Messagepar frederic danjon » 11 Déc 2024, 09:37
Bonjour,
je m'excuse, j'étais parti sur d'autres dossiers. j'espère vous fournir un code reproductible : la question et les résultats restent les mêmes (voir mon premier envoi), à part : survSplit(Surv(time10, status == 1) ~ ., data= dfmat, cut=c(2), episode= "tgroup", id="id") où j'ai enlevé le status == 1 pour le remplacer par status.
voilà mon environnement ========================================================
sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Linux Mint 20.2
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Paris
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] survival_3.7-0
loaded via a namespace (and not attached):
[1] compiler_4.4.2 Matrix_1.7-1 tools_4.4.2 splines_4.4.2 grid_4.4.2 lattice_0.22-5
==============================================================================
Le code utilisé : ===================================================================
colnames(dfmat) <- c("Id","tree","cont","soilPrepN","blocN","time10","status"); head(dfmat);
detach(dfmat)
detach(dfmat2)
dfmat <- data.frame(dfmat,row.names="Id", check.rows = TRUE, check.names = TRUE); attach(dfmat); head(dfmat)
dfmat$cont <- factor(cont); dfmat$soilPrepN <- factor(soilPrepN); dfmat$blocN <- factor(blocN);
library(survival)
# 3 SIMPLE COX ANALYSIS ######################
fit1 <- coxph(Surv(time10, status) ~ cont + soilPrepN + blocN, dfmat, x = TRUE, y = TRUE, model = T); print(fit1, digits = 2); summary(fit1); cox.zph(fit1); cox.zph(fit1, terms=F); #; tbl_regression(fit1) #, method = "efron" fit1 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex) + poly(age,3), lung); levels(strata(cont))
# paramètres graphiques ############################
ltyCont <- 1:3; Lty <- 1:3;
colSoilPrep <- c("black","orange","red","green"); colBloc <- c("red","blue","green"); colCont <- c("red","green","black"); XLAB <- "Age (years)"; CEXlegend <- 1; textWidth <- 1.5; experiment <- "AAAK"; legendCont <- c("container", "turf plug", "seeded"); legendSoilPrep <- c("no plough", "33%", "66%","full plough"); legendBloc <- c("bloc 1", "bloc 2", "bloc 3");
nameConts <- c("multi","plug","seeded"); nameSoilPreps <- c("noPlough","narrowPlough","largePlough","fullPlough"); nameBlocs <- c("bloc 1", "bloc 2","bloc 3");
# 3 STEP FUNCTIONS ###################### ========== survival model with several variables violating proportional hazard assumption
dfmat2 <- survSplit(Surv(time10, status) ~ ., data= dfmat, cut=c(2), episode= "tgroup", id="id"); dfmat2[,"tgroup"]; head(dfmat2);
dfmat2 <- transform(dfmat2, tgroup = factor(tgroup)); dfmat2[,"tstart"]
detach(dfmat)
detach(dfmat2)
attach(dfmat2)
fitS2 <- coxph(Surv(tstart, time10, status) ~ cont:strata(tgroup) + soilPrepN:strata(tgroup) + blocN, dfmat2, model = T); summary(fitS2); zphS2 <- cox.zph(fitS2); zphS2; cox.zph(fitS2, terms=F); fitS2$means;
plot(survfit(fitS2, data = dfmat2, newdata=NDS), col = colSoilPrep[NDS[,"soilPrepN"]], lty = ltyCont[NDS[,"cont"]], ylim = c(0.37,1)); legend("bottomright", nameSoilPreps, fill = colSoilPrep[4:1]); legend(8,0.7, nameConts, lty = Lty)
merci
et je colle la matrice d'entrée ci dessous.
