{"id":431,"date":"2019-08-14T20:44:56","date_gmt":"2019-08-14T11:44:56","guid":{"rendered":"https:\/\/best-biostatistics.com\/toukei-er\/entry\/competing-risk-analysis-gray-test-in-r\/"},"modified":"2024-09-19T23:25:23","modified_gmt":"2024-09-19T14:25:23","slug":"competing-risk-analysis-gray-test-in-r","status":"publish","type":"post","link":"https:\/\/best-biostatistics.com\/toukei-er\/entry\/competing-risk-analysis-gray-test-in-r\/","title":{"rendered":"R \u3067\u7af6\u5408\u30ea\u30b9\u30af\u5206\u6790 Gray \u691c\u5b9a\u3092\u884c\u3046\u65b9\u6cd5"},"content":{"rendered":"\n

\u7af6\u5408\u30ea\u30b9\u30af\u3068\u306f\u4f55\u304b\uff1f<\/p>\n\n\n\n

Gray \u691c\u5b9a\u306e\u5b9f\u884c\u65b9\u6cd5<\/p>\n\n\n\n\n\n\n\n

\u7af6\u5408\u30ea\u30b9\u30af\u3068\u306f\uff1f<\/h2>\n\n\n\n

\u518d\u767a\u304c\u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\u3067\u3042\u3063\u305f\u304c\u3001\u518d\u767a\u3059\u308b\u524d\u306b\u6b7b\u4ea1\u3057\u3066\u3057\u307e\u3063\u305f\u306e\u3067\u3001\u89b3\u5bdf\u3067\u304d\u306a\u304b\u3063\u305f\u3002<\/p>\n\n\n\n

\u8133\u6897\u585e\u306e\u767a\u73fe\u304c\u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\u3060\u3063\u305f\u304c\u3001\u5148\u306b\u80ba\u708e\u3067\u304a\u4ea1\u304f\u306a\u308a\u306b\u306a\u308a\u3001\u89b3\u5bdf\u3067\u304d\u306a\u304b\u3063\u305f\u3002<\/p>\n\n\n\n

\u3053\u306e\u3088\u3046\u306b\u3001\u518d\u767a\u3092\u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\u306b\u3057\u305f\u5834\u5408\u306e\u518d\u767a\u524d\u306e\u6b7b\u4ea1\u3001\u3042\u308b\u3044\u306f\u3001\u8133\u6897\u585e\u306e\u767a\u751f\u3092\u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\u306b\u3057\u305f\u5834\u5408\u306e\u305d\u306e\u4ed6\u306e\u539f\u56e0\u306b\u3088\u308b\u6b7b\u4ea1\u3001\u3053\u3093\u306a\u3075\u3046\u306a\u30a4\u30d9\u30f3\u30c8\u304c\u767a\u751f\u3059\u308b\u30ea\u30b9\u30af\u3092\u7af6\u5408\u30ea\u30b9\u30af\u3068\u547c\u3076\u3002<\/p>\n\n\n\n

\u751f\u5b58\u6642\u9593\u89e3\u6790\u306b\u304a\u3044\u3066\u3001\u7af6\u5408\u30ea\u30b9\u30af\u304c\u3042\u308b\u5834\u5408\u3001\u3069\u306e\u3088\u3046\u306b\u89e3\u6790\u3059\u308c\u3070\u3088\u3044\u304b\uff1f<\/p>\n\n\n\n

\u7af6\u5408\u30ea\u30b9\u30af\u5206\u6790\u306e\u30b5\u30f3\u30d7\u30eb\u30c7\u30fc\u30bf\u306e\u6e96\u5099<\/h2>\n\n\n\n

\u7af6\u5408\u30ea\u30b9\u30af\u304c\u3042\u308b\u5834\u5408\u3001\u751f\u5b58\u78ba\u7387\u304c\u4e0b\u304c\u3063\u3066\u3044\u304f\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u306e\u4ee3\u308f\u308a\u306b\u3001\u7d2f\u7a4d\u7684\u306b\u30a4\u30d9\u30f3\u30c8\u304c\u767a\u73fe\u3057\u3066\u3044\u304f\u69d8\u3092\u7d2f\u7a4d\u767a\u73fe\u30b0\u30e9\u30d5\u306b\u63cf\u304f\u3002<\/p>\n\n\n\n

\u7d71\u8a08\u30bd\u30d5\u30c8R\u306e riskRegression \u30d1\u30c3\u30b1\u30fc\u30b8\u306e Melanoma \u30c7\u30fc\u30bf\u3092\u7528\u3044\u308b\u3002<\/p>\n\n\n\n

