{"id":2,"date":"2025-05-01T16:26:43","date_gmt":"2025-05-01T16:26:43","guid":{"rendered":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/?page_id=2"},"modified":"2025-06-20T14:02:37","modified_gmt":"2025-06-20T14:02:37","slug":"software","status":"publish","type":"page","link":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/software\/","title":{"rendered":"Software Accompanying Eugene&#8217;s Publications"},"content":{"rendered":"\n<h4><strong>Note: No warranty and use at your own risk<\/strong><\/h4>\n<ul>\n<li>cequre: Censored Quantile Regression &amp; Monotonicity-Respecting Restoring [<a href=\"https:\/\/cran.r-project.org\/package=cequre\">\u00a0<span style=\"color: #0033a0\">R package &#8220;cequre&#8221; @ CRAN<\/span><\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/cequre\/cequre.pdf\">reference manual<\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/cequre\/vignettes\/cequre.html\">vignette<\/a>]<br \/>Implementation of\u00a0<span style=\"color: #f2a900\">Huang<\/span>\u00a0(2010,\u00a0<em><span style=\"color: #d14124\">The Annals of Statistics<\/span><\/em>\u00a038, pp 1607&#8211;1637) and\u00a0<span style=\"color: #f2a900\">Huang<\/span>\u00a0(2017,\u00a0<em><span style=\"color: #d14124\">Journal of the American Statistical Association<\/span><\/em>\u00a0112, pp 613&#8211;622).<\/li>\n<\/ul>\n<ul>\n<li>fastAFT: Fast Regression for the Accelerated Failure Time (AFT) Model [<a href=\"https:\/\/cran.r-project.org\/package=fastAFT\">\u00a0<span style=\"color: #0033a0\">R package &#8220;fastAFT&#8221; @ CRAN<\/span><\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/fastAFT\/fastAFT.pdf\">reference manual<\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/fastAFT\/vignettes\/fastAFT.html\">vignette<\/a>]<br \/>Implementation of\u00a0<span style=\"color: #f2a900\">Huang<\/span>\u00a0(2013,\u00a0<em><span style=\"color: #d14124\">Scandinavian Journal of Statistics<\/span><\/em>\u00a040, pp 789&#8211;806).<\/li>\n<\/ul>\n<ul>\n<li>coxerr: Cox regression with dependent error in covariates [<a href=\"https:\/\/cran.r-project.org\/package=coxerr\">\u00a0<span style=\"color: #0033a0\">R package &#8220;coxerr&#8221; @ CRAN<\/span><\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/coxerr\/coxerr.pdf\">reference manual<\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/coxerr\/vignettes\/coxerr.html\">vignette<\/a>]<br \/>Implementation of\u00a0<span style=\"color: #f2a900\">Huang and Wang<\/span>\u00a0(2018,\u00a0<em><span style=\"color: #d14124\">Biometrics<\/span><\/em>\u00a074, pp 118&#8211;126).<\/li>\n<\/ul>\n<ul>\n<li>SenSpe: Estimating Specificity at Controlled Sensitivity, or Vice Versa [<a href=\"https:\/\/cran.r-project.org\/package=SenSpe\">\u00a0<span style=\"color: #0033a0\">R package &#8220;SenSpe&#8221; @ CRAN<\/span><\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/SenSpe\/SenSpe.pdf\">reference manual<\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/SenSpe\/vignettes\/SenSpe.html\">vignette<\/a>]<br \/>Implementation of\u00a0<span style=\"color: #f2a900\">Huang, Parakati, Patil, and Sanda<\/span>\u00a0(2023,\u00a0<em><span style=\"color: #d14124\">Statistica Sinica<\/span>\u00a0<\/em>33, pp 193&#8211;214).<\/li>\n<\/ul>\n<ul>\n<li>caROC: Continuous Biomarker Evaluation with Adjustment of Covariates. [<a href=\"https:\/\/cran.r-project.org\/package=caROC\">\u00a0<span style=\"color: #0033a0\">R package &#8220;caROC&#8221; @ CRAN<\/span><\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/caROC\/caROC.pdf\">reference manual<\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/caROC\/vignettes\/caROC.html\">vignette<\/a>]<br \/>Implementation of\u00a0<span style=\"color: #f2a900\">Li, Huang, Patil, and Sanda<\/span>\u00a0(2023,\u00a0<em><span style=\"color: #d14124\">Biometrics<\/span><\/em>\u00a079, pp 39&#8211;48) and\u00a0<span style=\"color: #f2a900\">Li, Huang, Patil, Rubin, and Sanda<\/span>\u00a0(2023,\u00a0<em><span style=\"color: #d14124\">Statistics in Medicine<\/span><\/em>\u00a042, 953&#8211;969) by Ziyi Li.<\/li>\n<\/ul>\n<ul>\n<li>lincom: Linear Biomarker Combination: Empirical Performance Optimization. [<a href=\"https:\/\/cran.r-project.org\/package=lincom\">\u00a0<span style=\"color: #0033a0\">R package &#8220;lincom&#8221; @ CRAN<\/span><\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/lincom\/lincom.pdf\">reference manual<\/a>,\u00a0<a href=\"https:\/\/cran.r-project.org\/web\/packages\/lincom\/vignettes\/lincom.html\">vignette<\/a>]<br \/>Implementation of\u00a0<span style=\"color: #f2a900\">Huang and Sanda<\/span>\u00a0(2022,\u00a0<em><span style=\"color: #d14124\">The Annals of Statistics<\/span><\/em>\u00a050, pp 2793&#8211;2815).<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>maxAUC: Empirical AUC maximization. [<a href=\"https:\/\/github.com\/yuxuanchn\/maxAUC\">\u00a0R package &#8220;maxAUC&#8221;<\/a>]<br>Implementation of\u00a0Chen and Huang (2025+,\u00a0<em>Statistica Sinica<\/em>, accepted) by Yuxuan Chen.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Note: No warranty and use at your own risk cequre: Censored Quantile Regression &amp; Monotonicity-Respecting Restoring [\u00a0R package &#8220;cequre&#8221; @ CRAN,\u00a0reference manual,\u00a0vignette]Implementation of\u00a0Huang\u00a0(2010,\u00a0The Annals of Statistics\u00a038, pp 1607&#8211;1637) and\u00a0Huang\u00a0(2017,\u00a0Journal of the American Statistical Association\u00a0112, pp 613&#8211;622). fastAFT: Fast Regression for the Accelerated Failure Time (AFT) Model [\u00a0R package &#8220;fastAFT&#8221; @ CRAN,\u00a0reference manual,\u00a0vignette]Implementation of\u00a0Huang\u00a0(2013,\u00a0Scandinavian Journal of <a class=\"more-link\" href=\"https:\/\/scholarblogs.emory.edu\/eugenehuang\/software\/\">Read More &#8230;<\/a><\/p>\n","protected":false},"author":5076,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-2","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/pages\/2","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/users\/5076"}],"replies":[{"embeddable":true,"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/comments?post=2"}],"version-history":[{"count":4,"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/pages\/2\/revisions"}],"predecessor-version":[{"id":67,"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/pages\/2\/revisions\/67"}],"wp:attachment":[{"href":"https:\/\/scholarblogs.emory.edu\/eugenehuang\/wp-json\/wp\/v2\/media?parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}