Stack Overflow
Stack Overflow

Questions tagged [cox]

67 questions
1
vote
1 answer

Error when model diagnostics on stratified variable with coxph (survival package) in R

I have a dataset where 3 groups have recieved exposure to different media. One group is exposed to 1 of the 3 media. Therefore, my coxph model is stratified: # My treatment variable is loaded as a factor. fullModel <- coxph(Surv(time, status) ~…
asellus
  • 59
  • 5
1
vote
0 answers

How to plot survival probability calibration with Lifelines?

I am trying to use survival_probability_calibration to visualize the performance of Cox model but the calibration curve would always stay flat as shown in the following plot: Calibration curve with cox model What can be the reason of this issue?…
Ali Fahmi
  • 21
  • 1
1
vote
0 answers

How to predict risk scores with Cox models using lifelines package?

I have made multiple cox models with Lifelines package and I am trying to predict the risk score of each individual following information in CoxPhFitter page. predict_hazard is a suggested command in that page, but when I use it to predict risk…
Ali Fahmi
  • 21
  • 1
1
vote
1 answer

Creating a full vs. reduced model with one explanatory variable

I am attempting to create a Cox proportional hazards model with only one explanatory variable. To perform a likelihood ratio test, I know I need a full and reduced model. I also know that a full model would be a separate mean for each group, and a…
dolly
  • 13
  • 3
1
vote
0 answers

What is the output of predict.coxph() using type = "survival"?

I am trying to learn what the various outputs of predict.coxph() mean. I am currently attempting to fit a cox model on a training set then use the resulting coefficients from the training set to make predictions in a test set (new set of data). I…
Mao Pineda
  • 11
  • 1
1
vote
0 answers

cox regression plot using R

I have a Cox proportional hazards model set up using the following code in R that predicts mortality. Covariates A, B and C are added simply to avoid confounding (i.e. age, sex, race) but we are really interested in the predictor X. Where X is a…
Khalid
  • 23
  • 2
1
vote
0 answers

cox model forest plot

I would like to generate a cox model forest plot for several models in one fit1 <- coxph(Surv(years, status2) ~ drug , data = pbc2.id) fit2 <- coxph(Surv(years, status2) ~ drug + sex, data = pbc2.id) fit3 <- coxph(Surv(years, status2) ~ drug +…
S Front
  • 333
  • 1
  • 8
1
vote
1 answer

How do I turn off safebrowsing.io that comes with the Cox Panoramic Wifi?

I recently upgraded my wifi with Cox Cable and after installing their Panoramic Wifi device (that is both a modem and a router), I kept getting an Unsafe destination message with a button to click that said "Proceed Anyway". I would get this message…
ProfPerry
  • 11
  • 2
1
vote
1 answer

Multivariable cox regression analysis in R with non-binary categorical variables

I have questions about multivariable cox regression analysis including non-binary categorical variables. My data consists of several variables, and some of them are binary (like sex, and age over 70, etc..) whereas the rest of them are not (for…
user11602587
  • 11
  • 2
1
vote
1 answer

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…
Brandon
  • 51
  • 1
  • 7
1
vote
1 answer

random effects Cox model

I am trying to plot the dose-response relation between pm2.5 exposure and hypertension incidence. I fitted a random effects cox model, in which a random effect was added for the study centers. Then I used the plotHR function to plot the…
epi
  • 25
  • 3
1
vote
0 answers

convert dataset to longitudinal data structure in R

I have a datset that looks something like this: > head(BurnData) Treatment Gender Race Surface head buttock trunk up.leg low.leg resp.tract type ex.time excision antib.time antibiotic 1 0 0 0 15 0 0 1 1 …
user1607
  • 531
  • 7
  • 28
1
vote
0 answers

including time dependent covariates in Cox's Regression in R

I have a datset that looks like: Treatment Surface ex.time excision antib.time antibiotic inf.time infection 1 0 15 12 0 12 0 12 0 2 0 20 9 0 9 0 …
user1607
  • 531
  • 7
  • 28
1
vote
1 answer

How to calculate hazard ratio with coxph output

I have successfully got summary output from 'coxph'. However, now I am curious how to get the hazard ratio from these numbers? Is there a calculation I can do with what I have, or is there a certain code in R that will produce what I want?Output…
Carson
  • 13
  • 3
1
vote
0 answers

How to test PH assumption with Schoenfeld residuals with simulated paths in presence of competing events

I've obtained Schoenfeld residuals for testing PH for Fine & Gray's Cox regression model in presence of competing events with cmprsk. Here's the code: fg<-crr( fu_m, event, diabetes, failcode=1, cencode=0, na.action=na.omit, gtol=1e-06,…
ArTu
  • 431
  • 4
  • 20
1
2
3 4 5