merci
bien cordialement
frederic
========== matrice d'entrée ===================
dfmat <- rbind(c(1,8203,1,2,1,2,0),c(2,8205,1,2,1,2,0),c(3,8210,1,2,1,3,0),c(4,8212,1,2,1,3,0),c(5,8217,1,2,1,4,0),c(6,8219,1,2,1,4,0),c(7,8223,1,2,1,1,1),c(8,8224,1,2,1,6,0),c(9,8225,1,2,1,6,0),c(10,8228,1,2,1,10,0),c(11,8229,1,2,1,1,1),c(12,8230,1,2,1,10,0)
,c(13,8130,2,2,1,10,0),c(14,8129,2,2,1,10,0),c(15,8128,2,2,1,10,0),c(16,8125,2,2,1,1,1),c(17,8124,2,2,1,6,0),c(18,8123,2,2,1,6,0),c(19,8119,2,2,1,4,0),c(20,8117,2,2,1,4,0),c(21,8113,2,2,1,3,0),c(22,8111,2,2,1,3,0),c(23,8109,2,2,1,3,0),c(24,8105,2,2,1,2,0),
c(25,8103,2,2,1,2,0),c(26,8023,1,2,1,6,0),c(27,8028,1,2,1,10,0),c(28,8030,1,2,1,10,0),c(29,7525,1,1,1,2,1),c(30,7523,1,1,1,6,0),c(31,7403,2,1,1,2,0),c(32,7405,2,1,1,2,0),c(33,7410,2,1,1,1,1),c(34,7411,2,1,1,3,0),c(35,7412,2,1,1,1,1),c(36,7413,2,1,1,3,0),
c(37,7417,2,1,1,4,0),c(38,7419,2,1,1,4,0),c(39,7423,2,1,1,2,1),c(40,7425,2,1,1,6,0),c(41,7428,2,1,1,10,0),c(42,7429,2,1,1,10,0),c(43,7430,2,1,1,1,1),c(44,7330,1,1,1,10,0),c(45,7328,1,1,1,10,0),c(46,7325,1,1,1,6,0),c(47,7323,1,1,1,6,0),c(48,7319,1,1,1,4,0),
c(49,7317,1,1,1,4,0),c(50,7312,1,1,1,3,0),c(51,7310,1,1,1,3,0),c(52,7305,1,1,1,2,0),c(53,7303,1,1,1,2,0),c(54,7223,2,1,1,6,0),c(55,7224,2,1,1,6,0),c(56,7228,2,1,1,10,0),c(57,7230,2,1,1,10,0),c(58,6913,1,3,1,3,0),c(59,6904,1,3,1,2,0),c(60,6802,2,3,1,2,0),
c(61,6829,2,3,1,10,0),c(62,6730,1,3,1,10,0),c(63,6728,1,3,1,10,0),c(64,6725,1,3,1,6,0),c(65,6723,1,3,1,6,0),c(66,6605,3,3,1,0.01,1),c(67,6610,3,3,1,0.01,1),c(68,6616,3,3,1,3,0),c(69,6624,2,3,1,6,0),c(70,6625,2,3,1,6,0),c(71,6628,2,3,1,10,0),c(72,6630,2,3,1,2,1),
c(73,6230,1,4,1,10,0),c(74,6229,1,4,1,1,1),c(75,6228,1,4,1,1,1),c(76,6225,1,4,1,2,1),c(77,6224,1,4,1,1,1),c(78,6223,1,4,1,1,1),c(79,6210,3,4,1,2,0),c(80,6123,2,4,1,6,0),c(81,6125,2,4,1,6,0),c(82,6128,2,4,1,5,1),c(83,6129,2,4,1,1,1),c(84,6130,2,4,1,1,1),
c(85,6033,3,4,1,10,0),c(86,6030,1,4,1,1,1),c(87,6029,1,4,1,1,1),c(88,6028,1,4,1,2,1),c(89,6025,1,4,1,1,1),c(90,6024,1,4,1,5,1),c(91,6023,1,4,1,3,1),c(92,6020,2,4,1,1,1),c(93,6019,2,4,1,1,1),c(94,6018,2,4,1,1,1),c(95,6017,2,4,1,4,0),c(96,6016,2,4,1,4,0),
