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

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Plotting fraction of NAs of a data frame [migrated]

Does anyone know how to plot the graphs of figure 23.1 of the example chapter of Steyerberg's book? The R-function is called "na.plot2" and Displays for example the fraction of missing values in data ...
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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 ...
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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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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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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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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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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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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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52 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
37 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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29 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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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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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 ...
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72 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 ...
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1answer
51 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
34 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?
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1answer
51 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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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.
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Meaning of R's coxph output

I am getting below output from coxph function in R. ...
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rms package, getting zero Dxy in validation of cph model

I'm doing Cox proportional hazards analysis using Frank Harrell's rms package (4.2.0), with 3 strata. My model seems reasonably predictive on training data (Dxy=-0.537), but somehow in bootstrap ...
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25 views

Compare Cox with ANN

I am trying to compare Cox model with ANN by R but I have some problems. the result of package coxph is hazard but the result of package ...
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1answer
29 views

Survfit function in R to score a new dataset

I have built a cox proportional hazards model in the R survival package. I want to score new data set using this model. I thought the survfit function would doing this using survfit(original model, ...
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How to use coxph for prediction of event?

I fitted a cox model as: cfit <- coxph(Surv(tr$start, tr$end, tr$event1) ~ imp+sec + cluster(tr$compid)) Now i want to get the probability of event1 for the ...
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Does R square of Cox Regression tells the same thing as Linear Regression R square?

My R square from cox regression is about 0.02, Does it tell me that model is doing really bad? I used coxph in R.
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Combining two separate Cox PH models into one model?

I have two Cox proportional hazards models (in R), using same outcomes and predictors, one for $n_m$ males and one for $n_f$ females. Is it possible to combine them into one equivalent model over all ...
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Complete interpretation of Cox regression output in R

I need help with complete interpretation of this output(below). Can someone explain all (almost all) estimators in this output: what they mean and what is the substantive interpretation. In ...
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Running time dependent covariate model in R, getting warning

I am trying to fit this model, but it's giving a warning message I don't understand: ...
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Assistance with hazard ratios

I want to compare car accident deaths in two groups of people aged 18-24 (lets use this as the reference) and 24-30 after a certain law was changed using a Cox hazard model using SPSS version 22. I ...
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How to translate R to SQL for a Cox Proportional Hazards model?

I have built a cox model in R using the coxph function in the survival package, and now I need to replicate the model in SQL for scoring. From my understanding, the model has the form described on ...
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Applying Cox proportional hazards model to new data to get absolute risk (Framingham risk score)

I'm trying to apply one of the Framingham cardiovascular event risk scores to a new dataset in order to get absolute risk. D'Agostino 2013 "Cardiovascular Disease Risk Assessment: Insights from ...
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Addition of time before commencement of radiotherapy to Cox Model

I have a dataset from a clinical trial for which all cancer patients received radiotherapy, but at different times following surgical removal of their tumour. So more simply, I have a variable, time ...
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Can someone help me with the interpretation of this cox proportional hazards model and how to cross-validate it?

The question I'm asking is related to this question here and here. And I apologize for asking so many questions here, as I am thoroughly a stats novice and probably my MD thinking is clouding my ...
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spss macro for calculating nri and idi

I try to analyze if the addition of a biomarker to an established model could improve reclassification. Usually I calculate the NRI manually, but I was wondering if there is a macro that could do this ...
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Cox regression problem with time varying covariates

I was working on a cox regression problem and was refering to this link: http://support.sas.com/documentation/cdl/en/statug/63347/HTML/default/viewer.htm#statug_phreg_sect050.htm I have few ...
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Survival analysis in R with left-truncated data

I am doing a survival analysis in R with the survival package. I think I am working with left-truncated data, but I'm not entirely sure how to handle it. I have a ...
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Predicting conditional expected lifetime by Cox model in R

I'm using a Cox proportional hazards model, estimate the hazard rate for Levamisole relative to 5-FU, adjusting for Age and Sex. ...
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Cumulative Hazard Function where “status” is dependent on “time”

This question is in relation to a dataset I've previously discussed here. I'm trying to determine whether a treatment affects not only the number of visits a patient has to the doctor, but also how ...
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Negative Regression Coefficent (Cox Regression)

I'm doing a Cox regression analysis in order to verify the role of two variables on the prediction of disease conversion. Previously, I did a ROC analysis and a logistic regression. All these methods ...
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Testing residuals from a cox model with time dependent covariates

I'm doing survival analysis with time dependent covariates, using the counting process style. I already have a set of models and I want to test de residuals. I'm having trouble with the lack of ...
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Model speedup using weights in R

I need to run a cox-regression on a huge data set (millions) with only a few unique rows (hundreds) and regressing on categorical variable group. I could use just ...
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Evaluating Proportional Hazards with time-dependent variables

I'm doing survival analysis and using the survival package from R to do it. I have 7 variables, 5 of which are time-dependent (all except sexo and peso). Here is my model: ...
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Simulate censored data cox model

I would like to simulate interval-censored data in a Cox model. In the R package intcox I found the following code: ...
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How was this deviance formula for Cox Proportional Hazard derived?

The gbm package in R documents the following deviance formula for CoxPH models http://gradientboostedmodels.googlecode.com/git/gbm/inst/doc/gbm.pdf $-2 \sum w_i \delta_i (f(x_i) - \log(R_i / w_i)$, ...
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When is best to set the origin (time=0) point in a cox-propotional hazard model change analysis

I would like to know the relationship between change in a variable in the three months after a disease, and survival time. I have change in the variable in the first three months. But I am not sure ...
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Cox regression, survival, comparison with historic group, follow-up time

I have two groups of patients, treated at two time periods. I'm comparing survival. In the later group I have 3 years follow up time. In the early group I have of course access to longer follow up ...
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Cox regression with time varying covariates

I am looking for resources on Cox proportional hazards model with time varying covariates. I'm new to survival analysis so I'm looking for something not overly mathematical. I would also appreciate ...
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How to perform a constrast in R for a cox proportional hazards model

I have the following model fit: ...
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Cox regression to see if distribution of disease predicts survival

I'm working with clinical data from a few hundred patients. Every patient was measured at 6 different timepoints with regular intervals. Each patient is assessed on 3 different domains and given a ...