\u30d1\u30c3\u30b1\u30fc\u30b8\u306fcmprsk \u3068 riskRegression \u3092\u4e8b\u524d\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u304a\u304f\u3002<\/p>\n\n\n\n

library<\/span>(<\/span>cmprsk)<\/span>\nlibrary<\/span>(<\/span>riskRegression)<\/span>\nlibrary<\/span>(<\/span>survival)<\/span>\nhead<\/span>(<\/span>Melanoma)<\/span>\n<\/code><\/pre>\n\n\n\n
Melanoma \u30c7\u30fc\u30bf\u306e\u3046\u3061\u3001\u4ee5\u4e0b\u306e 3 \u3064\u306e\u5909\u6570\u3092\u4e3b\u306b\u4f7f\u3046\u3002<\/p>\n\n\n\n
    \n
  1. \u30a4\u30d9\u30f3\u30c8\u307e\u3067\u306e\u6642\u9593\u5909\u6570 time<\/li>\n\n\n\n
  2. \u72b6\u614b\u306e\u5909\u6570 status (0\u304c\u5358\u306a\u308b\u7814\u7a76\u7d42\u4e86\u306e\u6253\u3061\u5207\u308a\u30011\u304c\u30e1\u30e9\u30ce\u30fc\u30de\u306b\u3088\u308b\u6b7b\u4ea1\uff08\u7814\u7a76\u3057\u305f\u3044\u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\uff09\u30012\u304c\u30e1\u30e9\u30ce\u30fc\u30de\u4ee5\u5916\u306b\u3088\u308b\u6b7b\u4ea1\uff08\u7af6\u5408\u30ea\u30b9\u30af\uff09)<\/li>\n\n\n\n
  3. \u6d78\u6f64 invasion \uff08\u30ec\u30d9\u30eb\uff10\uff0c\uff11\uff0c\uff12\u3067\u30012\u304c\u91cd\u75c7\uff09<\/li>\n<\/ol>\n\n\n\n
    ><\/span> head<\/span>(<\/span>Melanoma)<\/span>\ntime status                    event invasion ici      epicel       ulcer thick\n1<\/span>   10<\/span>      2<\/span>       death.other.causes  level.1   2<\/span>     present     present  6.76<\/span>\n2<\/span>   30<\/span>      2<\/span>       death.other.causes  level.0   0<\/span> not present not present  0.65<\/span>\n3<\/span>   35<\/span>      0<\/span>                 censored  level.1   2<\/span> not present not present  1.34<\/span>\n4<\/span>   99<\/span>      2<\/span>       death.other.causes  level.0   2<\/span> not present not present  2.90<\/span>\n5<\/span>  185<\/span>      1<\/span> death.malignant.melanoma  level.2   2<\/span>     present     present 12.08<\/span>\n6<\/span>  204<\/span>      1<\/span> death.malignant.melanoma  level.2   2<\/span> not present     present  4.84<\/span>\nsex age   logthick\n1<\/span>   Male  76<\/span>  1.9110229<\/span>\n2<\/span>   Male  56<\/span> -<\/span>0.4307829<\/span>\n3<\/span>   Male  41<\/span>  0.2926696<\/span>\n4<\/span> Female  71<\/span>  1.0647107<\/span>\n5<\/span>   Male  52<\/span>  2.4915512<\/span>\n6<\/span>   Male  28<\/span>  1.5769147<\/span>\n<\/code><\/pre>\n\n\n\n
    \uff1e\uff1e\u3082\u3046\u7d71\u8a08\u3067\u60a9\u3080\u306e\u306f\u7d42\u308f\u308a\u306b\u3057\u307e\u305b\u3093\u304b\uff1f\u00a0<\/a><\/strong><\/span><\/p>\r\n\"\"<\/a>\r\n
    \u21911\u4e07\u4eba\u4ee5\u4e0a\u306e\u533b\u7642\u5f93\u4e8b\u8005\u304c\u8cfc\u8aad\u4e2d<\/span><\/strong><\/span><\/p><\/div>
    \u7af6\u5408\u30ea\u30b9\u30af\u306e\u7d2f\u7a4d\u767a\u73fe\u66f2\u7dda\u3092\u63cf\u3044\u3066\u307f\u308b<\/h2>\n\n\n\n
