[Cox proportional hazards regression][1] is a very popular, semi-parametric method for survival analysis.

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Possible time-dependent mediation effect in Cox regression

I'm quite new to survival analysis, but would appreciate any advice on how to deal with the following finding in my data analysis/ results interpretation. I have been using R and have used a ...
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10 views

How to plot adjusted Kaplan-Meier Curves?

I am trying to plot adjusted Kaplan-Meier curves. I know publications like to see something graphical. But using R, I don't know how to go about adjusting for something like age, gender, income when ...
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How to use time dependent covariates with cox regression in R

I don't know how to generate time dependent covariates in R for use cox regression. I know you need to reorganize your dataset into intervals between event times. This I believe I can do with the ...
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Interpretation of coefficients in Cox model with time varying covariates and coefficients

I have a data set on survival times for individuals that may or may not develop a disease during the course of the study. Disease status is a time varying covariate, since individuals may become ...
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7 views

Observed information matrix in Cox model with constant baseline hazard

I am trying to explore properties of Cox model with (parametric) constant baseline hazard function. So the hazard function for the model is $\lambda(t|Z_i) = \lambda_0(t) ...
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1answer
19 views

Why doesn't a Cox model with time-dependent co-variates lead to pseudoreplication?

In survival analysis, if we have a time-dependent covariate, it is recommended to split data for each individual into multiple time-periods, with start and end dates for each, such that each time ...
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How to get 95% CI from R's coxph? [migrated]

I have used the following function in R's coxph() to fit a cox hazard model. I want to report the proper statistics; however, there is no 95% CI in the output. ...
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1answer
26 views

Applying Cox's Porportional Hazard model

I have a dataset on two groups. Group 1 (18 subjects) and group 2 (5 subjects). Each subject in the groups had to perform a number of tasks which was timed. The time restriction was 60 seconds. If ...
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1answer
38 views

Optimal Cutpoint for Predicted Results from Kaplan Meier and Cox Regression

Is there anyway to get the optimal cutpoint for predicted survival probabilities of the aforementioned survival analysis approaches? Something like the optimal cutpoint from ...
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1answer
23 views

Can coxph be used for categorical data?

I'm doing some survival analysis and I got the idea to change a binary variable into three-category variable by sub-dividing one category of the binary variable into two new categories. Here's a ...
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1answer
59 views

predict from a Cox model with beta coefficients

I fitted a Cox PH model in R with the survival package and the coxph function. I get the beta estimates from this model. How can I use these coefficients to ...
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12 views

C-index of a fitted cox model in validation data set

I know that c-index of a cox model can be obtained using survival::survConcordance. Below is an example, ...
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1answer
22 views

How to get Cox p-value for 20,000 genes?

If you run the following code, you will have a data frame real.dat which has 1063 samples for 20531 genes. There are 2 extra columns named ...
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How to structure data for repeated measures Cox model in R?

I am looking the relationship between a patient's lab values (measured at baseline and post-treatment) and their survival. The lab values are measuring the concentration of the same protein, they are ...
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1answer
24 views

Forecasting survival probability using Cox Regression

I'm able to obtain predicted survival probabilities of cox regression using either survfit.coxph or predictSurvProb from ...
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Cox Regression When Event is Uncertain

Hypothetical Situation: I'm trying to create a cox model on data set with some serious quality issues. Sometimes the event goes unreported in our data set. Some patients have a treatment regime that ...
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1answer
39 views

Multivariable survival analysis: adding another variable lowers the p value?

When I was performing the Cox survival analysis on my data, I tried to look at the predictive value of different variables to survival. For example, here I have two variables: 'size' and 'surface'. ...
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1answer
39 views

What kind of model should I use for churn risk prediction?

I have a data set containing many client's id, and its behavior characteristics measured each month before churn or censored. Data looks like: id || lifetime period || folow-up time before churn of ...
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17 views

Cox PH model with quadratic effect interpretation

I'm fitting a Cox model with non-linear continuous variable with and without a time varying effect (to correct non-PH). My goal is to get risk ratio (hazard ratio) associated with X. I have the Cox PH ...
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1answer
16 views

Validity of PH test using Schoenfeld residuals from Cox model on parametric models

I need to use parametric models to model survival data. If the PH assumption holds, I would fit the data for my two intervention groups using a single covariate for treatment effect. I fit a Cox PH ...
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1answer
32 views

Weibull Survival Model with Time Varying Covariates in R

I am trying to run a survival model using the Weibull approach, but the wrinkle is that I have time varying covariates. I am using the survival package in R. My call is: output <- ...
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1answer
38 views

time varying coefficients in cox proportional hazard model

I am trying to fit a coxph model in R. The study can be described as follows: I have a very large dataset, in counting process form, containing whether or not someone responded to a survey or not. ...
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4answers
611 views

Machine learning methods which takes time-to-event into account?

My vague understanding is that machine learning methods are based on classification labels. How about a survival type of problem? That is to say, not only "have event" or "have no event", but also ...
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8 views

Using results from spline estimation in cox model

Is it possible to incorporate the results from estimating splines into a logistic or proportional hazards model? That is, I'd like to try to use the spline function as a weight for my exposure ...
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2answers
54 views

What is the reference point for a Cox proprtional hazard spline model?

When trying to fit a Cox model to a continuous term we have a problem interpreting the result. When fitting a linear model the hazard ratio is referenced to the mean of the predictor values, and at ...
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How do you calculate the compared populations in cox hazard ratio problems?

