Tagged Questions

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

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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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1answer
16 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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1answer
23 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, observational data frequently report that also ...
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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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11 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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1answer
26 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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6 views

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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19 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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1answer
27 views

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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17 views

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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1answer
51 views

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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1answer
39 views

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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0answers
25 views

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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1answer
30 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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0answers
34 views

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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1answer
32 views

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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1answer
54 views

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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23 views

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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1answer
59 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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2answers
43 views

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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0answers
45 views

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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0answers
24 views

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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1answer
96 views

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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1answer
83 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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1answer
103 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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26 views

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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1answer
31 views

different HRs and corresponding CIs with cph and coxph

I tried a model using cph and coxph: ...
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0answers
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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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1answer
46 views

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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16 views

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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9 views

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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3answers
67 views

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 ...
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2answers
43 views

HR of a continuous variable and manipulation of its interval

I am a medical intern trying to understand Cox regression modelling using R. I am using the pbc data of the survival package with the following code: ...
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2answers
32 views

Using time to event data to predict future time to event data

Design: People get drug A and time to an event is measured. Not everyone has the event. Later, most of those people get drug B (those censored and uncensored) and again, time to event is measured. ...
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1answer
153 views

Calculate incidence rates using poisson model: relation to hazard ratio from Cox PH model

I want to calculate incidence rates to present along hazard ratio's in order to present both relative and absolute measures of risk. I saw in other studies that such incidence rates can be calculated ...
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1answer
36 views

Standardising input parameters in coxph models

I'm trying to standardize the input variables of my coxph analysis to make outputs more easily interpretable. I've used the following function (Which was ...
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5answers
198 views

Adjust for everything you have in propensity score?

I have a methodological question, and therefore no sample dataset is attached. I'm planning to do a propensity score adjusted Cox regression that aims to examine whether a certain drug will reduce ...
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2answers
31 views

Use of data from ROC curve

In order to find an optimal time for initiation of treatment post surgery (oncologic patients) I created a ROC curve with death defined as event. The AUC was not significant. However, I decided to use ...
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Propensity score in time-updated (counting process) Cox regression

Suppose I aim to examine if treatment A is better than treatment B. My dataset consists of 10,000 individuals with a total of 100,000 observations. Thus each individual is observed 10 times and his ...
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1answer
63 views

How to assess the proportional hazards assumption for a continous variable

I am having a problem with checking the assumptions for a continuous variable in a proportional hazards model. If a variable were a factor with many levels, then I could use the logrank test or check ...
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1answer
50 views

Comparing Cox Proportional Hazards Models (variable selection)

I am using a cox proportional hazards model to run a survival analysis in r on a number of non-nested, distinct covariates such as Age, Blood Type, Cancer, etc: ...
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39 views

Model assumptions and diagnostics for proportional hazard regression model with frailty in R

I am wondering are there any assumptions that must be met in the proportional hazard regression model with frailty? I remember that in regular proportional hazard model without frailty all variables ...
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0answers
22 views

Result of the summary of the proportional hazard model with frailty in R

I am trying to fit coxph a model with frailty with syntax below: ...
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0answers
28 views

Martingale residuals

I have read in a recent article that, with the use of Martingale residuals in a Cox regression analysis, one can better categorize a variable (different cut-offs). I have computed them using SPSS v19 ...
3
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1answer
83 views

Create age and sexmatched pairs to balance Cox regression further (updated)

I analyze ethnic differences in risk of cardiovascular events (CVD) in a cohort study of patients with coronary heart disease. It is known that immigrants have higher risk of CVD and I intend to show ...
2
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2answers
79 views

Objective test for proportionality assumption in Cox Regression Model (SAS)?

I was trying to fit Cox Regression (aka Proportional Hazard) model on some cancer data (N=2288). I got the following output from SAS proc phreg: ...
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1answer
41 views

Logrank test for trend (proportional hazards)

How one can create a logrank test for trend and does it differ from normal logrank test? Any suggestions or literature? Maybe some R examples and functions?
2
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1answer
77 views

What’s wrong with this way of fitting time-dependent coefficients in a Cox regression?

I have a Cox proportional hazards model. Judging by Schoenfeld residual vs. time plots and corresponding tests for zero slope, there is clear violation of the PH assumption for several of the ...
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0answers
26 views

Outliers in proportional hazards model

How can one easily found an outlier in PH model and why are they so important? Can anybody give me some advice or suggest which R function may I use? Thanks for comments and help.