CoxPH refers to Cox proportional hazards regression, a semi-parametric method of survival analysis. It is semi-parametric in that the baseline hazard is left unspecified, but parameters for the effects of covariates are estimated. Eliminating the possibility of misspecifying the baseline makes the ...
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32 views
extended cox model with continuous time dependent covariate - how to structure data?
I need to run an extended cox model with a time-varying covariate in R: let’s call it the number of doses (X). I am interested in the hazard ratio associated with each level of X, ie. how an ...
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22 views
How to interpret the frailty terms in a coxph.penal model?
I have the following coxph model:
Surv(Y) ~ genotype + treatment + age + frailty(batch) + genotype:frailty(batch)
...
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40 views
Does case control ratio matter in Cox regression?
I am trying a Cox regression model to do survival analysis/hazard ratio of developing diabetes. But my case control ratio is like 9:1 (i.e. 900 cases and and 100 controls). Will this big difference in ...
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38 views
Median survival time for stratified Cox model
I have a dataset of 30,000 patients who are matched by surgical procedure. My main exposure of interest is if the patient got regional anesthesia during surgery or did not. I have 27 different ...
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50 views
How can I manually calculate Score and Schoenfield residuals for a coxph fit in R?
I am trying to develop a solid understanding of Martingales and various survival residuals calculated using Martingales. To do that, I am attempting to explicitly calculate them for the below dataset ...
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3answers
162 views
Two significant covariates in coxph analysis: exploring whether the two covariates interact significantly
I am using R 2.15.2 GUI1.53 64-bit on MacOSX 10.5.8 to perform these analyses. I am a molecular biologist by training, not a statistician, so all this analysis represents my own bootstrapped learning ...
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173 views
Cox proportional hazards with time-dependent covariates: predict in R
I would like to use the predict function (or something similar) in R to generate expected values from a Cox proportional hazards model with time-dependent covariates. The model takes the form
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1answer
366 views
Cox Baseline Hazard
Let's say I have a 'kidney catheter' data set. I'm actually trying to model a survival curve using a Cox model. If I consider a Cox model
...
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147 views
How to generate predicted survivor curves from frailty models (using R coxph)?
I want to compute predicted survivor function for a Cox proportional hazards
model with frailty terms [using survival package]. It appears that when
frailty terms are in the model, the predicted ...
4
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1answer
430 views
How to interpret the output of predict.coxph?
After fitting a coxmodel it is possible to make predictions and retrieve the relative risk of new data. What I don't understand is how the relative risk is computed for an individual and what is it ...
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1answer
96 views
Creating formula object for coxph()
I am trying to create the formula object for coxph() manually, as I want to reproduce it in RSRuby. Note that the response variable needs to be a ...
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46 views
R CCH CI Univariable Analysis
Using the survival package in R I am trying to calculate 95% confidence interval (CI) of the proportional hazards model coefficient. Normally this is pretty simple to do with the survival package.
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1answer
189 views
Schoenfeld residuals
In a Cox proportional hazards model with many variables, if the Schoenfeld residuals are not flat for one of the variables, does this invalidate the entire model or can just the poorly-performing ...
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154 views
What are the options in proportional hazard regression model when Schoenfeld residuals are not good?
I am doing a Cox proportional hazards regression in R using coxph, which includes many variables. The Martingale residuals look great, and the Schoenfeld residuals ...
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1answer
200 views
Proportional hazard ratio formula in R
I'm new proportional hazard ratio models and new-ish to R, so I suspect this is a basic question:
The scenario is modeling the speed of an effect through hazard ratios. People are joining an ...
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1answer
710 views
Which model should I use for Cox proportional hazards with paired data?
I am hoping someone can help me with which model (frailty, strata or cluster) I should use for my data. I have paired data so I need to take that into account when modelling the Cox PH and am unsure ...
6
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1answer
135 views
How important is using the exact method for ties in a Cox model, and how long should this take?
I'm analyzing the results of some simulation work using a Cox proportional hazard model, and I have what I perceive are a great many ties in the data, representing when a particular individual in the ...
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1answer
883 views
Difference between survdiff log-rank and coxph log-rank
I'm using the survival package in R to analyze clinical data. I am analyzing two different groups of patients, when I calculate survdiff in order to compare the curves, I got p= 0.135, but when I ...
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2answers
1k views
How to calculate predicted hazard rates from a Cox PH model?
I have the following Cox PH model
(Time, Event) ~ X + Y + Z
I would like to get the predicted hazard rates (i am talking about hazard rates NOT hazard ratios) ...
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1answer
2k views
Interpretation and validation of a Cox proportional hazards regression model using R in plain English
Can someone explain my Cox model to me in plain English? I fitted the following Cox regression model to all of my data using the cph function. My data are saved in an object called "Data". The ...
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371 views
Sample size and cross-validation methods for Cox regression predictive models
I have a question I would like to pose to the community. I have recently been asked to provide statistical analysis for a tumor marker prognostic study. I have primarily used these two references to ...
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1answer
1k views
Different prediction plot from survival coxph and rms cph
I've created my own slightly enhanced version of the termplot that I use in this example, you can find it here. I've previously posted on SO but the more I think about it I believe that this probably ...
5
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3answers
287 views
How best to analyze length of stay data in a hospital-based RCT?
I am interested in knowing whether or not there is a consensus about the optimal way to analyze hospital length of stay (LOS) data from a RCT. This is typically a very right-skewed distribution, ...
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1answer
196 views
Sampling distribution is skewed in a fully Bayesian inference of MCMC in Cox PH models
I used the MCMC method to estimate linear models with a fully Bayesian inference previously, and had no problem from estimated coefficients. Recently I use the same way in a semiparametric Cox PH ...
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2answers
983 views
How to get convergence using coxph (R) given that model converges using proc phreg (SAS)
I have a data set
...
