Stack Overflow
Stack Overflow

Questions tagged [cox-regression]

The term Cox regression model (omitting proportional hazards) is sometimes used to describe the extension of the Cox model to include time-dependent factors. However, this usage is potentially ambiguous since the Cox proportional hazards model can itself be described as a regression model.

476 questions
3
votes
0 answers

Error when running coxph on gene expression data

I am getting an error when running coxph on my data. Have anyone of you seen this before? coxph(Surv(OS,Survival_dead0_alive1)~.,data=data.frame(Bind)) Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in…
user2300940
  • 2,355
  • 1
  • 22
  • 35
3
votes
0 answers

Conditional Logisitc regression analysis with mgcv gam models

I am running a GAM model through the mgcv package with family = cox.ph() and have my data grouped by strata (strata = id). The data corresponds to one use location for an individual animal and 20 random locations associated with that individual that…
P. Farrell
  • 31
  • 3
3
votes
1 answer

R session aborted when trying to run coxph

Every time I run model<– coxph(enter,exit, event)~X1+X2+GDP the session crashes suddenly with no error message. It is only when I add the gap variable that it crashes. I wonder if it has to do with the GDP variable? I tried different sources and…
FKG
  • 285
  • 1
  • 4
  • 17
3
votes
1 answer

Multistate Survival Analysis using R package "Survival"

I am trying to estimate Cox proportional hazards model for transition from state 1 to state 2 using R survival package as follows: Altman <- coxph(Surv(Tstart, Tstop, to == 2) ~ wWCTA + wRETA + wEBITTA + wMETL + wSTA, data=Multistate,…
Jairaj Gupta
  • 347
  • 4
  • 16
3
votes
1 answer

Testing multicollinearity in cox proportional hazards using R

I would like to assess multicollinearity in a cox proportional hazards model by calculating Variance Inflation Factor (VIF). The vif-functions in packages like {car} does not accept coxph objects. Is there a way to calculate VIF for cox models in…
Erik
  • 308
  • 1
  • 3
  • 11
3
votes
1 answer

R object of type 'environment' is not subsettable

I'm doing survival analysis with interval censored data and I'm trying to use intcox() function from the incox package to do a Cox regression. I've already done part of the analysis with survfit() and everything worked fine. When I try to use…
JMarcelino
  • 904
  • 4
  • 13
  • 30
3
votes
1 answer

Stratified cox regression in R using package namespace

I'm doing stratified cox regression in R with the survival package: cox <- coxph(response~strata(x), data=data) This works fine, but when using the sampling package the strata function from the survival package is hidden and cannot be used…
DeltaKappa
  • 171
  • 7
2
votes
0 answers

Cox model selection: Test all variable combination

I need to test, which cox model fits the best based on partial AIC. Below you see the code, that I am using to test the combination of 5 parameters. How can I adjust my code, to test all possible variables combinations? parameters = ['v1', 'v3',…
Mischa
  • 83
  • 1
  • 10
2
votes
0 answers

How to use Predict in rms package for a multiple values?

I used cox model for Predict function rms package for individual values they are returning the correct result where as when I give multiple values it gives me weired…
user2110417
2
votes
1 answer

Wrangle data from long to wide format for cox regression in R

I am trying to wrangle some data for a cox regression... #generate some data set.seed(1) ID <- sort(rep(1:10, times = 5)) conditions <- rep(c("asthma", "copd", "af", "cvd", "ckd"), times = 10) day <- sample(1:100, 50) #assign to dataframe df <-…
Richard Summers
  • 143
  • 1
  • 10
2
votes
1 answer

comparing svycoxph models with likelihood ratio test

To find the optimal multivariate-adjusted Cox model (svycoxph) I'd like to compare different models with a likelihood ratio test to learn which model is better. Comparing to models with anova(model1, model2) or AIC doesn't work with survey weighted…
Sasi
  • 53
  • 3
2
votes
0 answers

Is there a way in R to include weights in a cox regression with Firth's penalized likelihood?

I am trying to fit a propensity score weighted cox regression model in R. However, one of the treatment groups has zero events, so I also need to use an adjustment method (Firth's penalized likelihood). I have been using the coxphf package just fine…
Jordan Hackett
  • 689
  • 3
  • 11
2
votes
1 answer

Adjusted Survival Curves in R From Cox Model at Specific Covariate Values

I'd like to plot adjusted survival curves from a Cox model at specific covariate values. The survfit function in the survival package and ggsurvplot in survminer allow one to easily plot adjusted survival curves from a model, but seem to only do so…
West_End_Line
  • 179
  • 6
2
votes
2 answers

Change axis ranges for a ggplot based on a Predict object (rms package)

I am using the rms package to perform Cox regression with age as restricted cubic splines with 4 knots, see reproducible code below from the rms package documentation. My problem is: How do I change the y axis interval for the ggplot-output? I tried…
Pontus Hedberg
  • 301
  • 1
  • 2
  • 9
2
votes
1 answer

Time-dependent covariates- is there something wrong with this code? (R program)

I am checking a few of my Cox multivariate regression analyses' proportional hazard assumptions using time-dependent co-variates, using the survival package. The question is looking at survival in groups with different ADAMTS13 levels (a type of…
Jobolo
  • 79
  • 6
1 2 3
…
31 32