c(97,6013,2,4,1,3,0),c(98,6012,2,4,1,1,1),c(99,6010,2,4,1,1,1),c(100,6009,2,4,1,3,0),c(101,6006,2,4,1,1,1),c(102,6005,2,4,1,1,1),c(103,6004,2,4,1,1,1),c(104,6003,2,4,1,1,1),c(105,6002,2,4,1,1,1),c(106,5902,1,4,1,1,1),c(107,5903,1,4,1,1,1),c(108,5904,1,4,1,2,0),
c(109,5905,1,4,1,2,0),c(110,5906,1,4,1,1,1),c(111,5910,1,4,1,1,1),c(112,5911,1,4,1,1,1),c(113,5913,1,4,1,3,0),c(114,5916,1,4,1,4,0),c(115,5917,1,4,1,1,1),c(116,5918,1,4,1,2,1),c(117,5919,1,4,1,1,1),c(118,5923,2,4,1,6,0),c(119,5924,2,4,1,6,0),c(120,5925,2,4,1,1,1),
c(121,5928,2,4,1,10,0),c(122,5930,2,4,1,10,0),c(123,5430,1,4,2,2,1),c(124,5429,1,4,2,2,1),c(125,5428,1,4,2,1,1),c(126,5425,1,4,2,6,0),c(127,5423,1,4,2,2,1),c(128,5420,1,4,2,2,1),c(129,5418,1,4,2,2,1),c(130,5416,1,4,2,4,0),c(131,5413,1,4,2,1,1),c(132,5412,1,4,2,2,1),
c(133,5410,1,4,2,2,1),c(134,5406,1,4,2,2,0),c(135,5404,1,4,2,2,0),c(136,5402,1,4,2,2,0),c(137,5302,2,4,2,2,0),c(138,5304,2,4,2,2,0),c(139,5305,2,4,2,1,1),c(140,5309,2,4,2,2,1),c(141,5310,2,4,2,3,0),c(142,5312,2,4,2,1,1),c(143,5316,2,4,2,1,1),c(144,5317,2,4,2,4,0),
c(145,5319,2,4,2,4,0),c(146,5323,2,4,2,1,1),c(147,5324,2,4,2,6,0),c(148,5325,2,4,2,2,1),c(149,5328,2,4,2,1,1),c(150,5329,2,4,2,10,0),c(151,5330,2,4,2,1,1),c(152,5229,1,4,2,10,0),c(153,5228,1,4,2,10,0),c(154,5225,1,4,2,5,0),c(155,5224,1,4,2,5,0),c(156,5223,1,4,2,5,1),
c(157,5103,3,4,2,0.01,1),c(158,5123,2,4,2,6,0),c(159,5125,2,4,2,6,0),c(160,5129,2,4,2,10,0),c(161,5130,2,4,2,10,0),c(162,4723,1,2,2,6,0),c(163,4725,1,2,2,6,0),c(164,4728,1,2,2,10,0),c(165,4730,1,2,2,10,0),c(166,4630,2,2,2,10,0),c(167,4628,2,2,2,10,0),
c(168,4625,2,2,2,6,0),c(169,4623,2,2,2,6,0),c(170,4619,2,2,2,4,0),c(171,4617,2,2,2,4,0),c(172,4612,2,2,2,3,0),c(173,4610,2,2,2,3,0),c(174,4605,2,2,2,2,0),c(175,4603,2,2,2,2,0),c(176,4503,1,2,2,2,0),c(177,4505,1,2,2,2,0),c(178,4510,1,2,2,3,0),c(179,4512,1,2,2,3,0),
c(180,4517,1,2,2,4,0),c(181,4519,1,2,2,4,0),c(182,4523,1,2,2,6,0),c(183,4524,1,2,2,6,0),c(184,4525,1,2,2,1,1),c(185,4528,1,2,2,10,0),c(186,4530,1,2,2,10,0),c(187,4430,2,2,2,10,0),c(188,4428,2,2,2,10,0),c(189,4425,2,2,2,10,1),c(190,4423,2,2,2,10,1),c(191,4103,1,1,2,2,0),
