demographic initialization. Achieved a more robust forecasting workflow through enhanced diagnostics and bug fixes, enabling reliable scenario analysis and decision support. Focused on business value by improving accuracy of disease progression, testing timing, and population dynamics while reducing run-time errors.
June 2025
19 Commits • 2 Features
Jun 1, 2025June 2025 (2025-06) monthly summary for tfojo1/jheem_analyses: Key SHIELD model enhancements completed to improve realism, calibration, and stability. Implemented start-year alignment and data-driven seeding for demographic initialization. Achieved a more robust forecasting workflow through enhanced diagnostics and bug fixes, enabling reliable scenario analysis and decision support. Focused on business value by improving accuracy of disease progression, testing timing, and population dynamics while reducing run-time errors.
May 2025
55 Commits • 20 Features
May 1, 2025May 2025 monthly summary for tfojo1/jheem_analyses: Delivered measurable improvements in code quality, calibration reliability, and experimental capability across the core analysis engine. Highlights include a comprehensive code cleanup and refactor clarifying data extraction vs model fitting, calibration workflow enhancements (including reading package choices from JHEEM, updated transmission parameters, dynamic weights, and improved result review), and SHIELD/Rockfish integration (new SHIELD path and shield prep script) along with Rockfish readiness. Documentation scaffolding was added to improve onboarding and governance. Engine tests confirmed all likelihoods compute reliably, supporting robust model outputs. A new Starting Point option (1940 vs 1970) was added, with 1940 runs validated. A parameter block structure was introduced for clarity, and stability improvements were pursued via solver tolerance tuning and likelihood weighting adjustments. Fixed immigration start year bug and several parameter-related issues; removed unintended immigration changes. Collaboration with Andrew advanced, and broader test coverage was expanded with MCMC test scripts. Business value: more stable, transparent, and faster calibration cycles, better historical scenario coverage, and easier maintenance.
55 Commits • 20 Features
May 1, 2025May 2025 monthly summary for tfojo1/jheem_analyses: Delivered measurable improvements in code quality, calibration reliability, and experimental capability across the core analysis engine. Highlights include a comprehensive code cleanup and refactor clarifying data extraction vs model fitting, calibration workflow enhancements (including reading package choices from JHEEM, updated transmission parameters, dynamic weights, and improved result review), and SHIELD/Rockfish integration (new SHIELD path and shield prep script) along with Rockfish readiness. Documentation scaffolding was added to improve onboarding and governance. Engine tests confirmed all likelihoods compute reliably, supporting robust model outputs. A new Starting Point option (1940 vs 1970) was added, with 1940 runs validated. A parameter block structure was introduced for clarity, and stability improvements were pursued via solver tolerance tuning and likelihood weighting adjustments. Fixed immigration start year bug and several parameter-related issues; removed unintended immigration changes. Collaboration with Andrew advanced, and broader test coverage was expanded with MCMC test scripts. Business value: more stable, transparent, and faster calibration cycles, better historical scenario coverage, and easier maintenance.
May 2025
April 2025
35 Commits • 12 Features
Apr 1, 2025Month: 2025-04 — In April, delivered significant robustness in the likelihood modeling stack, improved performance, and expanded sampling capabilities. The work focused on stabilizing the core probability machinery, fixing calibration aging integration, and accelerating the end-to-end workflow, enabling larger-scale experiments with reduced setup time. Key business value includes more reliable models, faster turnarounds for experiments, and scalable MCMC pipelines for planning and decision support.
April 2025
35 Commits • 12 Features
Apr 1, 2025Month: 2025-04 — In April, delivered significant robustness in the likelihood modeling stack, improved performance, and expanded sampling capabilities. The work focused on stabilizing the core probability machinery, fixing calibration aging integration, and accelerating the end-to-end workflow, enabling larger-scale experiments with reduced setup time. Key business value includes more reliable models, faster turnarounds for experiments, and scalable MCMC pipelines for planning and decision support.
March 2025
19 Commits • 2 Features
Mar 1, 2025This month focused on advancing prenatal care modeling and stabilizing the likelihood engine, delivering robust priors, improved projection accuracy, and diagnostic uncertainty integration. Key activities included completing Prenatal Care Data Modeling, Priors, and Likelihoods enhancements with priors fitted from Wonder and fixes to age dimension and weighted-mean handling; addressing misclassification and diagnostics in Syphilis and prenatal estimates; refining the Likelihood Engine and HIV Testing Priors to improve initialization and validation; migrating to the jheem2 package to resolve desolve-related issues and stabilize engine runs; and introducing preliminary variance estimation at the MSA level for prenatal projections. The work has improved model fidelity, reduced runtime issues, and positioned the project for Todd's review and broader deployment.
19 Commits • 2 Features
Mar 1, 2025This month focused on advancing prenatal care modeling and stabilizing the likelihood engine, delivering robust priors, improved projection accuracy, and diagnostic uncertainty integration. Key activities included completing Prenatal Care Data Modeling, Priors, and Likelihoods enhancements with priors fitted from Wonder and fixes to age dimension and weighted-mean handling; addressing misclassification and diagnostics in Syphilis and prenatal estimates; refining the Likelihood Engine and HIV Testing Priors to improve initialization and validation; migrating to the jheem2 package to resolve desolve-related issues and stabilize engine runs; and introducing preliminary variance estimation at the MSA level for prenatal projections. The work has improved model fidelity, reduced runtime issues, and positioned the project for Todd's review and broader deployment.
March 2025
February 2025
10 Commits • 3 Features
Feb 1, 2025February 2025 monthly summary for tfojo1/jheem_analyses. Focused on solidifying SHIELD model integration, delivering consolidated parameterization and specification for SYPHILIS progression, congenital syphilis parameters, and contact tracing, while improving accuracy, maintainability, and visualization.