    \u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\uff08status==1\uff09\u3068\u7af6\u5408\u30ea\u30b9\u30af\uff08status==2\uff09\u306e\u7d2f\u7a4d\u767a\u73fe\u66f2\u7dda\uff08Cumulative Incidence Curve\uff09\u3092\u63cf\u3044\u3066\u307f\u308b\u3002<\/p>\n\n\n\n
    Surv()\u3068survfit()\u306e\u7d44\u307f\u5408\u308f\u305b\u3067fun=”event”\u3092\u4f7f\u3063\u3066\u7c21\u6613\u7684\u306b\u63cf\u304f\u3053\u3068\u306f\u3067\u304d\u308b\u304c\u3001cmprsk \u30d1\u30c3\u30b1\u30fc\u30b8\u306ecuminc()\u3092\u4f7f\u3046\u307b\u3046\u304c\u9069\u5207\u3002<\/p>\n\n\n\n
    cuminc()\u3092\u3088\u308a\u4f7f\u3044\u3084\u3059\u304f\u3057\u305fCumIncidence()\u3082\u3042\u308b\u3002<\/p>\n\n\n\n
    survfit0.1 <-<\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status==<\/span>1<\/span>)<\/span>~<\/span>1<\/span>,<\/span>\ndata=<\/span>Melanoma)<\/span>\nsurvfit0.2 <-<\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status==<\/span>2<\/span>)<\/span>~<\/span>1<\/span>,<\/span>\ndata=<\/span>Melanoma)<\/span>\nlayout<\/span>(<\/span>matrix<\/span>(<\/span>1<\/span>:<\/span>4<\/span>,<\/span>nr=<\/span>2<\/span>))<\/span>\nplot<\/span>(<\/span>survfit0.1,<\/span> fun=<\/span>\"event\"<\/span>,<\/span> conf.int=<\/span>FALSE<\/span>)<\/span>\nplot<\/span>(<\/span>survfit0.2,<\/span> fun=<\/span>\"event\"<\/span>,<\/span> conf.int=<\/span>FALSE<\/span>,<\/span> col=<\/span>2<\/span>)<\/span>\ncuminc0 <-<\/span> cuminc<\/span>(<\/span>ftime=<\/span>Melanoma$<\/span>time,<\/span>\nfstatus=<\/span>Melanoma$<\/span>status)<\/span>\nplot<\/span>(<\/span>cuminc0)<\/span>\nsource<\/span>(<\/span>\"http:\/\/www.stat.unipg.it\/luca\/misc\/CumIncidence.R\"<\/span>)<\/span>\nCumIncidence<\/span>(<\/span>ftime=<\/span>Melanoma$<\/span>time,<\/span> fstatus=<\/span>Melanoma$<\/span>status)<\/span>\n<\/code><\/pre>\n\n\n\n
    \"\"<\/figure>\n\n\n\n
    <\/span><\/p>\n\n\n\n
    \u5de6\u5074\u306e\u4e0a\u4e0b2\u3064\u304cSurv()\u3068survfit()\u3092\u4f7f\u3063\u305f\u30b0\u30e9\u30d5\u3002<\/p>\n\n\n\n
    \u53f3\u4e0a\u304ccuminc()\u306e\u30c7\u30d5\u30a9\u30eb\u30c8\u30b0\u30e9\u30d5\u3002\u53f3\u4e0b\u304cCumIncidence()\u306e\u30b0\u30e9\u30d5\u3002<\/p>\n\n\n\n
    cuminc()\u306f\u3001status\u306e2\u3064\u304cline types (lty)\u3067\u63cf\u304d\u5206\u3051\u3089\u308c\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
    \u4e00\u65b9\u3067CumIncidence()\u306e\u30b0\u30e9\u30d5\u306f\u3001status\u304c\u9ed2\u3068\u8d64\u3067\u5857\u308a\u5206\u3051\u3089\u308c\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
    \u7af6\u5408\u30ea\u30b9\u30af\u306e\u8981\u56e0\u5225\u7d2f\u7a4d\u767a\u73fe<\/h2>\n\n\n\n
    \u6b21\u306b\u3001invasion\u306e3\u30ec\u30d9\u30eb\u5225\u306e\u7d2f\u7a4d\u767a\u73fe\u3068\u691c\u5b9a\u306e\u7d50\u679c\u3002<\/p>\n\n\n\n
    \u7d2f\u7a4d\u767a\u73fe\u30b0\u30e9\u30d5\u306f\u3001\u4ee5\u4e0b\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3067\u66f8\u3051\u308b\u3002<\/p>\n\n\n\n
