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

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Change in destribution af variable with time - doing cox regression

A hopefully a question that has a simple answer:) I'm doing cox regression on a large dataset. Event=death. Destribution of the main variable change a lot during the timespand (10years) - i.e type of ...
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calculus of predicted number of failures in cox regression

Suppose we rank the prognosis index (the linear product beta*X) of the individuals in a Cox regression and divide this set in a number G of groups. It is trivial to count the number of observed ...
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how to deal with dependence/interaction among covariates in a cox regression model

In case of a linear regression, if we are to account for interaction between two regressors x1 and x2, we write a model like ...
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Is oversampling done for Cox regression data?

I have a dataset consisting of about 48000 people, about 40,000 of which die before the end of the study and get a failed = 1 and the remaining 8000 have a failed = 0 because they're either lost to ...
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Cox PH model - Time-independent vs time-dependent covariates

I am trying to fit two different Cox PH models to some data I have, and get strange results when I consider the same variable as time-independent as opposed to when I consider it time-dependent. More ...
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114 views

Cox discrete time regression model question

Cox's 1972 publication Regression Models and Life Tables links logistic regression to an extension of the discrete time proportional hazard model. I do not understand how Equation (21) in the ...
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Is it possible to gain point survival estimates from a coxme object?

I have a coxme object: (Age, status) ~ F + X1 + X2 + (1|R1) + (1|R2) + (1|R3) Where F is an individual's level of inbreeding, X1 ...
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Model Selection with Competing risks in Cox regression

When doing cox proportional hazards regression one often has competing risks. The typical approach for this is to fit separate cox proportional hazards models for each risk, censoring the competing ...
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R adds unexpected variable to interaction model

Not sure if this is more of a programming question (in which case please move to stack overflow) or a statistical model question (in which case, please read on!) I'm exploring a data set and doing ...
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Study Length Over-Estimating Hazard Ratio?

Are cox model studies over too long a time-scale at risk of over estimating (or under estimating) a covariate's effect on hazard? I'm studying inbreeding in a captive animal population. Some ...
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Survival analysis for matched set cohort data - Methods for absolute and relative risks?

BACKGROUND I have a matched data set with 10,000 cases and 20,000 controls. Cases are defined as such due to a diagnosis of COPD (Chronic Obstructive Pulmonary Disease - a lung disease caused by ...
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Survival Analysis on Telecom Churn in R

I am working on Telecom Churn problem and here is my dataset. http://www.sgi.com/tech/mlc/db/churn.data Names - http://www.sgi.com/tech/mlc/db/churn.names I'm new to survival analysis.Given the ...
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Prediction with categorical variables in Cox regression

I'm doing survival analysis with Cox PH. I have my final model based on averaged models and I have four categorical variables with multiple levels each. I computed the fitted values using ...
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Cox Models treatments depending on time until event

I'm trying to get the "productivity" of treatments like sending an email, calling or sending an SMS and their combinations in the paying debtor's probability. I couldn't find one model that satisfies ...
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Violation of Cox Proportional Hazards by a continuous variable

[This question is related to 1 and 2 on this site.] I fit a Cox model with these three time dependent variables: {s:numeric, C:binary, l:numeric }. I have 1069 ...
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32 views

Akaike information criterion for Cox proportional hazard models

I am conducting an analysis of survival data using Cox proportional hazard (CPH) models, to figure out what is the best model to use. The models I am comparing are non-nested. My plan is to compute ...
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How can parameter expansion be applied to cox proportional hazard models with random effects?

Parameter expansion is used in various GLMMs to accelerate e.g. EM or Gibbs convergence. Is anybody aware of a paper/work which implements PX for CPH?
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Cox proportional hazards (setting a reference level and an interaction with time)

I am currently trying to analysis some data in R using Cox proportional hazards. I have been able to get my coxph model to run but, I am having some coding difficulties. I have two factors (individual ...
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35 views

Discrepancy between Kaplan-Meier curves and Cox Model

I have plotted Kaplan-Meier curves of survival times for cancer patients with above and below average levels of Copy Number Variation (CNV), and performed a log-rank test for each cancer type. I have ...
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141 views

Determine where hazards starts to increase for a continuous variable

I'm interested in a continuous variable, namely blood pressure. The higher the blood pressure, the greater the risk of heart attack and stroke. However, studies frequently report that also low blood ...
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Relating the effect of a composite variable to multiple causative variables

I have the following scenario: I am measuring Copy Number Variation (CNV) in various types of cancer. To explain: the genome is essentially like one long sentence, with genes as words, and each cell ...
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20 views

How do I report the data from a Cox proportional hazard regression model on SPSS

I was just wondering if there is a set way to write the results within a CPH model, I have obtained results from SPSS and I have values for Sig B and the 95% Confidence interval. What I am after is ...
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Approximating cox model with time varying covariates using poisson

How do you reformat a dataset in order to perform a cox regression with time-varying covariates as a poisson regression. I'm trying to run a survival analysis regression in python with time varying ...
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41 views

How to assess the functional form of covariates in the Cox model with martingale residuals in R?

I want to find if the functional forms of covariates in my Cox model are linear. I understand the way to do this is to plot the Martingale residuals against the covariate of interest. I have found ...
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Is calculating r2 appropriate for cox mixed effect models?

