{"id":434,"date":"2019-07-28T20:46:07","date_gmt":"2019-07-28T11:46:07","guid":{"rendered":"https:\/\/best-biostatistics.com\/toukei-er\/entry\/kaplan-meier-curve-by-group-in-r\/"},"modified":"2024-10-09T08:11:58","modified_gmt":"2024-10-08T23:11:58","slug":"kaplan-meier-curve-by-group-in-r","status":"publish","type":"post","link":"https:\/\/best-biostatistics.com\/toukei-er\/entry\/kaplan-meier-curve-by-group-in-r\/","title":{"rendered":"R \u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u30b0\u30eb\u30fc\u30d7\u3054\u3068\u306b\u66f8\u304f\u65b9\u6cd5"},"content":{"rendered":"\n

R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u304f\u65b9\u6cd5\u306e\u7d39\u4ecb\u3002<\/p>\n\n\n\n

survfit \u3092\u4f7f\u3063\u305f\u30b0\u30eb\u30fc\u30d7\u3054\u3068\u306e\u66f2\u7dda\u306e\u66f8\u304d\u65b9\u3002<\/p>\n\n\n\n\n\n\n\n

R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u304f\u305f\u3081\u306e\u30b5\u30f3\u30d7\u30eb\u30c7\u30fc\u30bf<\/h2>\n\n\n\n

\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u304f\u305f\u3081\u306e\u30b5\u30f3\u30d7\u30eb\u30c7\u30fc\u30bf\u306f\u3001survival \u30d1\u30c3\u30b1\u30fc\u30b8\u306e lung \u3092\u4f7f\u3046\u3002<\/p>\n\n\n\n

\u3053\u308c\u306f\u3001North Central Cancer Treatment Group, NCCTG \u63d0\u4f9b\u306e\u9032\u884c\u80ba\u304c\u3093\u60a3\u8005\u3055\u3093\u306e\u751f\u5b58\u30c7\u30fc\u30bf\u3002<\/p>\n\n\n\n

\u307e\u305a\u3001survival \u30d1\u30c3\u30b1\u30fc\u30b8\u306e\u95a2\u6570\u53ca\u3073\u30b5\u30f3\u30d7\u30eb\u30c7\u30fc\u30bf\u304c\u4f7f\u3048\u308b\u3088\u3046\u306b\u3059\u308b\u3002<\/p>\n\n\n\n

library<\/span>(<\/span>survival)<\/span>\n<\/code><\/pre>\n\n\n\n
head()\u3067\u5148\u982d\u90e8\u5206\u3092\u898b\u3066\u307f\u308b\u3068\u4ee5\u4e0b\u306e\u901a\u308a\u3002time\u304c\u751f\u5b58\u6642\u9593\uff08\u65e5\u6570\uff09\u3001status\u304c\u6253\u3061\u5207\u308a(1)\u304b\u6b7b\u4ea1(2)\u304b\u3001ph.ecog\u304cECOG performance score\u3067good(0)\u304b\u3089dead(5)\u307e\u3067\u306e\u30b0\u30ec\u30fc\u30c7\u30a3\u30f3\u30b0\u3002<\/p>\n\n\n\n
><\/span> head<\/span>(<\/span>lung)<\/span>\ninst time status age sex ph.ecog ph.karno pat.karno meal.cal wt.loss\n1<\/span>    3<\/span>  306<\/span>      2<\/span>  74<\/span>   1<\/span>       1<\/span>       90<\/span>       100<\/span>     1175<\/span>      NA<\/span>\n2<\/span>    3<\/span>  455<\/span>      2<\/span>  68<\/span>   1<\/span>       0<\/span>       90<\/span>        90<\/span>     1225<\/span>      15<\/span>\n3<\/span>    3<\/span> 1010<\/span>      1<\/span>  56<\/span>   1<\/span>       0<\/span>       90<\/span>        90<\/span>       