February 2025
10 Commits • 3 Features
Feb 1, 2025February 2025 monthly summary for tfojo1/jheem_analyses. Focused on solidifying SHIELD model integration, delivering consolidated parameterization and specification for SYPHILIS progression, congenital syphilis parameters, and contact tracing, while improving accuracy, maintainability, and visualization.
January 2025
8 Commits • 2 Features
Jan 1, 2025January 2025 monthly summary for tfojo1/jheem_analyses: Delivered substantial SHIELD model enhancements to improve disease progression modeling, staging, and transition rates, with calibration refinements and integration of HIV testing calculations to strengthen policy impact assessments. Parametrized congenital syphilis transmission by stage and prenatal screening timing, aligning HIV testing and contact tracing parameters with congenital syphilis modeling improvements. Fixed critical stability issues observed during HIV testing outcome and data-pull workflows, restoring reliable runs and enabling policy scenario analyses. Prepared the model for Todd's contact tracing work and established groundwork for Nick's engine run readiness. Overall impact: higher model accuracy, better policy insight for public health interventions, and improved data workflows for reproducibility and collaboration.
8 Commits • 2 Features
Jan 1, 2025January 2025 monthly summary for tfojo1/jheem_analyses: Delivered substantial SHIELD model enhancements to improve disease progression modeling, staging, and transition rates, with calibration refinements and integration of HIV testing calculations to strengthen policy impact assessments. Parametrized congenital syphilis transmission by stage and prenatal screening timing, aligning HIV testing and contact tracing parameters with congenital syphilis modeling improvements. Fixed critical stability issues observed during HIV testing outcome and data-pull workflows, restoring reliable runs and enabling policy scenario analyses. Prepared the model for Todd's contact tracing work and established groundwork for Nick's engine run readiness. Overall impact: higher model accuracy, better policy insight for public health interventions, and improved data workflows for reproducibility and collaboration.
January 2025
December 2024
2 Commits • 2 Features
Dec 1, 2024Month: 2024-12. Key features delivered: - Enhanced Calibration and Plotting for USA Demographics: updated calibration to use US location and US calibration code; adjusted data loading date; extended plotting outputs to include deaths and fertility.rate; configured plots by race and age. Commits: 05691a71678701db94cfd3cf26a70c27d5525bd8 (tracking issue with the fertility rate outcome). - Automated Synchronization with JHEEM_ANALYSIS Repository: added automation to shield_source_code.R to detect JHEEM_ANALYSIS directory and automatically pull latest analysis code. Commits: ca88c4d852ae7cee089977a4c048e41939284cee (adding script to pull JHEEM_analysis). Major bugs fixed: None reported this month. Overall impact and accomplishments: Improved accuracy of US demographic analyses and richer visual outputs, with automated code synchronization reducing manual steps and drift, enabling faster iteration and more reliable reporting. Technologies/skills demonstrated: R scripting (shield_source_code.R and US calibration code), data loading workflow adjustments, plotting by race and age, automation scripting for repository synchronization, Git-based traceability and issue tracking.
December 2024
2 Commits • 2 Features
Dec 1, 2024Month: 2024-12. Key features delivered: - Enhanced Calibration and Plotting for USA Demographics: updated calibration to use US location and US calibration code; adjusted data loading date; extended plotting outputs to include deaths and fertility.rate; configured plots by race and age. Commits: 05691a71678701db94cfd3cf26a70c27d5525bd8 (tracking issue with the fertility rate outcome). - Automated Synchronization with JHEEM_ANALYSIS Repository: added automation to shield_source_code.R to detect JHEEM_ANALYSIS directory and automatically pull latest analysis code. Commits: ca88c4d852ae7cee089977a4c048e41939284cee (adding script to pull JHEEM_analysis). Major bugs fixed: None reported this month. Overall impact and accomplishments: Improved accuracy of US demographic analyses and richer visual outputs, with automated code synchronization reducing manual steps and drift, enabling faster iteration and more reliable reporting. Technologies/skills demonstrated: R scripting (shield_source_code.R and US calibration code), data loading workflow adjustments, plotting by race and age, automation scripting for repository synchronization, Git-based traceability and issue tracking.
November 2024
16 Commits • 2 Features
Nov 1, 2024Summary for 2024-11: Focused on stabilizing aging parameterization, integrating fertility rate calibration, and strengthening data workflow automation. These efforts reduced calibration failures, improved forecast accuracy for demographic scenarios, and elevated data integrity and reproducibility. Notable technical work included creating a Slurm-based calibration script for rockfish, refining calibration pipelines, and enhancing ontology mappings. Business value: more reliable planning data, faster turnaround on model runs, and reduced risk from pipeline failures.
16 Commits • 2 Features
Nov 1, 2024Summary for 2024-11: Focused on stabilizing aging parameterization, integrating fertility rate calibration, and strengthening data workflow automation. These efforts reduced calibration failures, improved forecast accuracy for demographic scenarios, and elevated data integrity and reproducibility. Notable technical work included creating a Slurm-based calibration script for rockfish, refining calibration pipelines, and enhancing ontology mappings. Business value: more reliable planning data, faster turnaround on model runs, and reduced risk from pipeline failures.
November 2024
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Quality Metrics
Correctness80.6%
Maintainability81.8%
Architecture76.8%
Performance66.4%
AI Usage20.8%
Skills & Technologies
Programming Languages
BashBatchRSQLShell
Technical Skills
Batch ScriptingBayesian AnalysisBug FixingCalibrationCluster ComputingCode RefactoringConditional LogicConfiguration ManagementCross-platform compatibilityData AnalysisData CalibrationData CleaningData EngineeringData IntegrationData Management
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