{"id":"https://openalex.org/W4415883036","doi":"https://doi.org/10.1371/journal.pcbi.1013647","title":"Calibration of transmission-dynamic infectious disease models: A scoping review and reporting framework","display_name":"Calibration of transmission-dynamic infectious disease models: A scoping review and reporting framework","publication_year":2025,"publication_date":"2025-11-04","ids":{"openalex":"https://openalex.org/W4415883036","doi":"https://doi.org/10.1371/journal.pcbi.1013647","pmid":"https://pubmed.ncbi.nlm.nih.gov/41187204"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013647","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013647","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013647","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106708854","display_name":"Emmanuelle A. Dankwa","orcid":"https://orcid.org/0000-0002-3084-5915"},"institutions":[{"id":"https://openalex.org/I4210156643","display_name":"Harvard Global Health Institute","ror":"https://ror.org/055avk103","country_code":"US","type":"education","lineage":["https://openalex.org/I4210156643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emmanuelle A. Dankwa","raw_affiliation_strings":["Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3084-5915","affiliations":[{"raw_affiliation_string":"Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210156643"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108977295","display_name":"L\u00e9a Cavalli","orcid":"https://orcid.org/0009-0005-2322-6971"},"institutions":[{"id":"https://openalex.org/I1338678786","display_name":"Center for Disease Dynamics, Economics & Policy","ror":"https://ror.org/01skhd946","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338678786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"L\u00e9a Cavalli","raw_affiliation_strings":["Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1338678786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013298277","display_name":"Ruchita Balasubramanian","orcid":"https://orcid.org/0000-0002-9151-9873"},"institutions":[{"id":"https://openalex.org/I1338678786","display_name":"Center for Disease Dynamics, Economics & Policy","ror":"https://ror.org/01skhd946","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338678786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruchita Balasubramanian","raw_affiliation_strings":["Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1338678786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101730533","display_name":"Melike Hazal Can","orcid":"https://orcid.org/0000-0001-6810-0356"},"institutions":[{"id":"https://openalex.org/I4210156643","display_name":"Harvard Global Health Institute","ror":"https://ror.org/055avk103","country_code":"US","type":"education","lineage":["https://openalex.org/I4210156643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Melike Hazal Can","raw_affiliation_strings":["Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6810-0356","affiliations":[{"raw_affiliation_string":"Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210156643"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110101784","display_name":"Hong Cui","orcid":"https://orcid.org/0000-0001-5734-825X"},"institutions":[{"id":"https://openalex.org/I4210156643","display_name":"Harvard Global Health Institute","ror":"https://ror.org/055avk103","country_code":"US","type":"education","lineage":["https://openalex.org/I4210156643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hening Cui","raw_affiliation_strings":["Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-5734-825X","affiliations":[{"raw_affiliation_string":"Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210156643"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067598681","display_name":"Katherine Min Jia","orcid":"https://orcid.org/0000-0001-8875-2415"},"institutions":[{"id":"https://openalex.org/I1338678786","display_name":"Center for Disease Dynamics, Economics & Policy","ror":"https://ror.org/01skhd946","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338678786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Katherine M. Jia","raw_affiliation_strings":["Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1338678786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080903903","display_name":"Yunfei Li","orcid":"https://orcid.org/0000-0002-6891-5392"},"institutions":[{"id":"https://openalex.org/I4210156643","display_name":"Harvard Global Health Institute","ror":"https://ror.org/055avk103","country_code":"US","type":"education","lineage":["https://openalex.org/I4210156643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yunfei Li","raw_affiliation_strings":["Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210156643"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069882478","display_name":"Sylvia K. Ofori","orcid":"https://orcid.org/0000-0002-9961-9975"},"institutions":[{"id":"https://openalex.org/I1338678786","display_name":"Center for Disease Dynamics, Economics & Policy","ror":"https://ror.org/01skhd946","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338678786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sylvia K. Ofori","raw_affiliation_strings":["Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1338678786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045687399","display_name":"Nicole A. Swartwood","orcid":"https://orcid.org/0000-0003-4116-9243"},"institutions":[{"id":"https://openalex.org/I4210156643","display_name":"Harvard Global Health Institute","ror":"https://ror.org/055avk103","country_code":"US","type":"education","lineage":["https://openalex.org/I4210156643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nicole