NA<\/span>      15<\/span>\n4<\/span>    5<\/span>  210<\/span>      2<\/span>  57<\/span>   1<\/span>       1<\/span>       90<\/span>        60<\/span>     1150<\/span>      11<\/span>\n5<\/span>    1<\/span>  883<\/span>      2<\/span>  60<\/span>   1<\/span>       0<\/span>      100<\/span>        90<\/span>       NA<\/span>       0<\/span>\n6<\/span>   12<\/span> 1022<\/span>      1<\/span>  74<\/span>   1<\/span>       1<\/span>       50<\/span>        80<\/span>      513<\/span>       0<\/span>\n<\/code><\/pre>\n\n\n\n
R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u304f\u305f\u3081\u306e\u6e96\u5099\u305d\u306e1\uff1aSurv()<\/h2>\n\n\n\n
Surv()\u306f\u3001\u751f\u5b58\u6642\u9593\u3068\u30b9\u30c6\u30fc\u30bf\u30b9\u3092\u4f7f\u3063\u3066\u3001\u751f\u5b58\u6642\u9593\u30c7\u30fc\u30bf\u306b\u5909\u63db\u3057\u3066\u304f\u308c\u308b\u95a2\u6570\u3002<\/p>\n\n\n\n
><\/span> with<\/span>(<\/span>data=<\/span>lung,<\/span> Surv<\/span>(<\/span>time,<\/span> status))[<\/span>1<\/span>:<\/span>20<\/span>]<\/span>\n[<\/span>1<\/span>]<\/span>  306<\/span>   455<\/span>  1010<\/span>+<\/span>  210<\/span>   883<\/span>  1022<\/span>+<\/span>  310<\/span>   361<\/span>   218<\/span>   166<\/span>   170<\/span>   654<\/span>\n[<\/span>13<\/span>]<\/span>  728<\/span>    71<\/span>   567<\/span>   144<\/span>   613<\/span>   707<\/span>    61<\/span>    88<\/span>\n<\/code><\/pre>\n\n\n\n
\u5148\u982d\u306e20\u500b\u3092\u53d6\u308a\u51fa\u3057\u3066\u307f\u308b\u3068\u4e0a\u8a18\u306e\u3088\u3046\u306b\u5909\u63db\u3055\u308c\u3066\u3044\u308b\u30021010\u30681022\u306b\uff0b\u304c\u3064\u3044\u3066\u3044\u308b\u306e\u306f\u3001\u6253\u3061\u5207\u308a\u4f8b\u3067\u3042\u308b\u3053\u3068\u3092\u793a\u3057\u3066\u3044\u308b\u3002<\/p>\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>
R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u304f\u305f\u3081\u306e\u6e96\u5099\u305d\u306e2\uff1asurvfit()<\/h2>\n\n\n\n
survfit()\u306f\u3001Surv()\u3067\u751f\u5b58\u6642\u9593\u30c7\u30fc\u30bf\u306b\u5909\u63db\u3055\u308c\u305f\u6570\u5024\u3092\u3082\u3068\u306b\u3001\u751f\u5b58\u6642\u9593\u306e\u63a8\u5b9a\u8a08\u7b97\u3092\u3059\u308b\u3002<\/p>\n\n\n\n
><\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span> status)<\/span>~<\/span>1<\/span>,<\/span> data=<\/span>lung)<\/span>\nCall:<\/span> survfit<\/span>(<\/span>formula =<\/span> Surv<\/span>(<\/span>time,<\/span> status)<\/span> ~<\/span> 1<\/span>,<\/span> data =<\/span> lung)<\/span>\nn  events  median 0.95<\/span>LCL 0.95<\/span>UCL\n228<\/span>     165<\/span>     310<\/span>     285<\/span>     363<\/span>\n<\/code><\/pre>\n\n\n\n
