My sessionInfo is as follows: R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit)
locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] mi_0.09-16 arm_1.5-05 foreign_0.8-50 abind_1.4-0 [5] R2WinBUGS_2.1-18 coda_0.15-2 lme4_0.999999-0 Matrix_1.0-6 [9] lattice_0.20-6 car_2.0-12 nnet_7.3-4 MASS_7.3-20 [13] MuMIn_1.7.11 survival_2.36-14 loaded via a namespace (and not attached): [1] grid_2.15.1 nlme_3.1-104 stats4_2.15.1 > It will be difficult to reproduce an example here as the data set I am using in very large. I can give you an example: fit3.1<- coxph(formula = y ~ sex + ns(ageyrs, df = 2) + AdmissionSource + + X1 + X2 + X3 + X5 + X6 + X7 + X11 + X12 + X13 + X14 + X15 + + X16 + X17 + X18 + X19 + X20 + X22 + X24 + X25 + X26 + X27 + + X28 + X29 + X32 + X33 + X35 + X38 + X39 + X40 + X41 + X42 + + X43 + X44 + X47 + X49 + X53 + X54 + X55 + X58 + X59 + X62 + + X68 + X69 + X78 + X80 + X81 + X84 + X85 + X86 + X93 + X95 + + X98 + X100 + X101 + X102 + X105 + X107 + X108 + X109 + X110 + + X112 + X113 + X114 + X115 + X116 + X117 + X121 + X122 + X125 + + X127 + X128 + X129 + X131 + X132 + X133 + X134 + X138 + X140 + + X143 + X145 + X146 + X148 + X150 + X151 + X153 + X157 + X158 + + X159 + X164 + X197 + X200 + X202 + X203 + X204 + X205 + X211 + + X214 + X217 + X224 + X228 + X233 + X237 + X244 + X249 + X254 + + X258 + X259 + X260 + CharlsonIndex + ethnic + day + season + + ln, data = dat2) haz<-basehaz(fit3.1) # gives 507 unique haz$time, time points fit2<-coxph(y~ns(ageyrs,df=2)+day+ln+sex+AdmissionSource+season+CharlsonIndex,data=dat1) haz<-basehaz(fit2) # gives 611 unique haz$time, time points I get the following warnings() with fit3.1: Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, : Loglik converged before variable ; beta may be infinite. Also the coefficients of the variables that the error occurs for are very high. The Wald test suggests dropping these terms where as the LRT suggests keeping them. What should I do in terms of model selection? -- View this message in context: http://r.789695.n4.nabble.com/basehaz-in-package-Survival-and-warnings-with-coxph-tp4639687p4639838.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.