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| [module] | |
| name = "pubtime" | |
| title = "Publication likelihood and timeliness" | |
| runtime = "python" | |
| entrypoint = "modules.pubtime:summarize_from_archive" | |
| imported_source = "modules/pubtime" | |
| [dependencies] | |
| required = ["pandas>=2.0"] | |
| optional = ["lifelines>=0.30"] | |
| [parity] | |
| reference_language = "R" | |
| reference_scripts = [ | |
| "modules/pubtime/analysis_Code/Cancer_code/0924_cancer analysis.Rmd", | |
| "modules/pubtime/analysis_Code/Covid_code/0924_covid analysis.Rmd", | |
| "modules/pubtime/analysis_Code/CVD_code/0924_cvd_analysis.Rmd", | |
| ] | |
| cox_model_status = "not-translated" | |
| data_prep_status = "verified-against-R" | |
| parity_harness = "tests/test_pubtime_r_parity.py" | |
| parity_report = "docs/ai/pubtime_parity.md" | |
| # Data prep matches R exactly except publication-date parsing of malformed strings, | |
| # where R's lubridate parse_date_time(exact=FALSE) is context-dependent and buggy (mangles | |
| # trailing-period dates, drops bare years, and parses the same month-range string to either | |
| # a date or NA depending on its neighbours). The Python port parses each string | |
| # independently and resolves month ranges to their first month, so it is at least as | |
| # correct as R on every value and strictly more correct on the divergences. Divergence is | |
| # bounded (11 cancer / 0 covid / 72 cvd trials) and fully attributable to malformed | |
| # pub_date values. See parity_report. | |
| known_divergence = "pub_date parsing of malformed strings (Python strictly more correct than R)" | |