{"id":"W4401357785","doi":"10.1371/journal.pcbi.1012324","title":"rtestim: Time-varying reproduction number estimation with trend filtering","year":2024,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"COVID-19 epidemiological studies","field":"Mathematics","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre for Advancing Health Outcomes; University of British Columbia","funders":"Centers for Disease Control and Prevention; Alliance de recherche numérique du Canada","keywords":"Computer science; Estimator; Mathematical optimization; Estimation; Mathematics; Statistics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003178695,0.0001620493,0.0002697146,0.00007097567,0.0001318381,0.00003105147,0.00008058274,0.00007536065,0.0002979935],"category_scores_gemma":[0.0015084,0.0001172598,0.00004920544,0.0002376585,0.0001122116,0.00009976892,0.00007511468,0.0001486426,0.0003197257],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009392041,"about_ca_system_score_gemma":0.00003317606,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009414153,"about_ca_topic_score_gemma":0.000002360188,"domain_scores_codex":[0.9987431,0.0001212097,0.0003141958,0.000505506,0.0001172706,0.0001986801],"domain_scores_gemma":[0.9961201,0.003556421,0.00008234956,0.0001403115,0.00006407165,0.00003677346],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0004303582,0.0009610918,0.02824284,0.002065192,0.002524783,0.000168589,0.002539547,0.3844818,0.01139855,0.3798667,0.03317292,0.1541476],"study_design_scores_gemma":[0.0001543869,0.0001162755,0.001813,0.0001257615,0.00006086475,0.00006719989,0.000005813058,0.5244407,0.0001510706,0.471856,0.001015547,0.0001934029],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.3727042,0.0003941517,0.6118653,0.009264442,0.0003607627,0.0005393485,0.00005687967,0.001525488,0.003289412],"genre_scores_gemma":[0.7786656,0.000005390025,0.2204469,0.0001979523,0.0002260663,0.00005931437,0.0001643801,0.0000216054,0.0002127744],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.4059614,"threshold_uncertainty_score":0.4781716,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1816824019543427,"score_gpt":0.4097063575667703,"score_spread":0.2280239556124276,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}