Error in coxModelFrame.coxph(object) : invalid object set x=TRUE in the call to coxph

The following example is for anyone who is building a Cox Proportional Hazards models and trying to produce prediction error curves, but get an error stating:

Error in coxModelFrame.coxph(object) : invalid object set x=TRUE in the call to coxph.

Here is the code to reproduce the error:

LIBRARIES

library(survival)
library(survminer)
library(pec)
library(Hmisc)
library(rms)
library(riskRegression)
#install.packages("doMC", repos="http://R-Forge.R-project.org")
library(doMC)

The Data

#Load and store the data
lcOrig <- read.csv("cancer.csv")

#Replace all the 1's with 0's (censored)
lcOrig$status <- gsub(pattern = "1", replacement = "0", x = lcOrig$status, fixed = TRUE)

#Replace all the 2's with 1's (death)
lcOrig$status <- gsub (pattern = "2", replacement = "1", x = lcOrig$status, fixed = TRUE)

#Do the same thing for sex (0 = Males, 1 = Females)
lcOrig$sex <- gsub(pattern = "1", replacement = "0", x = lcOrig$sex, fixed = TRUE)

lcOrig$sex <- gsub(pattern = "2", replacement = "1", x = lcOrig$sex, fixed = TRUE)

#Change the class of these variables to integer.
lcOrig$status <- as.integer(lcOrig$status)
lcOrig$sex <- as.integer(lcOrig$sex)
lcOrig$ph.ecog <- as.integer(lcOrig$ph.ecog)

#Remove missing values and column with over 20% missing data.
apply(lcOrig, 2, function(x) sum(is.na(x))/length(x))
lcOrig <- lcOrig[, c(1:9, 11)]
lc <- lcOrig[complete.cases(lcOrig), ]

Cox Proportional Hazards

fitform1 <- Surv(time, status) ~ inst + age + sex + ph.ecog + ph.karno + pat.karno + wt.loss

cox1 <- coxph(fitform1, data = lc)

PREDICTION ERROR CURVES

extends <- function(...) TRUE
library("doMC")
registerDoMC()

set.seed(0692)
fitpec1 <- pec(list("CPH" = cox1), data = lc, formula = fitform1, splitMethod = "cv10", B = 5, keep.index = TRUE, keep.matrix = TRUE)

The last line of code results in the following error: Error in coxModelFrame.coxph(object) : invalid object set x=TRUE in the call to coxph

SOLUTION

Change:

cox1 <- coxph(fitform1, data = lc)

To:

cox1 <- coxph(fitform1, data = lc, x = TRUE)

This did not use to be a requirement 2 years ago, but is now. I hope this helps save you some time!