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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.

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R coxph() warning: Loglik converged before variable

I'm having some trouble using coxph(). I've two categorical variables: Sex and Probable Cause, that I want to use as predictor variables. Sex is just the typical male/female but Probable Cause has 5 options. I don't know what is the problem with the…
JMarcelino
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coxph() X matrix deemed to be singular;

I'm having some trouble using coxph(). I've two categorical variables:"tecnologia" and "pais", and I want to evaluate the possible interaction effect of "pais" on "tecnologia"."tecnologia" is a variable factor with 2 levels: gps and convencional.…
JMarcelino
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What does is.na() applied to non-(list or vector) of type 'NULL' mean?

I want to select a Cox model with the forward procedure from a data.frame with no NA. Here is some sample data: test <- data.frame( x_1 = runif(100,0,1), x_2 = runif(100,0,5), x_3 = runif(100,10,20), time = runif(100,50,200), event…
Vincent
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Cox regression python

Are there any packages in Python for survival analysis? Specifically, I am interested in performing a Cox regression? I know this example but it's in R. Could we just interface Python with R (using, for example, rpy2)?
Edward
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How to handle Recurrent event Survival analysis (Counting Process Approach) in Python

I am trying to find a way to model Survival Models for Recurrent Events in Python, especially the Counting process approach using CoxPH. In Counting Process Approach, it is expecting start-time and stop-time. But the fit method of CoxPHFitter in…
B K
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Plot Kaplan-Meier for Cox regression

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. X is a…
Hims
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Plotting estimated HR from coxph object with time-dependent coefficient and splines

I want to plot the estimated hazard ratio as a function of time in the case of a coxph model with a time-dependent coefficient that is based on a spline term. I created the time-dependent coefficient using function tt, analogous to this example that…
half-pass
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Pooling Cox PH results after multiple imputation with the MICE package

I have a dataset with survival data and a few missing covariates. I've successfully applied the mice-package to imputate m-numbers of datasets using the mice() function, created an imputationList object and applied a Cox PH model on each m-dataset.…
Kjetil Loland
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Cox regression output in xtable - choosing rows/columns and adding a confidence interval

I wan't to export the output from a cox regression to a table that I then can put into my article. I guess the best way to go about it is with xtable: library(survival) data(pbc) fit.pbc <- coxph(Surv(time, status==2) ~ age + edema + log(bili) + …
Max Gordon
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Violation of PH assumption

Running a survival analysis, assume the p-value regarding a variable is statistically significant - let's say with a positive association with the outcome. However, according to the Schoenfeld residuals, the proportional hazard (PH) assumption has…
Slouei
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Error in aeqSurv(Y) : aeqSurv exception, an interval has effective length 0

I'm using R's coxph function to fit a survival regression model, and I'm trying to model time dependent covariates (see this vignette). When fitting the model, I get the following error: Error in aeqSurv(Y) : aeqSurv exception, an interval has…
Adam Haber
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How to model interaction of covariate with time when proportionality assumption is violated in survival analysis in R

In R, what is the best way to incorporate the interaction term between a covariate and time, when the proportionality test (with coxph) shows that the proportionality assumption in the Cox model is violated? I know that you can either use strata or…
B.Z.
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How does cox.zph deal with time-dependent covariates?

I have a coxph model with 5 time-dependent and 2 time-independent variables. I want to test the proportional hazards assumption and besides martingale and deviance residuals, using cox.zph. My question is, how does this function deal with…
JMarcelino
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Time-Dependent Cox Model

Consider the attached (dummy) sample csv file where two methods (i.e. Method A and Method B) are used to evaluate time to progression (PFS) in cancer patients. For each patient we also have the overall survival (OS). data available as CSV from…
user86533
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NA/NaN/Inf in foreign function call (arg 5)

I don't know if I need to get rid of some data, or what is going on here. Models 1 and 2 work perfectly fine. Model 3 won't run. model1 <- clogit(Used ~ Slope + strata(OBJECTID), data=old) model2 <- clogit(Used ~ Aspect + strata(OBJECTID),…
Dan Graham
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