A. Swartwood","raw_affiliation_strings":["Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210156643"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Carrie G. Wade","orcid":null},"institutions":[{"id":"https://openalex.org/I2802436442","display_name":"Boston Public Library","ror":"https://ror.org/00n5y3d41","country_code":"US","type":"archive","lineage":["https://openalex.org/I2802436442"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carrie G. Wade","raw_affiliation_strings":["Countway Library, Harvard School of Medicine, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Countway Library, Harvard School of Medicine, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I2802436442"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033364470","display_name":"Caroline O. Buckee","orcid":"https://orcid.org/0000-0002-8386-5899"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Caroline O. Buckee","raw_affiliation_strings":["Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033519595","display_name":"Jeffrey W. Eaton","orcid":"https://orcid.org/0000-0001-7728-728X"},"institutions":[{"id":"https://openalex.org/I1338678786","display_name":"Center for Disease Dynamics, Economics & Policy","ror":"https://ror.org/01skhd946","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1338678786"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Jeffrey W. Imai-Eaton","raw_affiliation_strings":["Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America","MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I1338678786"]},{"raw_affiliation_string":"MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068219287","display_name":"Nicolas A. Menzies","orcid":"https://orcid.org/0000-0002-2571-016X"},"institutions":[{"id":"https://openalex.org/I4210156643","display_name":"Harvard Global Health Institute","ror":"https://ror.org/055avk103","country_code":"US","type":"education","lineage":["https://openalex.org/I4210156643"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nicolas A. Menzies","raw_affiliation_strings":["Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-2571-016X","affiliations":[{"raw_affiliation_string":"Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210156643"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5013298277","https://openalex.org/A5033364470","https://openalex.org/A5033519595","https://openalex.org/A5045687399","https://openalex.org/A5067598681","https://openalex.org/A5068219287","https://openalex.org/A5069882478","https://openalex.org/A5080903903","https://openalex.org/A5101730533","https://openalex.org/A5106708854","https://openalex.org/A5108977295","https://openalex.org/A5110101784"],"corresponding_institution_ids":["https://openalex.org/I1338678786","https://openalex.org/I136199984","https://openalex.org/I2802436442","https://openalex.org/I4210156643","https://openalex.org/I47508984"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8257,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.75341181,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"21","issue":"11","first_page":"e1013647","last_page":"e1013647"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.4867999851703644,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10410","display_name":"COVID-19 epidemiological studies","score":0.4867999851703644,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.11779999732971191,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.10029999911785126,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.7390000224113464},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.6985999941825867},{"id":"https://openalex.org/keywords/credibility","display_name":"Credibility","score":0.5479000210762024},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.367900013923645},{"id":"https://openalex.org/keywords/reproducibility","display_name":"Reproducibility","score":0.3343000113964081},{"id":"https://openalex.org/keywords/emerging-infectious-disease","display_name":"Emerging infectious disease","score":0.3009999990463257}],"concepts":[{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.7390000224113464},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.6985999941825867},{"id":"https://openalex.org/C2780224610","wikidata":"https://www.wikidata.org/wiki/Q1530061","display_name":"Credibility","level":2,"score":0.5479000210762024},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4564000070095062},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4462999999523163},{"id":"https://openalex.org/C19527891","wikidata":"https://www.wikidata.org/wiki/Q1120908","display_name":"Medical physics","level":1,"score":0.3799999952316284},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.367900013923645},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36739999055862427},{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.3343000113964081},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32280001044273376},{"id":"https://openalex.org/C2779973787","wikidata":"https://www.wikidata.org/wiki/Q609748","display_name":"Emerging infectious disease","level":3,"score":0.3009999990463257},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.2863999903202057},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.2858000099658966},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.27000001072883606},{"id":"https://openalex.org/C2985496182","wikidata":"https://www.wikidata.org/wiki/Q1773974","display_name":"Disease prevention","level":2,"score":0.2612999975681305},{"id":"https://openalex.org/C177713679","wikidata":"https://www.wikidata.org/wiki/Q679690","display_name":"Intensive care