    survfit1.1 <-<\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status==<\/span>1<\/span>)<\/span>~<\/span>invasion,<\/span>\ndata=<\/span>Melanoma)<\/span>\nsurvfit1.2 <-<\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status==<\/span>2<\/span>)<\/span>~<\/span>invasion,<\/span>\ndata=<\/span>Melanoma)<\/span>\nlayout<\/span>(<\/span>matrix<\/span>(<\/span>1<\/span>:<\/span>4<\/span>,<\/span>nr=<\/span>2<\/span>))<\/span>\nplot<\/span>(<\/span>survfit1.1,<\/span> fun=<\/span>\"event\"<\/span>,<\/span> conf.int=<\/span>FALSE<\/span>,<\/span> lty=<\/span>1<\/span>:<\/span>3<\/span>)<\/span>\nplot<\/span>(<\/span>survfit1.2,<\/span> fun=<\/span>\"event\"<\/span>,<\/span> conf.int=<\/span>FALSE<\/span>,<\/span> lty=<\/span>1<\/span>:<\/span>3<\/span>,<\/span>col=<\/span>2<\/span>)<\/span>\ncuminc1 <-<\/span> cuminc<\/span>(<\/span>ftime=<\/span>Melanoma$<\/span>time,<\/span>\nfstatus=<\/span>Melanoma$<\/span>status,<\/span> group=<\/span>Melanoma$<\/span>invasion)<\/span>\nplot<\/span>(<\/span>cuminc1)<\/span>\n(<\/span>CumInc1 <-<\/span> CumIncidence<\/span>(<\/span>ftime=<\/span>Melanoma$<\/span>time,<\/span>\nfstatus=<\/span>Melanoma$<\/span>status,<\/span> group=<\/span>Melanoma$<\/span>invasion))<\/span>\n<\/code><\/pre>\n\n\n\n
    \"\"<\/figure>\n\n\n\n
    <\/span><\/p>\n\n\n\n
    \u5de6\u306e\u4e0a\u4e0b\u4e8c\u3064\u306fSurv()\u3068survfit()\u3067\u63cf\u3044\u305f\u30b0\u30e9\u30d5\u3002<\/p>\n\n\n\n
    invasion\u306e3\u30ec\u30d9\u30eblty\u3067\u63cf\u304d\u5206\u3051\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
    \u53f3\u4e0a\u306fcuminc()\u3067\u63cf\u3044\u305fCumulative Incidence\u306e\u30b0\u30e9\u30d5\u3002<\/p>\n\n\n\n
    status\u304c2\u3064\u3068invasion\u304c3\u30ec\u30d9\u30eb\u306e\u5408\u8a086\u672c\u304clty\u3067\u63cf\u304d\u5206\u3051\u3089\u308c\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
    \u53f3\u4e0b\u306fCumIncidence()\u3067\u63cf\u304b\u308c\u305f\u3082\u306e\u3002status\u304c\u9ed2\u3068\u8d64\u3067\u5206\u3051\u3089\u308c\u3066\u3044\u3066\u3001\u305d\u308c\u305e\u308clty\u3067invasion\u306e\u30ec\u30d9\u30eb\u304c\u308f\u304b\u308b\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
    CumIncidence()\u304c\u4e00\u756a\u898b\u3084\u3059\u3044\u3002<\/p>\n\n\n\n
    \u7af6\u5408\u30ea\u30b9\u30af\u306e Gray \u691c\u5b9a\uff08\u30ed\u30b0\u30e9\u30f3\u30af\u691c\u5b9a\u3068\u306e\u6bd4\u8f03\uff09<\/h2>\n\n\n\n
    survdiff()\u306e\u7d50\u679c\u3068cuminc()\u306e\u7d50\u679c\u3092\u6bd4\u3079\u3066\u307f\u308b\u3002<\/p>\n\n\n\n
    survdiff1.1 <-<\/span> survdiff<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status==<\/span>1<\/span>)<\/span>~<\/span>invasion,<\/span>\ndata=<\/span>Melanoma)<\/span>\nsurvdiff1.2 <-<\/span> survdiff<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status==<\/span>2<\/span>)<\/span>~<\/span>invasion,<\/span>\ndata=<\/span>Melanoma)<\/span>\nsurvdiff1.1\nsurvdiff1.2\ncuminc1\nCumInc1\n<\/code><\/pre>\n\n\n\n