c(192,4105,1,1,2,2,0),c(193,4109,1,1,2,1,1),c(194,4110,1,1,2,3,0),c(195,4112,1,1,2,3,0),c(196,4117,1,1,2,4,0),c(197,4119,1,1,2,4,0),c(198,4123,1,1,2,6,0),c(199,4124,1,1,2,1,1),c(200,4125,1,1,2,6,0),c(201,4128,1,1,2,10,0),c(202,4130,1,1,2,10,0),c(203,4030,2,1,2,10,0),
c(204,4028,2,1,2,5,1),c(205,4025,2,1,2,3,1),c(206,4023,2,1,2,6,0),c(207,4019,2,1,2,4,0),c(208,4017,2,1,2,4,0),c(209,4012,2,1,2,3,0),c(210,4010,2,1,2,3,0),c(211,4005,2,1,2,2,0),c(212,4003,2,1,2,2,0),c(213,3923,1,1,2,6,0),c(214,3925,1,1,2,6,0),c(215,3928,1,1,2,10,0),
c(216,3930,1,1,2,2,1),c(217,3830,2,1,2,10,0),c(218,3828,2,1,2,10,0),c(219,3825,2,1,2,6,0),c(220,3823,2,1,2,6,0),c(221,3423,1,3,2,6,0),c(222,3424,1,3,2,1,1),c(223,3425,1,3,2,6,0),c(224,3428,1,3,2,1,1),c(225,3429,1,3,2,1,1),c(226,3430,1,3,2,10,0),c(227,3330,2,3,2,1,1),
c(228,3329,2,3,2,1,1),c(229,3328,2,3,2,10,0),c(230,3325,2,3,2,5,1),c(231,3323,2,3,2,6,0),c(232,3203,2,3,2,2,0),c(233,3205,2,3,2,2,0),c(234,3210,2,3,2,3,0),c(235,3212,2,3,2,3,0),c(236,3217,2,3,2,4,0),c(237,3219,2,3,2,4,0),c(238,3223,1,3,2,6,0),c(239,3225,1,3,2,6,0),
c(240,3228,1,3,2,10,0),c(241,3229,1,3,2,10,0),c(242,3230,1,3,2,1,1),c(243,3130,2,3,2,10,0),c(244,3128,2,3,2,10,0),c(245,3125,2,3,2,6,0),c(246,3123,2,3,2,6,0),c(247,3119,1,3,2,4,0),c(248,3117,1,3,2,4,0),c(249,3112,1,3,2,3,0),c(250,3110,1,3,2,3,0),c(251,3105,1,3,2,2,0),
c(252,3103,1,3,2,2,0),c(253,2603,1,3,3,2,0),c(254,2605,1,3,3,2,0),c(255,2610,1,3,3,3,0),c(256,2612,1,3,3,3,0),c(257,2617,1,3,3,4,0),c(258,2619,1,3,3,4,0),c(259,2624,1,3,3,6,0),c(260,2625,1,3,3,6,0),c(261,2628,1,3,3,10,0),c(262,2629,1,3,3,10,0),c(263,2630,1,3,3,1,1),
c(264,2530,2,3,3,10,0),c(265,2528,2,3,3,10,0),c(266,2525,2,3,3,6,0),c(267,2524,2,3,3,1,1),c(268,2523,2,3,3,6,0),c(269,2519,2,3,3,4,0),c(270,2517,2,3,3,4,0),c(271,2512,2,3,3,3,0),c(272,2510,2,3,3,3,0),c(273,2505,2,3,3,2,0),c(274,2503,2,3,3,2,0),c(275,2423,1,3,3,6,0),
c(276,2425,1,3,3,6,0),c(277,2429,1,3,3,10,0),c(278,2430,1,3,3,10,0),c(279,2329,2,3,3,10,0),c(280,2328,2,3,3,10,0),c(281,2325,2,3,3,6,0),c(282,2324,2,3,3,6,0),c(283,2323,2,3,3,1,1),c(284,1930,1,4,3,10,0),c(285,1929,1,4,3,1,1),c(286,1928,1,4,3,1,1),c(287,1925,1,4,3,6,0),
