{"id":"W3188731060","doi":"10.1101/2021.07.25.21261097","title":"regentrans: a framework and R package for using genomics to study regional pathogen transmission","year":2021,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Canadian Institutes of Health Research; Michigan Institute for Clinical and Health Research; National Institutes of Health; National Science Foundation","keywords":"Transmission (telecommunications); Data science; Genomics; Genome; Health care; Open source; Computer science; Biology; Telecommunications; Genetics; Political science","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01225942,0.004375443,0.003096634,0.003875742,0.0009777732,0.004433325,0.005291241,0.001901307,0.05093503],"category_scores_gemma":[0.06691157,0.003017332,0.005093128,0.003385782,0.001781211,0.002649992,0.00567729,0.004879396,0.03549483],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001250099,"about_ca_system_score_gemma":0.005977278,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00656289,"about_ca_topic_score_gemma":0.006985328,"domain_scores_codex":[0.9939981,0.002918778,0.0005545203,0.001198127,0.001011546,0.0003189091],"domain_scores_gemma":[0.9735735,0.01963171,0.001968951,0.002292905,0.001859839,0.0006730673],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001201361,0.0001831794,0.01710013,0.007570608,0.004300862,0.001582278,0.001163551,0.04542593,0.004874529,0.04116587,0.7865303,0.08890135],"study_design_scores_gemma":[0.001685089,0.0003610008,0.0107989,0.001787117,0.001502922,0.001329473,0.0003977137,0.1581081,0.009633617,0.1351179,0.6786849,0.0005933903],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.005783923,0.001735437,0.5491571,0.002694201,0.001040005,0.001011648,0.1532961,0.2794037,0.005877814],"genre_scores_gemma":[0.046847,0.001735133,0.6949966,0.00300434,0.0004353932,0.007097349,0.09530825,0.1452712,0.005304745],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.05093503,"threshold_uncertainty_score":0.1703947,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03173608711911292,"score_gpt":0.3024202778742899,"score_spread":0.270684190755177,"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."}}