\u30b5\u30f3\u30d7\u30eb\u30b5\u30a4\u30ba\u304c228\u3001\u30a4\u30d9\u30f3\u30c8\u304c165\u3001\u751f\u5b58\u671f\u9593\u4e2d\u592e\u5024\u304c310\u65e5\u300195%\u4fe1\u983c\u533a\u9593\u304c285\u65e5\u304b\u3089363\u65e5\u3068\u8a08\u7b97\u3055\u308c\u3066\u3044\u308b\u3002<\/p>\n\n\n\n
R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u3044\u3066\u307f\u308b\uff1aplot()<\/h2>\n\n\n\n
survfit()\u306b\u4f55\u304b\u540d\u524d\u3092\u4ed8\u3051\u3066\uff08\u3053\u3053\u3067\u306f survfit1 \u304c\u4ed8\u3051\u305f\u540d\u524d\uff09\u3001\u305d\u306e\u540d\u524d\u3092plot()\u306b\u5165\u308c\u308b\u3060\u3051\u3067\u3001\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u304c\u66f8\u3051\u308b\u3002<\/p>\n\n\n\n
survfit1 <-<\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span> status)<\/span>~<\/span>1<\/span>,<\/span> data=<\/span>lung)<\/span>\nplot<\/span>(<\/span>survfit1)<\/span>\n<\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/span><\/p>\n\n\n\n
\u5b9f\u7dda\u306e\u4e0a\u4e0b\u306e\u7834\u7dda\u306f95%\u4fe1\u983c\u533a\u9593\u3092\u793a\u3057\u3066\u3044\u308b\u3002\u8868\u793a\u3092\u6d88\u3059\u306b\u306fconf.int=FALSE\u3092\u8ffd\u52a0\u3059\u308b\u3002<\/p>\n\n\n\n
plot<\/span>(<\/span>survfit1,<\/span> conf.int=<\/span>FALSE<\/span>)<\/span>\n<\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/span><\/p>\n\n\n\n
Y\u8ef8\u306e\u76ee\u76db\u308a\u6570\u5024\u3092\u7e26\u306b\u3059\u308b\u306b\u306f las=1\u3001X\u8ef8\u3068Y\u8ef8\u306e\u8aac\u660e\u306f xlab=””, ylab=””\u3067\u66f8\u304d\u5165\u308c\u308b\u3002<\/p>\n\n\n\n
plot<\/span>(<\/span>survfit1,<\/span> conf.int=<\/span>FALSE<\/span>,<\/span> las=<\/span>1<\/span>,<\/span>\nxlab=<\/span>\"Survival Time (days)\"<\/span>,<\/span> ylab=<\/span>\"Overall Survival\"<\/span>)<\/span>\n<\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/span><\/p>\n\n\n\n
\u751f\u5b58\u6642\u9593\u4e2d\u592e\u5024\u3092\u56f3\u306b\u66f8\u304d\u5165\u308c\u308b\u306b\u306f\u3001arrows()\u3092\u4f7f\u3046\u3002\u59cb\u70b9\u3068\u7d42\u70b9\u3092\u5ea7\u6a19\u3067\u793a\u3057\u3066\u3001\u77e2\u5370\u306e\u5927\u304d\u3055\u3092\u30bc\u30ed\u306b\u3059\u308b\u3002<\/p>\n\n\n\n
\u307e\u305f\u3001\u56f3\u4e2d\u306b\u30b3\u30e1\u30f3\u30c8\u3092\u5165\u308c\u308b\u306b\u306f text()\u3092\u4f7f\u3046\u3002\u6307\u5b9a\u3057\u305fX\u5ea7\u6a19\u304c\u3001\u30c6\u30ad\u30b9\u30c8\u306e\u4e2d\u70b9\u306b\u306a\u308b\u3002<\/p>\n\n\n\n
