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{"title"=>"Using a web-based application to define the accuracy of diagnostic tests when the gold standard is imperfect", "type"=>"journal", "authors"=>[{"first_name"=>"Cherry", "last_name"=>"Lim"}, {"first_name"=>"Prapass", "last_name"=>"Wannapinij"}, {"first_name"=>"Lisa", "last_name"=>"White"}, {"first_name"=>"Nicholas P J", "last_name"=>"Day"}, {"first_name"=>"Ben S.", "last_name"=>"Cooper"}, {"first_name"=>"Sharon J.", "last_name"=>"Peacock"}, {"first_name"=>"Direk", "last_name"=>"Limmathurotsakul"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24265775", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0079489", "issn"=>"19326203"}, "id"=>"8f1df9e2-9c1f-3786-bd59-a6ca1cd201aa", "abstract"=>"BACKGROUND: Estimates of the sensitivity and specificity for new diagnostic tests based on evaluation against a known gold standard are imprecise when the accuracy of the gold standard is imperfect. Bayesian latent class models (LCMs) can be helpful under these circumstances, but the necessary analysis requires expertise in computational programming. Here, we describe open-access web-based applications that allow non-experts to apply Bayesian LCMs to their own data sets via a user-friendly interface.\\n\\nMETHODS/PRINCIPAL FINDINGS: Applications for Bayesian LCMs were constructed on a web server using R and WinBUGS programs. The models provided (http://mice.tropmedres.ac) include two Bayesian LCMs: the two-tests in two-population model (Hui and Walter model) and the three-tests in one-population model (Walter and Irwig model). Both models are available with simplified and advanced interfaces. In the former, all settings for Bayesian statistics are fixed as defaults. Users input their data set into a table provided on the webpage. Disease prevalence and accuracy of diagnostic tests are then estimated using the Bayesian LCM, and provided on the web page within a few minutes. With the advanced interfaces, experienced researchers can modify all settings in the models as needed. These settings include correlation among diagnostic test results and prior distributions for all unknown parameters. The web pages provide worked examples with both models using the original data sets presented by Hui and Walter in 1980, and by Walter and Irwig in 1988. We also illustrate the utility of the advanced interface using the Walter and Irwig model on a data set from a recent melioidosis study. The results obtained from the web-based applications were comparable to those published previously.\\n\\nCONCLUSIONS: The newly developed web-based applications are open-access and provide an important new resource for researchers worldwide to evaluate new diagnostic tests.", "link"=>"http://www.mendeley.com/research/using-webbased-application-define-accuracy-diagnostic-tests-gold-standard-imperfect-4", "reader_count"=>18, "reader_count_by_academic_status"=>{"Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Mathematics"=>2, "Medicine and Dentistry"=>11, "Agricultural and Biological Sciences"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>11}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

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• http://doi.org/10.1371/journal.pone.0223832
• http://doi.org/10.1099/jmm.0.001108
• http://doi.org/10.1016/j.jviromet.2016.08.015
• http://doi.org/10.12688/f1000research.10068.1
• http://doi.org/10.1128/JCM.02744-15
• http://doi.org/10.1016/j.cmi.2017.10.017
• http://doi.org/10.3201/eid2102.141045
• http://doi.org/10.1016/j.eimce.2017.03.029
• http://doi.org/10.1016/j.eimc.2017.03.009
• http://doi.org/10.1016/j.cmi.2018.11.014
• http://doi.org/10.3389/fmicb.2020.00457
• http://doi.org/10.1111/liv.13207
• http://doi.org/10.1371/journal.pone.0114930
• http://doi.org/10.1371/journal.pone.0129236
• http://doi.org/10.1016/j.molmed.2015.08.001

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• {"id"=>"403228832993660928", "text"=>"Using a Web-Based Application to Define the Accuracy of Diagnostic Tests When the Gold Standard Is Imperfect: PLoSONE http://t.co/dW3KoLeCtr", "created_at"=>"2013-11-20T18:30:20Z", "user"=>"info_TGHN", "user_name"=>"GlobalHealthNetwork", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000085601617/1198adecb890f73e565f065a7e196bae_normal.jpeg"}