c(288,1923,1,4,3,6,0),c(289,1802,2,4,3,2,0),c(290,1804,2,4,3,1,1),c(291,1805,2,4,3,2,0),c(292,1809,2,4,3,3,0),c(293,1810,2,4,3,3,0),c(294,1811,2,4,3,1,1),c(295,1812,2,4,3,1,1),c(296,1813,2,4,3,1,1),c(297,1816,2,4,3,1,1),c(298,1817,2,4,3,4,0),c(299,1819,2,4,3,4,0),
c(300,1820,2,4,3,1,1),c(301,1823,2,4,3,6,0),c(302,1824,2,4,3,6,0),c(303,1825,2,4,3,1,1),c(304,1828,2,4,3,10,0),c(305,1829,2,4,3,10,0),c(306,1830,2,4,3,1,1),c(307,1730,1,4,3,1,1),c(308,1729,1,4,3,1,1),c(309,1728,1,4,3,1,1),c(310,1725,1,4,3,1,1),c(311,1724,1,4,3,1,1),
c(312,1723,1,4,3,6,0),c(313,1720,1,4,3,4,0),c(314,1719,1,4,3,1,1),c(315,1718,1,4,3,1,1),c(316,1716,1,4,3,2,1),c(317,1713,1,4,3,3,0),c(318,1711,1,4,3,3,0),c(319,1705,1,4,3,2,0),c(320,1703,1,4,3,2,0),c(321,1623,2,4,3,6,0),c(322,1624,2,4,3,1,1),c(323,1625,2,4,3,6,0),
c(324,1628,2,4,3,2,1),c(325,1630,2,4,3,1,1),c(326,1330,1,2,3,9,1),c(327,1328,1,2,3,10,0),c(328,1325,1,2,3,6,0),c(329,1323,1,2,3,6,0),c(330,1319,1,2,3,4,0),c(331,1317,1,2,3,4,0),c(332,1312,1,2,3,3,0),c(333,1310,1,2,3,3,0),c(334,1305,1,2,3,2,0),c(335,1303,1,2,3,2,0),
c(336,1203,2,2,3,2,0),c(337,1205,2,2,3,2,0),c(338,1210,2,2,3,3,0),c(339,1211,2,2,3,1,1),c(340,1212,2,2,3,3,0),c(341,1217,2,2,3,4,0),c(342,1219,2,2,3,4,0),c(343,1223,2,2,3,6,0),c(344,1225,2,2,3,6,0),c(345,1228,2,2,3,10,0),c(346,1230,2,2,3,10,0),c(347,1130,1,2,3,2,1),
c(348,1128,1,2,3,10,0),c(349,1125,1,2,3,6,0),c(350,1123,1,2,3,6,0),c(351,1023,2,2,3,6,0),c(352,1025,2,2,3,5,1),c(353,1028,2,2,3,10,0),c(354,1030,2,2,3,10,0),c(355,630,1,1,3,10,0),c(356,628,1,1,3,10,0),c(357,625,1,1,3,6,0),c(358,623,1,1,3,6,0),c(359,523,2,1,3,6,0),
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c(372,405,2,1,3,2,0),c(373,403,2,1,3,2,0),c(374,302,1,1,3,2,0),c(375,303,1,1,3,1,1),c(376,304,1,1,3,1,1),c(377,305,1,1,3,2,0),c(378,310,1,1,3,3,0),c(379,312,1,1,3,3,0),c(380,317,1,1,3,4,0),c(381,319,1,1,3,4,0),c(382,323,2,1,3,6,0),c(383,325,2,1,3,6,0),
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