arrows<\/span>(<\/span>310<\/span>,<\/span>0<\/span>,<\/span>310<\/span>,<\/span>0.5<\/span>,<\/span>0<\/span>)<\/span>\narrows<\/span>(<\/span>0<\/span>,<\/span>0.5<\/span>,<\/span>310<\/span>,<\/span>0.5<\/span>,<\/span>0<\/span>)<\/span>\ntext<\/span>(<\/span>550<\/span>,<\/span>0.5<\/span>,<\/span>\"Median Survival = 310 days\"<\/span>)<\/span>\n<\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/span><\/p>\n\n\n\n
R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u30b0\u30eb\u30fc\u30d7\u3054\u3068\u306b\u66f8\u304f\u306b\u306f\uff1f<\/h2>\n\n\n\n
\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u3044\u304f\u3064\u304b\u306e\u30b0\u30eb\u30fc\u30d7\u306b\u5206\u3051\u3066\u66f8\u304f\u306b\u306f\u3069\u3046\u3057\u305f\u3089\u3088\u3044\u304b\uff1f<\/p>\n\n\n\n
\u30b0\u30eb\u30fc\u30d7\u306b\u5206\u3051\u308b\u306b\u306f survfit() \u3067\u300c~\u300d\u306e\u5f8c\u306b\u3001\u30b0\u30eb\u30fc\u30d7\u308f\u3051\u306e\u5909\u6570\u3092\u5165\u308c\u308b\u3002<\/p>\n\n\n\n
ECOG\u306e\u30d1\u30d5\u30a9\u30fc\u30de\u30f3\u30b9\u30b9\u30b3\u30a2\u3067\u5206\u3051\u3066\u66f8\u304f\u306a\u3089\u3001~ph.ecog\u3068\u66f8\u304f\u3002<\/p>\n\n\n\n
survfit2 <-<\/span> survfit<\/span>(<\/span>Surv<\/span>(<\/span>time,<\/span>status)<\/span>~<\/span>ph.ecog,<\/span> data=<\/span>lung)<\/span>\n<\/code><\/pre>\n\n\n\n
\u307e\u305a\u3001survfit2\u3092\u78ba\u8a8d\u3057\u3066\u307f\u308b\u3068\u3001ECOG Performance Score\u306f0\u304b\u30893\u307e\u3067\u306e\u60a3\u8005\u3055\u3093\u3057\u304b\u3044\u306a\u304b\u3063\u305f\u3002\u307e\u305f\u30013\u306e\u4eba\u306f\u4e00\u4eba\u306e\u307f\u3067\u3042\u3063\u305f\u3002<\/p>\n\n\n\n
><\/span> survfit2\nCall:<\/span> survfit<\/span>(<\/span>formula =<\/span> Surv<\/span>(<\/span>time,<\/span> status)<\/span> ~<\/span> ph.ecog,<\/span> data =<\/span> lung)<\/span>\n1<\/span> observation deleted due to missingness\nn events median 0.95<\/span>LCL 0.95<\/span>UCL\nph.ecog=<\/span>0<\/span>  63<\/span>     37<\/span>    394<\/span>     348<\/span>     574<\/span>\nph.ecog=<\/span>1<\/span> 113<\/span>     82<\/span>    306<\/span>     268<\/span>     429<\/span>\nph.ecog=<\/span>2<\/span>  50<\/span>     44<\/span>    199<\/span>     156<\/span>     288<\/span>\nph.ecog=<\/span>3<\/span>   1<\/span>      1<\/span>    118<\/span>      NA<\/span>      NA<\/span>\n<\/code><\/pre>\n\n\n\n
plot()\u3067\u4f5c\u56f3\u3059\u308b\u3002legend()\u3067\u3001\u56f3\u4e2d\u306b\u6ce8\u91c8\u3092\u5165\u308c\u308b\u3002<\/p>\n\n\n\n
