R/coxRegressionResiduals.R

In milescsmith/WGCNA: Weighted Correlation Network Analysis

## The function is currently defined as

coxRegressionResiduals <- function(time, event, datCovariates = NULL) {
  if (eval(parse(text = '!require("survival")'))) {
    stop("This function requires package survival. Please install it first.")
  }

  if (length(time) != length(event)) {
    stop("Error: The length of the vector event is unequal to the length of the time vector. In R language: length(time) != length(event)")
  }
  if (is.null(datCovariates)) {
    coxmodel <- eval(parse(text = "survival:::coxph(Surv(time, event) ~ 1 , na.action = na.exclude)"))
  }
  if (!is.null(datCovariates)) {
    if (dim(as.matrix(datCovariates))[[1]] != length(event)) stop("Error: the number of rows of the input matrix datCovariates is unequal to the number of observations specified in the vector event. In R language: dim(as.matrix(datCovariates))[[1]] !=length(event)")
    coxmodel <- eval(parse(
      text = paste(
        "survival:::coxph(Surv(time, event) ~ . , data=datCovariates,",
        "na.action = na.exclude, model = TRUE)"
      )
    ))
  } # end of if
  datResiduals <- data.frame(
    martingale = residuals(coxmodel, type = "martingale"),
    deviance = residuals(coxmodel, type = "deviance")
  )
  datResiduals
} # end of function