medicine","level":1,"score":0.2578999996185303}],"mesh":[{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013647","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013647","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41187204","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41187204","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:79b136017ed1476095a430509d88fa9f","is_oa":true,"landing_page_url":"https://doaj.org/article/79b136017ed1476095a430509d88fa9f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 11, p e1013647 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11413076","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12604776","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013647","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013647","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4727752154","display_name":null,"funder_award_id":"T32 AI007535","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8729796487","display_name":null,"funder_award_id":"200-2016-91779","funder_id":"https://openalex.org/F4320332162","funder_display_name":"Centers for Disease Control and Prevention"}],"funders":[{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1482581820","https://openalex.org/W1973090847","https://openalex.org/W1986346806","https://openalex.org/W1988555439","https://openalex.org/W2034380059","https://openalex.org/W2057127516","https://openalex.org/W2116416291","https://openalex.org/W2131553265","https://openalex.org/W2151729750","https://openalex.org/W2594816818","https://openalex.org/W2751317214","https://openalex.org/W2783040364","https://openalex.org/W2794521555","https://openalex.org/W2889970632","https://openalex.org/W2891378911","https://openalex.org/W2903321323","https://openalex.org/W2949690026","https://openalex.org/W2951092176","https://openalex.org/W3012797136","https://openalex.org/W3014427260","https://openalex.org/W3023721945","https://openalex.org/W3041385952","https://openalex.org/W3161540023","https://openalex.org/W3164986408","https://openalex.org/W4306318790","https://openalex.org/W4327568792","https://openalex.org/W4387972449","https://openalex.org/W4402473670"],"related_works":[],"abstract_inverted_index":{"OBJECTIVE/BACKGROUND:":[0],"Transmission-dynamic":[1],"models":[2,95,125,150,157],"are":[3],"commonly":[4],"used":[5,232],"to":[6,85,116,128,164,194,201],"study":[7],"infectious":[8,55,298],"disease":[9,56,299],"epidemiology.":[10],"Calibration":[11],"involves":[12],"identifying":[13],"model":[14,19,204,218],"parameter":[15],"values":[16],"that":[17],"align":[18],"outputs":[20],"with":[21,143,217,226,233,239],"observed":[22],"data":[23,130],"or":[24,131,181,187,267],"other":[25],"evidence.":[26],"Inaccurate":[27],"calibration":[28,53,63,76,87,212,293,308],"and":[29,35,58,78,89,99,106,114,151,221,235,265,314],"inconsistent":[30],"reporting":[31,51,75,91,243,306],"produce":[32],"inference":[33],"errors":[34],"limit":[36],"reproducibility,":[37],"compromising":[38],"confidence":[39],"in":[40,81,93,251,260,270,282,296],"the":[41,70,195,203,278],"validity":[42],"of":[43,54,61,96,168,211,256,288,307,316],"modeled":[44,317],"results.":[45],"No":[46],"standardized":[47],"framework":[48,73,247,304],"exists":[49],"for":[50,74,305],"on":[52,292],"models,":[57,142,169],"an":[59],"understanding":[60],"current":[62],"approaches":[64,88,309],"is":[65,294],"lacking.":[66],"METHODS:":[67],"We":[68,110,135],"developed":[69],"Purpose-Inputs-Process-Outputs":[71],"(PIPO)":[72],"practices":[77],"applied":[79],"it":[80],"a":[82],"scoping":[83],"review":[84],"assess":[86],"evaluate":[90,165],"comprehensiveness":[92],"transmission-dynamic":[94],"tuberculosis,":[97],"HIV":[98],"malaria":[100],"published":[101,132],"between":[102],"January":[103,107],"1,":[104],"2018,":[105],"16,":[108],"2024.":[109],"searched":[111],"relevant":[112,193],"databases":[113],"websites":[115],"identify":[117],"eligible":[118,138],"publications,":[119],"including":[120],"peer-reviewed":[121],"studies":[122,139],"where":[123],"these":[124],"were":[126,174,179,249],"calibrated":[127,175],"empirical":[129],"estimates.":[133],"RESULTS:":[134],"identified":[136],"411":[137],"encompassing":[140],"419":[141],"74%":[144],"(n":[145,153,253,262,272,285],"=":[146,154,171,185,207,224,254,263,273,286],"309)":[147],"being":[148,199],"compartmental":[149,240],"20%":[152,284],"81)":[155],"individual-based":[156],"(IBMs).":[158],"The":[159,209],"predominant":[160],"analytical":[161],"purpose":[162],"was":[163,192,214,277],"interventions":[166],"(71%":[167],"n":[170,184,206],"298).":[172],"Parameters":[173],"mainly":[176],"because":[177,188],"they":[178],"unknown":[180],"ambiguous":[182],"(40%,":[183],"168),":[186],"determining":[189],"their":[190],"value":[191],"scientific":[196],"question":[197],"beyond":[198],"necessary":[200],"run":[202],"(20%,":[205],"85).":[208],"choice":[210],"method":[213],"significantly":[215],"associated":[216],"structure":[219],"(p-value<0.001)":[220],"stochasticity":[222],"(p-value":[223],"0.006),":[225],"approximate":[227],"Bayesian":[228],"computation":[229],"more":[230],"frequently":[231],"IBMs":[234],"Markov-Chain":[236],"Monte":[237],"Carlo":[238],"models.":[241,289],"Regarding":[242],"comprehensiveness,":[244],"all":[245],"PIPO":[246],"items":[248,259,269],"reported":[250],"4%":[252],"18)":[255],"models;":[257],"11-14":[258],"66%":[261],"277),":[264],"10":[266],"fewer":[268],"28%":[271],"124).":[274],"Implementation":[275],"code":[276],"least":[279],"reported,":[280],"available":[281],"only":[283],"82)":[287],"CONCLUSIONS:":[290],"Reporting":[291],"heterogeneous":[295],"recent":[297],"modeling":[300],"literature.":[301],"Our":[302],"proposed":[303],"could":[310],"support":[311],"improved":[312],"reproducibility":[313],"credibility":[315],"analyses.":[318]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-11-04T00:00:00"}