plot<\/span>(<\/span>survfit2,<\/span>las=<\/span>1<\/span>,<\/span>xlab=<\/span>\"Survival Time (days)\"<\/span>,<\/span>\nylab=<\/span>\"Overall Survivial\"<\/span>,<\/span>col=<\/span>2<\/span>:<\/span>5<\/span>)<\/span>\nlegend<\/span>(<\/span>\"topright\"<\/span>,<\/span> paste<\/span>(<\/span>\"ECOG PS=\"<\/span>,<\/span>0<\/span>:<\/span>3<\/span>,<\/span> sep=<\/span>\"\"<\/span>),<\/span> lty=<\/span>1<\/span>,<\/span>\ncol=<\/span>2<\/span>:<\/span>5<\/span>)<\/span>\n<\/code><\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/span><\/p>\n\n\n\n
\u3053\u308c\u3067\u3001\u30b0\u30eb\u30fc\u30d7\u5225\u306e\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u304c\u66f8\u3051\u305f\u3002<\/p>\n\n\n\n
\u51e1\u4f8b\u5185\u306e\u8a18\u8f09\u3092\u30c7\u30fc\u30bf\u304b\u3089\u6301\u3063\u3066\u304f\u308b\u3053\u3068\u3082\u3067\u304d\u308b\u3002legend=, names(), $strata \u3092\u4f7f\u3063\u3066\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u66f8\u3051\u308b\u3002<\/p>\n\n\n\n
plot<\/span>(<\/span>survfit2,<\/span>las=<\/span>1<\/span>,<\/span> xlab=<\/span>\"Survival Time (days)\"<\/span>,<\/span>\nylab=<\/span>\"Overall Survivial\"<\/span>,<\/span>col=<\/span>2<\/span>:<\/span>5<\/span>)<\/span>\nlegend<\/span>(<\/span>\"topright\"<\/span>,<\/span> legend=<\/span>names<\/span>(<\/span>survfit2$<\/span>strata),<\/span> lty=<\/span>1<\/span>,<\/span>\ncol=<\/span>2<\/span>:<\/span>5<\/span>)<\/span>\n<\/code><\/pre>\n\n\n\n
\u30b0\u30e9\u30d5\u306f\u3053\u306e\u3088\u3046\u306b\u306a\u308b\u3002<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
<\/span><\/p>\n\n\n\n
\u307e\u3068\u3081<\/h2>\n\n\n\n
R\u3067\u30ab\u30d7\u30e9\u30f3\u30de\u30a4\u30e4\u30fc\u66f2\u7dda\u3092\u66f8\u304f\u65b9\u6cd5\u3092\u7d39\u4ecb\u3057\u305f\u3002<\/p>\n\n\n\n
survival \u30d1\u30c3\u30b1\u30fc\u30b8\u3092\u547c\u3073\u51fa\u3057\u3066\u3001Surv(), survfit(), plot()\u306e3\u3064\u3067\u57fa\u672c\u306f\u66f8\u3051\u308b\u3002<\/p>\n\n\n\n
\u30b0\u30eb\u30fc\u30d7\u3054\u3068\u306b\u66f8\u304b\u305b\u308b\u305f\u3081\u306b\u306f\u3001survfit()\u4e2d\u306b\u300c~\u30b0\u30eb\u30fc\u30d7\u540d\u300d\u3092\u5165\u308c\u308b\u3002<\/p>\n\n\n\n
plot()\u306e\u30ab\u30c3\u30b3\u5185\u306b las=, xlab=, ylab= \u3092\u4f7f\u3046\u3068\u6700\u4f4e\u9650\u306e\u898b\u6804\u3048\u306e\u30b0\u30e9\u30d5\u306b\u306f\u306a\u308b\u3002<\/p>\n\n\n\n
\u5fc5\u8981\u306b\u5fdc\u3058\u3066\u3001arrows(), text(), legend()\u3067\u3055\u3089\u306b\u304d\u308c\u3044\u306a\u30b0\u30e9\u30d5\u3092\u63cf\u304f\u3053\u3068\u3082\u53ef\u80fd\u3002<\/p>\n\n\n\n
\u53c2\u8003\u306b\u306a\u308c\u3070\u3002<\/p>\n\n\n\n
\u95a2\u9023\u8a18\u4e8b<\/h2>\n\n\n
\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\u3042\u308f\u305b\u3066\u8aad\u307f\u305f\u3044<\/span>\n\t\t\t\t\t
\"\"<\/figure><\/div>\t\t\t\t\t
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