Take a look at the following open-access paper http://www.ncbi.nlm.nih.gov/pubmed/26506242 I've tried doing cox regression in both R and SPSS but I cannot get ...
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Cox regression with penalized package in R

Although I have visited this site several times, this is the first time I make a question, so be kind if it is not in a appropriate form. My problem is part statistical and part R. I am trying to ...
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Computing c-index for an external validation of a Cox PH model with Stata

I have developed a Cox prognostic model based and internally validated it using bootstrapping. I also evaluated its calibration using Harrell’s $c$ statistic and Somers' $D$. I have also checked ...
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Calibration test of cox-model in external validation using stata

I'm planning to validate a cox-risk prediction model in external dataset. As a pert of the validation process, I want to test the calibration of my model in the external dataset. I would appreciate if ...
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Reposted: Calibration and Discrimination of Cox prognostic model with Stata [duplicate]

I'm planning to do an external validation of a Cox-prognostic model against another study and a published risk prediction equation. Yet, my previous exposure is limited validation of logistic model. ...
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43 views

Failure to converge after including and interaction between time and a covariate (in survival analysis) in R

I have fit a Cox proportional hazards model to some survival data. I then checked assumption of proportionality of hazards by checking plots of scaled Schoenfeld residuals. based on this, it ...
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34 views

Determine if covariate is confounding in Cox proportional hazards model

I've developed a risk score that predicts patient survival. Now I want to see whether my risk score is independent of cancer stage. I've already determined that there's no interaction between the two, ...
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232 views

Cox proportional hazards model: response to reviewer's comment on prognostic significance

I am answering a reviewer's comments on a manuscript (medical). In one analysis I run a univariate Cox regression analysis on the variable "has disease vs hasn't disease" as stated by a clinical ...
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1answer
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Violation of proportional hazard for covariate but not for interaction it's part of in a Cox Proportional Hazards model

I have a problem in which one of the covariates in my model violates the assumption of proportional hazards, but the interaction it is part of does not. Data info: Lifespan - mosquito time to death ...
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43 views

KM versus Cox model

This question is in general, but I would also like to know how the answer pertains to building the model in R. I have some time to event data and want to do some ...
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2answers
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Generating data from KM curves

I have some survival data from different cohorts and can fit Kaplan Meier curves and cox proportional hazard models. I want to be able to simulate data that resembles the data found in say the KM ...
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1answer
40 views

Cox-Proportional Hazards Survival Curve has too many lines - can binning the continuous variable help?

I am doing survival analysis on some continuous variables and am finding that some of my plots are difficult to interpret because there are too many lines. Here is an example: I am interested in ...
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107 views

How can machine learning models (GBM, NN etc.) be used for survival analysis?

I know that traditional statistical models like Cox Proportional Hazards regression & some Kaplan-Meier models can be used to predict days till next occurrence of an event say failure etc. i.e ...
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21 views

Max and min survival “phenotypes” in coxph model R

I have made a cox prop hazards model from continuous survival time data and covariates selected from a larger set using lasso/L1 reg, and I want to visually demonstrate how my selected covariates can ...
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Comparing plot from survfit with plot of cox baseline hazard converted to survival rate

Based on the initial question: Cox Baseline Hazard I would like to plot survival curves by gender for this model using the kidney dataset. Following the example codes, I subset the dataset by gender, ...
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56 views

Categorical variable with hierarchical structure - Cox regression

What is the best way to build a cox model with a categorical variable that has a hierarchical structure (20 levels).
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Survival analysis book with R language

I am looking for a good book for survival analysis in R . Also, I wnat the focus to be on cox model and its extensions). Better if free
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235 views

Layman's explanation of censoring in survival analysis

I have read about what censoring is and how it needs to be accounted for in survival analysis but I would like to hear a less mathematical definition of it and a more intuitive definition (pictures ...
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1answer
26 views

Many categorical variables in Cox regression model

I am using Cox regression to model my data (time to an event). One of the covariates has 29 categories. I would like to compare the categories to one another and identify which category has shortest ...
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27 views

How to plot splines in a coxph model that includes a frailty term?

I have a Cox PH model including a smoothing spline and a frailty term as follows: fit<-coxph(Surv(start,end,exit) ~ x + pspline(z) + frailty(a)) When I run a ...
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53 views

P-values for spline terms in coxph in R

I have a Cox PH model including a smoothing spline as follows, where x and z are covariates: fit<-coxph(Surv(start,end,exit) ~ x + pspline(z)) While I ...
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26 views

Need help to simulate Survival Times with a time-varying Covariate

I would really appreciate if someone can help me figure this out as I have been working on it for few days now and I don't know what I'm missing that it's not working. Basically, my goal is to sample ...
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Confusion about coxph function/model

When comparing two arms of a trial, the idea is to imagine that each patient receives both treatment A (control) and treatment B essentially in two parallel worlds. Obviously this can't work and so a ...
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How would I use sample weights in a Cox proportional hazards model?

I was asked to run a Cox proportional hazards model with sample weights. The sample weights are for respondent company, but I'm only running on an overall and regional level. How would I incorporate ...
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Should I use GEE, Multilevel or Cox regression?

I am interested in the relationship between the number of hours worked per week and the chances of getting an illness. My dataset consists of 47 subjects, the predictor variable hours worked per week ...