{"id":3427,"date":"2024-03-31T08:54:33","date_gmt":"2024-03-30T23:54:33","guid":{"rendered":"https:\/\/plaza.umin.ac.jp\/~OIO\/?p=3427"},"modified":"2024-03-31T08:54:33","modified_gmt":"2024-03-30T23:54:33","slug":"r-epibasix%e3%82%92%e8%a7%a6%e3%81%a3%e3%81%a6%e3%81%bf%e3%81%9f","status":"publish","type":"post","link":"https:\/\/plaza.umin.ac.jp\/~OIO\/?p=3427","title":{"rendered":"R epibasix\u3092\u89e6\u3063\u3066\u307f\u305f"},"content":{"rendered":"<h1>epibasix\u30d1\u30c3\u30b1\u30fc\u30b8\u306e\u95a2\u6570\u3092\u8a66\u3057\u3066\u898b\u307e\u3057\u305f<\/h1>\n<h2>sensSpec\u95a2\u6570<\/h2>\n<p>\u3053\u306eR\u30b3\u30fc\u30c9\u306f\u3001\u75ab\u5b66\u7814\u7a76\u306b\u304a\u3044\u3066\u65b0\u3057\u3044\u691c\u67fb\u6cd5\u3084\u81ea\u5df1\u5831\u544a\u3092\u73fe\u884c\u306e\u30b4\u30fc\u30eb\u30c9\u30b9\u30bf\u30f3\u30c0\u30fc\u30c9\u3068\u6bd4\u8f03\u3059\u308b\u969b\u306b\u3001\u611f\u5ea6\u3001\u7279\u7570\u5ea6\u3001Youden\u6307\u6570\u3001\u304a\u3088\u3073\u4e00\u81f4\u7387\u3092\u8a08\u7b97\u3059\u308b\u305f\u3081\u306e\u3082\u306e\u3067\u3059\u3002<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">library(epibasix)\r\n\r\n# This function is designed to calculate Sensitivity, Specificity, Youden\u2019s J and Percent Agreement.\r\n# These tools are used to assess the validity of a new instrument or self-report against the current\r\n# gold standard. In general, self-report is less expensive, but may be subject to information bias.\r\n# Computational formulae can be found in the reference.\r\n\r\ndat &lt;- cbind(c(18,1), c(19,11))\r\nsummary(sensSpec(dat))\r\n\r\n# Szklo M and Nieto FJ. Epidemiology: Beyond the Basics, Jones and Bartlett: Boston, 2007 P.315<\/pre>\n<ul>\n<li><strong>\u611f\u5ea6 (Sensitivity)<\/strong>: \u691c\u67fb\u6cd5\u304c\u75be\u60a3\u3092\u6b63\u3057\u304f\u691c\u51fa\u3059\u308b\u80fd\u529b\u3092\u8a55\u4fa1\u3057\u307e\u3059\u3002\u611f\u5ea6\u306f\u3001\u75be\u60a3\u306e\u5b58\u5728\u3059\u308b\u4eba\u3005\u306e\u3046\u3061\u3001\u691c\u67fb\u3067\u967d\u6027\u3068\u5224\u5b9a\u3055\u308c\u305f\u5272\u5408\u3092\u793a\u3057\u307e\u3059\u3002<\/li>\n<li><strong>\u7279\u7570\u5ea6 (Specificity)<\/strong>: \u691c\u67fb\u6cd5\u304c\u5065\u5eb7\u306a\u4eba\u3005\u3092\u6b63\u3057\u304f\u9670\u6027\u3068\u5224\u5b9a\u3059\u308b\u80fd\u529b\u3092\u8a55\u4fa1\u3057\u307e\u3059\u3002\u7279\u7570\u5ea6\u306f\u3001\u5065\u5eb7\u306a\u4eba\u3005\u306e\u3046\u3061\u3001\u691c\u67fb\u3067\u9670\u6027\u3068\u5224\u5b9a\u3055\u308c\u305f\u5272\u5408\u3092\u793a\u3057\u307e\u3059\u3002<\/li>\n<li><strong>Youden\u6307\u6570 (J)<\/strong>: Youden\u6307\u6570\u306f\u3001\u611f\u5ea6\u3068\u7279\u7570\u5ea6\u306e\u30d0\u30e9\u30f3\u30b9\u3092\u793a\u3059\u6307\u6a19\u3067\u3059\u3002Youden\u6307\u6570\u306f\u3001\u611f\u5ea6\u3068\u7279\u7570\u5ea6\u306e\u548c\u304b\u30891\u3092\u5f15\u3044\u305f\u5024\u3067\u8a08\u7b97\u3055\u308c\u307e\u3059\u3002Youden\u6307\u6570\u304c\u9ad8\u3044\u307b\u3069\u3001\u691c\u67fb\u6cd5\u306e\u6027\u80fd\u304c\u826f\u3044\u3053\u3068\u3092\u610f\u5473\u3057\u307e\u3059\u3002<\/li>\n<li><strong>\u4e00\u81f4\u7387 (Percent Agreement)<\/strong>: \u73fe\u884c\u306e\u30b4\u30fc\u30eb\u30c9\u30b9\u30bf\u30f3\u30c0\u30fc\u30c9\u3068\u65b0\u3057\u3044\u691c\u67fb\u6cd5\u306e\u7d50\u679c\u304c\u4e00\u81f4\u3059\u308b\u5272\u5408\u3092\u793a\u3057\u307e\u3059\u3002\u4e00\u81f4\u7387\u306f\u3001\u4e21\u8005\u306e\u7d50\u679c\u304c\u540c\u3058\u3068\u5224\u5b9a\u3055\u308c\u305f\u5272\u5408\u3067\u3059\u3002<\/li>\n<\/ul>\n<p><a