    \u4ee5\u4e0b\u306e 4 \u3064\u306e\u51fa\u529b\u306e\u584a\u306e\u3046\u3061\u3001\u4e0a\u4e8c\u3064\u304csurvdiff()\u306e\u7d50\u679c\u3001\u3064\u307e\u308a\u30ed\u30b0\u30e9\u30f3\u30af\u691c\u5b9a\u306e\u7d50\u679c\u3067\u3042\u308b\u3002<\/p>\n\n\n\n
    \u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8(status==1)\u3068\u7af6\u5408\u30ea\u30b9\u30af(status==2)\u3092\u5225\u3005\u306b\u89e3\u6790\u3057\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
    \u4e0b\u306e\u4e8c\u3064 cuminc1 \u53ca\u3073 CumInc1\u306f\u3068\u3082\u306b\u540c\u3058\u7d50\u679c\u3067\u3053\u3061\u3089\u306f Gray \u691c\u5b9a\u306e\u7d50\u679c\u3002<\/p>\n\n\n\n
    ><\/span> survdiff1.1\nCall:<\/span>\nsurvdiff<\/span>(<\/span>formula =<\/span> Surv<\/span>(<\/span>time,<\/span> status ==<\/span> 1<\/span>)<\/span> ~<\/span> invasion,<\/span> data =<\/span> Melanoma)<\/span>\nChisq=<\/span> 18.8<\/span>  on 2<\/span> degrees of freedom,<\/span> p=<\/span> 8e-05<\/span>\n><\/span> survdiff1.2\nCall:<\/span>\nsurvdiff<\/span>(<\/span>formula =<\/span> Surv<\/span>(<\/span>time,<\/span> status ==<\/span> 2<\/span>)<\/span> ~<\/span> invasion,<\/span> data =<\/span> Melanoma)<\/span>\nChisq=<\/span> 0.5<\/span>  on 2<\/span> degrees of freedom,<\/span> p=<\/span> 0.8<\/span>\n><\/span> cuminc1\nTests:<\/span>\nstat           pv df\n1<\/span> 17.9441643<\/span> 0.0001269037<\/span>  2<\/span>\n2<\/span>  0.8846449<\/span> 0.6425424207<\/span>  2<\/span>\n><\/span> CumInc1\n$<\/span>test\nStatistic df   p-<\/span>value\n1<\/span> 17.9441643<\/span>  2<\/span> 0.0001269<\/span>\n2<\/span>  0.8846449<\/span>  2<\/span> 0.6425424<\/span>\n<\/code><\/pre>\n\n\n\n
    Gray \u691c\u5b9a\u306e\u307b\u3046\u304c\u3001\u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\u306e\u6709\u610f\u78ba\u7387\u304c\u82e5\u5e72\u9ad8\u3044\u7a0b\u5ea6\u3067\u307b\u3068\u3093\u3069\u540c\u3058\u3067\u3042\u3063\u305f\u304c\u3001\u7406\u5c48\u306e\u4e0a\u3067\u306f\u3001Gray \u691c\u5b9a\u3092\u884c\u3046\u306e\u304c\u671b\u307e\u3057\u3044\u3002<\/p>\n\n\n\n
    \u307e\u3068\u3081<\/h2>\n\n\n\n
    \u30a8\u30f3\u30c9\u30dd\u30a4\u30f3\u30c8\u3092\u89b3\u5bdf\u3057\u305f\u304f\u3066\u3082\u3001\u305d\u306e\u524d\u306b\u89b3\u5bdf\u3067\u304d\u306a\u304f\u306a\u308b\u4e8b\u8c61\u304c\u8d77\u304d\u308b\u3053\u3068\u304c\u3042\u308a\u3001\u305d\u3046\u3044\u3046\u4e8b\u8c61\u3092\u7af6\u5408\u30ea\u30b9\u30af\u3068\u547c\u3076\u3002<\/p>\n\n\n\n
    \u7af6\u5408\u30ea\u30b9\u30af\u3092\u52a0\u5473\u3057\u305f\u7d2f\u7a4d\u767a\u73fe\u3067\u30b0\u30e9\u30d5\u3092\u63cf\u304d\u3001\u30b0\u30eb\u30fc\u30d7\u9593\u306e\u5dee\u3092\u898b\u308b\u5834\u5408\u306f Gray \u691c\u5b9a\u3092\u884c\u3046\u3002<\/p>\n\n\n\n
    \u7d71\u8a08\u30bd\u30d5\u30c8R\u306e\u5834\u5408\u3001survival \u30d1\u30c3\u30b1\u30fc\u30b8\u306b\u52a0\u3048\u3001cmprsk \u30d1\u30c3\u30b1\u30fc\u30b8\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u304c\u5fc5\u8981\u3068\u306a\u308b\u3002<\/p>\n\n\n\n
    \u89e3\u8aac\u52d5\u753b\uff1aEZR \u3067 Gray \u691c\u5b9a\u3092\u884c\u3046\u65b9\u6cd5<\/h2>\n\n\n\n