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• {"files"=>["https://ndownloader.figshare.com/files/1277430"], "description"=>"<p>See text for details. </p>", "links"=>[], "tags"=>["simplified", "interface", "two-tests", "two-population", "walter", "website"], "article_id"=>847987, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Cherry Lim", "Prapass Wannapinij", "Lisa White", "Nicholas P. J. Day", "Ben S. Cooper", "Sharon J. Peacock", "Direk Limmathurotsakul"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0079489.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Input_and_output_screen_for_the_simplified_interface_of_the_two_tests_in_two_population_model_Hui_and_Walter_model_provided_on_the_website_http_mice_tropmedres_ac_/847987", "title"=>"Input and output screen for the simplified interface of the two-tests in two-population model (Hui and Walter model) provided on the website (http://mice.tropmedres.ac).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-12 03:39:49"}
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• {"files"=>["https://ndownloader.figshare.com/files/1277440", "https://ndownloader.figshare.com/files/1277441", "https://ndownloader.figshare.com/files/1277442", "https://ndownloader.figshare.com/files/1277443", "https://ndownloader.figshare.com/files/1277444", "https://ndownloader.figshare.com/files/1277445", "https://ndownloader.figshare.com/files/1277446"], "description"=>"<div><p>Background</p><p>Estimates of the sensitivity and specificity for new diagnostic tests based on evaluation against a known gold standard are imprecise when the accuracy of the gold standard is imperfect. Bayesian latent class models (LCMs) can be helpful under these circumstances, but the necessary analysis requires expertise in computational programming. Here, we describe open-access web-based applications that allow non-experts to apply Bayesian LCMs to their own data sets via a user-friendly interface.</p> <p>Methods/Principal Findings</p><p>Applications for Bayesian LCMs were constructed on a web server using R and WinBUGS programs. The models provided (<u><a href=\"http://mice.tropmedres.ac\" target=\"_blank\">http://mice.tropmedres.ac</a></u>) include two Bayesian LCMs: the two-tests in two-population model (Hui and Walter model) and the three-tests in one-population model (Walter and Irwig model). Both models are available with simplified and advanced interfaces. In the former, all settings for Bayesian statistics are fixed as defaults. Users input their data set into a table provided on the webpage. Disease prevalence and accuracy of diagnostic tests are then estimated using the Bayesian LCM, and provided on the web page within a few minutes. With the advanced interfaces, experienced researchers can modify all settings in the models as needed. These settings include correlation among diagnostic test results and prior distributions for all unknown parameters. The web pages provide worked examples with both models using the original data sets presented by Hui and Walter in 1980, and by Walter and Irwig in 1988. We also illustrate the utility of the advanced interface using the Walter and Irwig model on a data set from a recent melioidosis study. The results obtained from the web-based applications were comparable to those published previously.</p> <p>Conclusions</p><p>The newly developed web-based applications are open-access and provide an important new resource for researchers worldwide to evaluate new diagnostic tests.</p> </div>", "links"=>[], "tags"=>["web-based", "diagnostic", "imperfect"], "article_id"=>847992, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Cherry Lim", "Prapass Wannapinij", "Lisa White", "Nicholas P. J. Day", "Ben S. Cooper", "Sharon J. Peacock", "Direk Limmathurotsakul"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0079489.s001", "https://dx.doi.org/10.1371/journal.pone.0079489.s002", "https://dx.doi.org/10.1371/journal.pone.0079489.s003", "https://dx.doi.org/10.1371/journal.pone.0079489.s004", "https://dx.doi.org/10.1371/journal.pone.0079489.s005", "https://dx.doi.org/10.1371/journal.pone.0079489.s006", "https://dx.doi.org/10.1371/journal.pone.0079489.s007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Using_a_Web_Based_Application_to_Define_the_Accuracy_of_Diagnostic_Tests_When_the_Gold_Standard_Is_Imperfect_/847992", "title"=>"Using a Web-Based Application to Define the Accuracy of Diagnostic Tests When the Gold Standard Is Imperfect", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-12 03:39:49"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Computer and information sciences", "average_usage"=>[297, 488, 616, 724, 828, 939, 1038, 1127, 1223, 1311, 1393, 1479, 1556]}, {"subject_area"=>"/Computer and information sciences/Computer software", "average_usage"=>[275, 441, 557, 690, 806, 929, 1029, 1117, 1218, 1286, 1349, 1438, 1506]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}, {"subject_area"=>"/Medicine and health sciences/Diagnostic medicine", "average_usage"=>[244, 425, 535, 636, 728, 814, 900, 982, 1063, 1139, 1221, 1296, 1361]}, {"subject_area"=>"/Medicine and health sciences/Infectious diseases", "average_usage"=>[297, 523, 655, 765, 866, 971, 1070, 1159, 1256, 1337, 1424, 1496, 1568]}]}

F1000Prime