We want to perform a survival analysis using time-dependent covariates in the Cox regression. In this analysis, ESRD1_END and ESRD1_TIME are the outcome and follow-up time,respectively. AKI_END is a binary time-dependent variable, while AKI_TIME is the time point for AKI_END measurement. The Cox model is some- thing like: Surv(tstart, tstop, ESRD1_END) ˜ AKI_END. However, it seems the formatted data were incorrect using the functions of event() and tdc(), mainly including two problems: 1, The output of event(y, x) is inconsistent with the input data x. 2, Missing value NA was generated from tdc(y, x).
> library(survival) > ori_data <- read.table("test_data.csv", sep=",", header=TRUE, stringsAsFactors=F) > str(ori_data) ' data.frame ' : 7 obs. of 5 variables: $ data95_Obs: int 10112 15 11 12 13 14 16 $ ESRD1_TIME: num 6.27 9.35 16.77 10.84 18.33 ... $ ESRD1_END : int 1 0 0 0 0 1 1 $ AKI_END : int 1 1 0 0 0 0 1 $ AKI_TIME : num 3.23 7.65 16.77 10.84 18.33 ... > dim(ori_data) [1] 7 5 > head(ori_data) data95_Obs ESRD1_TIME ESRD1_END AKI_END AKI_TIME 10112 6.267 1 1 3.233 15 9.347 0 1 7.654 11 16.775 0 0 16.775 12 10.836 0 0 10.836 13 18.330 0 0 18.330 14 6.971 1 0 6.971 > #generate the variables "tstart", "tstop" and "status". However, the "status" is different > #from "ESRD1_END" > ori_data <- tmerge(ori_data, ori_data, id=data95_Obs, status=event(ESRD1_TIME, ESRD1_END)) > dim(ori_data) [1] 7 9 > head(ori_data) data95_Obs ESRD1_TIME ESRD1_END AKI_END AKI_TIME id tstart tstop status 10112 6.267 1 1 3.233 10112 0 6.267 1 15 9.347 0 1 7.654 15 0 9.347 0 11 16.775 0 0 16.775 11 0 16.775 1 12 10.836 0 0 10.836 12 0 10.836 0 13 18.330 0 0 18.330 13 0 18.330 0 14 6.971 1 0 6.971 14 0 6.971 0 > #generate the time-dependent variable "AKI_TC". However, why there are some NAs. > ori_data <- tmerge(ori_data, ori_data, id=data95_Obs, AKI_TC=tdc(AKI_TIME, AKI_END)) > dim(ori_data) [1] 9 10 > head(ori_data) data95_Obs ESRD1_TIME ESRD1_END AKI_END AKI_TIME id tstart tstop status 10112 6.267 1 1 3.233 10112 0.000 3.233 0 10112 6.267 1 1 3.233 10112 3.233 6.267 1 15 9.347 0 1 7.654 15 0.000 7.654 0 15 9.347 0 1 7.654 15 7.654 9.347 0 11 16.775 0 0 16.775 11 0.000 16.775 1 12 10.836 0 0 10.836 12 0.000 10.836 0 AKI_TC NA 1 NA 0 NA NA [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.