I'm looking at the effects of inbreeding on survival in a captive animal species. I'm trying to clearly distinguish the effects of inbreeding from other possible random genetic factors on survival. ...
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68 views

Fitting Cox Regression / Proportional Hazard Model with x time interaction term in R

I am asking this in the context of wanting to diagnose for violation of proportional hazard assumption and its correction. (Schemper 1992) On p.179 of Hosmer, Lemeshow and May, it says that we can ...
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Specifying the LHS for a proportional-hazards survival regression

This is a basic question to understand how datasets for survival analysis are constructed. I understand the terms in the model, given by this equation: (P.41, G. Brostrom, "Event History Analysis ...
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Hazard ratios for three groups - does deleting one group affect the remaining ratio?

My study originally had 3 groups, x , y and z. Hazard ratios were reported for x vs y, x vs z and y vs z. If we remove group z from the study, would the x vs y hazard ratio change? If someone can ...
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Ignore strata in external validation of stratified Cox prop hazards model?

I've fit a stratified Cox proportional hazards model to some survival data, where I've stratified by a potential confounder which is the batch the data comes from (there are three batches). Now, I'd ...
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What does a negative Somers' D say about model discriminative power?

I developed a Cox proportional hazard regression model in R. Then I tried using validate in Professor Harrell's rms package to ...
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Difference in Chi-square calculated by anova from cph and coxph

Is there a difference between Chi-square (from coxph -> anova) and Wald Chi-square (from cph ...
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39 views

Calculating probabilities using cox regression [duplicate]

I have done a multivariate Cox regression in R. The model fits to my data very well. Now, I would like to use my model and predict the survival probabilities of new observations. I am unclear how to ...
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Plotting the effect of a variable estimated by a regression model fit

Plotting the effect of a variable estimated by a regression model fit is quite interesting. However, I have some questions regarding this subject. Here is some example code: ...
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Bootstrapping coxph after model averaging

I have selected 7 coxph models using AIC, and did model averaging to obtain model averaged parameter estimates. I wanted to plot the survival curve from the averaged model, and I found someone with my ...
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Bootstrapping Hmisc::rcorrp.cens for paired concordance?

As Frank Harrell says here and other places, it's better to compare two predictive models (Cox proportional hazards in this case) wrt discrimination (C-index) using the paired U-statistic ...
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Cox Proportional Hazards Assumptions - Simplest Tests in R

I have no stats background, and have been looking into Cox models. $$ h(t) = h_0(t)e^{\beta_1 x_1 + \beta_2 x_2 + ...}$$ (Where $h$ is an individual hazard function, $h_0$ is the baseline hazard ...
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193 views

How to interpret the output of Cox regression with categorical nominal variables in SPSS?

When I enter a nominal categorical variable as independent variable into the Cox regression procedure, SPSS gives cloaked results. It just reports something like the following: ...
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Estimating expected lifetime from hazard ratio and estimated base hazard function

Apologies if this is a basic question, I am not very familiar with survival analysis ... I have trained a gradient boosted Cox proportional hazards model in R, and have been able to obtain reasonable ...
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covariate selection for a cox model by Lasso using glmnet

I would like to use model selection through shrinkage (Lasso) using glmnet. So far I did the following: ...
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How can I make decisions from the output of predict.coxph()?

I'm studying Survival Analysis for the purposes of customer churn modeling. I've managed to put together a model, but I'm confused about what to do with the output. As I understand it, the output is a ...
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model selection through shrinkage (Lasso) using glmnet

I would like to use model selection through shrinkage (Lasso) using glmnet. After trying the example of the glmnet manual and tried the procedure with my data. ...
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123 views

Impute missing values using aregImpute

I have a data frame with 61 columns. Some data is missing. I read in Steyerberg's book about aregImpute in Hmisc. I used it with ...
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115 views

How to assess the incremental additive information of a new predictor in a Cox model using R?

I want to check whether the addition of the new predictor x3 improves the predictive information of a Cox model significantly or not. So far I have: ...
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Joint Models vs the 'usual' time-dependent Cox regression for time-varying predictors

I've got a methodological question, and no data set attached. Suppose I aim to fit a proportional hazards model (Cox) for survival data. I have multiple observations for each individual (data in long ...
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different HRs and corresponding CIs with cph and coxph

I tried a model using cph and coxph: ...
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Validation of the gene-signature predictor reconstructed using Cox PH

I reconstructed a prognostic gene model including four genes using univariate and then multivariate Cox PH model. The model is used for predicting prognosis in patients with a specific cancer ...
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plotting “log relative hazard” against continuous covariate: what are knots when using cph

I try to get into in Cox Regression and read the example chapter from Steyerberg's book. Afterwards I tried to plot log relative hazards against continuous variables using the rms package: ...
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Predicting dropout in an ordered process: Cox regression, autoregressive model, multilevel modeling?

I am working on a project in which I collected data about 100 people’s steps in an ordered process. All took at least one step, with some continuing up to a fourth step. Each person either drops out ...
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Is it possible to add 2 ore more Hazard factors?

I'm a general practicioner and I'm trying to estabilish a conection between interarm sistolic blood pressure difference with cardiovascular disease but i dont have time to wait 10 years or more to ...
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backward selection multivariate analysis usind R

I want to perform an exploratory Cox regression analysis of medical data using R. I am practicing using the pbc data from the survival function. How would you recommand performing a backward ...