href=\"https:\/\/rdocumentation.org\/packages\/epibasix\/versions\/1.5\/topics\/sensSpec\" class=\"tooltip-target\" data-citationid=\"691cd294-09f8-3bb3-b36a-96544a33eebf-17-group\" h=\"ID=SERP,5017.1\" target=\"_blank\" rel=\"noopener\">\u3053\u306e\u30b3\u30fc\u30c9\u3067\u306f\u3001<code>epibasix<\/code>\u30d1\u30c3\u30b1\u30fc\u30b8\u3092\u4f7f\u7528\u3057\u3066\u3001\u4e0e\u3048\u3089\u308c\u305f\u30c7\u30fc\u30bf\u30bb\u30c3\u30c8\u304b\u3089\u611f\u5ea6\u3001\u7279\u7570\u5ea6\u3001Youden\u6307\u6570\u3001\u304a\u3088\u3073\u4e00\u81f4\u7387\u3092\u8a08\u7b97\u3057\u3066\u3044\u307e\u3059\u3002\u5177\u4f53\u7684\u306a\u8a08\u7b97\u5f0f\u306f\u3001\u53c2\u8003\u6587\u732e\u3067\u78ba\u8a8d\u3067\u304d\u307e\u3059<\/a><a href=\"https:\/\/rdocumentation.org\/packages\/epibasix\/versions\/1.5\/topics\/sensSpec\" class=\"ac-anchor sup-target\" target=\"_blank\" data-citationid=\"691cd294-09f8-3bb3-b36a-96544a33eebf-17\" aria-label=\"1: epibasix\" h=\"ID=SERP,5017.1\" rel=\"noopener\"><sup class=\"citation-sup\">1<\/sup><\/a>\u3002<\/p>\n<p>\u3053\u306e\u3088\u3046\u306a\u6307\u6a19\u3092\u4f7f\u7528\u3059\u308b\u3053\u3068\u3067\u3001\u65b0\u3057\u3044\u691c\u67fb\u6cd5\u306e\u6709\u52b9\u6027\u3092\u8a55\u4fa1\u3057\u3001\u75ab\u5b66\u7814\u7a76\u306b\u304a\u3044\u3066\u9069\u5207\u306a\u5224\u65ad\u3092\u884c\u3046\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n<h2>sensSpec\u95a2\u6570\u306e\u5b9f\u884c\u7d50\u679c<\/h2>\n<pre aria-label=\"Console Output\" role=\"document\" class=\"GND-IWGDH3B\" id=\"rstudio_console_output\" tabindex=\"0\"><span class=\"GND-IWGDI3B\" role=\"document\" tabindex=\"-1\"><span style=\"color: #0000ff;\"><span class=\"GND-IWGDO3B ace_keyword\">&gt; <\/span><span class=\"GND-IWGDN2B ace_keyword\">summary(sensSpec(dat))\r\n<\/span><\/span><span class=\"GND-IWGDH3B\">\r\n Detailed Sensitivity and Specitivity Output \r\n \r\nInput Matrix: \r\n           Gold Standard A Gold Standard B\r\nReported A              18              19\r\nReported B               1              11\r\n\r\nThe sample sensitivity is: 94.7% \r\n95% Confidence Limits for true sensitivity are: [84.7, 104.8]\r\n\r\nThe sample of specificity is: 36.7% \r\n95% Confidence Limits for true specificity are: [19.4, 53.9]\r\n\r\nThe sample value of Youden's J is: 31.4\r\n95% Confidence Limits for Youden's J are: [11.4, 51.4]\r\n\r\nSample value for Percent Agreement (PA) is: 59.2% \r\n95% Confidence Limits for PA are: [45.4, 72.9]\r\n\r\n<\/span><\/span><\/pre>\n<p>\u307e\u3001\u305d\u3046\u3044\u3046\u4e8b\u307f\u305f\u3044\u3067\u3059\u3002<\/p>\n<h2>univar\u95a2\u6570<\/h2>\n<p>\u3053\u306eR\u30b3\u30fc\u30c9\u306f\u3001<strong>\u5358\u4e00\u306e\u5909\u6570\u306b\u5bfe\u3059\u308b\u8a73\u7d30\u306a\u5358\u5909\u91cf\u89e3\u6790<\/strong>\u3092\u63d0\u4f9b\u3057\u307e\u3059\u3002\u5177\u4f53\u7684\u306b\u306f\u3001\u4ee5\u4e0b\u306e\u7d71\u8a08\u91cf\u3092\u8a08\u7b97\u3057\u307e\u3059\uff1a<\/p>\n<ul>\n<li><strong>\u5e73\u5747 (mean)<\/strong>: \u89b3\u6e2c\u5024\u306e\u5e73\u5747\u5024\u3002<\/li>\n<li><strong>\u4e2d\u592e\u5024 (median)<\/strong>: \u89b3\u6e2c\u5024\u306e\u4e2d\u592e\u5024\u3002<\/li>\n<li><strong>\u6a19\u6e96\u504f\u5dee (standard deviation)<\/strong>: \u89b3\u6e2c\u5024\u306e\u3070\u3089\u3064\u304d\u306e\u5c3a\u5ea6\u3002<\/li>\n<li><strong>\u7bc4\u56f2 (range)<\/strong>: \u89b3\u6e2c\u5024\u306e\u6700\u5c0f\u5024\u304b\u3089\u6700\u5927\u5024\u307e\u3067\u306e\u5e45\u3002<\/li>\n<li><strong>\u4eee\u8aac\u691c\u5b9a\u3068\u4fe1\u983c\u533a\u9593\u306e\u30c4\u30fc\u30eb<\/strong>\u3002<\/li>\n<\/ul>\n<p>\u5177\u4f53\u7684\u306a\u4f7f\u7528\u65b9\u6cd5\u306f\u6b21\u306e\u901a\u308a\u3067\u3059\uff1a<\/p>\n<pre class=\"EnlighterJSRAW\" data-enlighter-language=\"generic\">#This function provides detailed univariate analysis for a single variable. Values include the sample\r\n# mean, median, standard deviation and range, as well as tools for hypothesis tests and confidence\r\n# intervals.\r\n\r\nx &lt;- rexp(100)\r\nunivar(x)\r\n\r\n# Casella G and Berger RL. Statistical Inference (2nd Ed.) Duxbury: New York, 2002.<\/pre>\n<h2>univar\u95a2\u6570\u306e\u5b9f\u884c\u7d50\u679c<\/h2>\n<pre aria-label=\"Console Output\" role=\"document\" class=\"GND-IWGDH3B\" id=\"rstudio_console_output\" tabindex=\"0\"><span class=\"GND-IWGDI3B\" role=\"document\" style=\"color: #0000ff;\" tabindex=\"-1\"><span class=\"GND-IWGDO3B ace_keyword\">&gt; <\/span><span class=\"GND-IWGDN2B ace_keyword\">x &lt;- rexp(100)\r\n<\/span><\/span><span class=\"GND-IWGDI3B\" role=\"document\" tabindex=\"-1\"><span style=\"color: #0000ff;\"><span class=\"GND-IWGDO3B ace_keyword\">&gt; <\/span><span class=\"GND-IWGDN2B ace_keyword\">univar(x)\r\n<\/span><\/span><span class=\"GND-IWGDH3B\">\r\nUnivariate Summary\r\n \r\nSample Size: 100\r\nSample Mean: 0.972 \r\nSample Median: 0.632 \r\nSample Standard Deviation: 0.986 <\/span><\/span><\/pre>\n<p>\u307e\u3001\u3053\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u306f\u4ed6\u306e\u3082\u306e\u3067\u30ab\u30d0\u30fc\u3067\u304d\u305d\u3046\u304b\u306a<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>epibasix\u30d1\u30c3\u30b1\u30fc\u30b8\u306e\u95a2\u6570\u3092\u8a66\u3057\u3066\u898b\u307e\u3057\u305f sensSpec\u95a2\u6570 \u3053\u306eR\u30b3\u30fc\u30c9\u306f\u3001\u75ab\u5b66\u7814\u7a76\u306b\u304a\u3044\u3066\u65b0\u3057\u3044\u691c\u67fb\u6cd5\u3084\u81ea\u5df1\u5831\u544a\u3092\u73fe\u884c\u306e\u30b4\u30fc\u30eb\u30c9\u30b9\u30bf\u30f3\u30c0\u30fc\u30c9\u3068\u6bd4\u8f03\u3059\u308b\u969b\u306b\u3001\u611f\u5ea6\u3001\u7279\u7570\u5ea6\u3001Youden\u6307\u6570\u3001\u304a\u3088\u3073\u4e00\u81f4\u7387\u3092\u8a08\u7b97&#8230;<\/p>\n","protected":false},"author":1,"featured_media":3428,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[5],"tags":[],"class_list":["post-3427","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-miscellaneous"],"jetpack_featured_media_url":"https:\/\/plaza.umin.ac.jp\/~OIO\/wp-content\/uploads\/2024\/03\/cat1.jpg","jetpack_shortlink":"https:\/\/wp.me\/p9b6zl-Th","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/posts\/3427","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=3427"}],"version-history":[{"count":0,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/posts\/3427\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=\/wp\/v2\/media\/3428"}],"wp:attachment":[{"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3427"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3427"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/plaza.umin.ac.jp\/~OIO\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3427"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}