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

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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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54 views

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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27 views

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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31 views

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 ...
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146 views

Violation Proportionality Cox model - Repeat analysis?

I'm new to survival analysis, but I've been reading some papers and books and I got a nice model. However, one of the variables (Sit) does not met the proportionality assumption for the Cox model. ...
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R package to handle gene expression and proportional hazards model

I have survival data with RNA expression. A lot of the data is censored. Is there an R package that does a proportional hazards model where the number of covariates is much larger than the number of ...
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1answer
56 views

Error term interpretation in the Cox PH model

I am preparing a presentation on Survival Analysis models, with specific focus on the Cox model. I have been using such model (including its competing risks generalization) for some time now, but I ...
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47 views

Selection correction variable (non-randomly selected sample / bias) and Cox regression

I found an approach to calculate a selection correction variable for a Cox regression (Lee 1983. Generalized econometric models with selectivity. Econometrica 51: 507–512.): $$ λ = \phi \frac{ ...
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Inferring the statistical tests performed in a paper

I am in great need of help in order to infer the statistical hypothesis tests performed in Xanthelasmata, arcus corneae, and ischaemic vascular disease and death in general population: prospective ...
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1answer
110 views

p-value zero in hypothesis testing for survival curves

I have done survival analysis. I used Kaplan-Meir to do the survival analysis. Description of data: My data set is large and data table has close 120,000 records of survival information belong to 6 ...
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cox.zph says the standard deviation is zero

I need to compare my observed point vs random points that have been constrained to be relevant to that observation. In my case, I am looking at habitat selection along transects of animal movements. ...
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Different time scales in time-dependent cox proportional hazards

I'm doing survival analysis with time-dependent variables and I have two types of data: birds followed in a biweekly basis and others followed randomly. I think that analysing both types of data ...
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19 views

How to have a captured response table for a 2-year prediction base Cox model in R?

My study is about "Churn Risk Evaluation of College Students". I decided to use R software, already had a result for the survival probability of an old data (all the students already left or ...
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39 views

Statistics of time dependent variable observable only at end-of-life, given survival data

I have a variable whose value I can only measure at the end-of-life of a product (which is not fixed). The variable's value, continuous and between 0 and 100, may be related to its age at that time. ...
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Cox PH model selection and validation

I am trying to analyze my data using survival CoX PH in SPSS v.19 and also attempting to make different prediction models (without and with a biomarker of interest). I am a clinician (not a ...
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Interaction in Survival analysis

I am a physician and clearly not a statistician (I try to understand why and how to perform the right analysis, but I don't understand the formulas). I am using SPSS v.19 in analyzing my data. I try ...
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How exactly can the Cox-model ignore exact times?

The Cox model does not depend on the times itself, instead it only needs an ordering of the events. How come it doesn't need the time, as all of the models I've seen so far are dependent on the exact ...
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Time-scale in cox porportinal hazards model with multiple time-dependent variables

I'm doing survival analysis and I have three time-dependent variables, with different time scales each. I've already done univariate analysis and I want to proceed with multivariate analysis. My ...
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External validation of a regression in Stata

What I'm essentially trying to do is a temporal external validation of a Cox Proportional Hazards model and also a logistic regression model on the newest year of a dataset that was not included ...
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1answer
51 views

How to analyze healing time when the follow up times are not equal and we are looking at a specific time?

I would really appreciate if you could help me with your expertise: I have a study in which I evaluate patients for healing after discharge. So I have two group, healed and non-healed patients. The ...
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2answers
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How to interpret standard errors in a Cox model?

I am running a multi-variate Cox regression and Stata provides the standard errors for each hazard ratio. How are theses to be interpreted? I know that I want my coefficients to be large compared to ...
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109 views

Sample size / power calculation for logrank survival test

I have really little idea of survival analysis. I am aware that logrank is a special case of Cox' proportional hazards model, and that tons of R packages and scripts address the problem of power / ...
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Is there any functional difference between an odds ratio and hazard ratio?

In logistic regression, an odds ratio of 2 means that the event is 2 time more probable given a one-unit increase in the predictor. In Cox regression, a hazard ratio of 2 means the event will occur ...
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Frailty conundrum: how can area effects be large when shared frailty variance for area is non-sig?

I’m running Cox proportional hazards models (in stata) to predict risk of teenage birth, where individuals (c. 50 000, c. 3000 births) are clustered within wards (>500). In null models with shared ...
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rms validate on models with a predict function such as coxph and glmnet

I would like to use bootstrapping to evaluate models generated by coxph and glmnet. Would that be somehow possible with rms validate ? From the documentation it seems limited to rms functions (cph, ...
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How to create a covariate × time interaction term in Cox regression?

In Cox regression, it is sometimes inevitable that the strength of a predictor will vary across time (Singer & Willett). This violates the proportionality assumption, but can be incorporated in ...
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Statistical significance seen with Kaplan-Meier but not with Cox. Need help with interpretation

I'll caveat this by saying that I am a novice in every sense of the word so I apologize if this is basic. I am currently working on a retrospective analysis where I am looking at patients to see if ...
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103 views

how to code and interpret categorical time varying variable in Cox PH model

I'm working on a project looking at the relationship between exposure to several different drugs on the risk of preterm delivery in a cohort of pregnant women with a particular disease. I'm confident ...
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39 views

Cox regression with interaction giving NA values, how to interpret? + Choosing covariates based on p-values

I am working with a dataset with 12 covariates(categorical). The covariates have different Levels, some are from 0-5, and one has as much as 0-11 categories. I started with a univariate analysis to ...
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1answer
195 views

Discrepancy between log likelihood Harrell's C Index and brier score for the evaluation of a Cox regression

I am evaluating a dataset of ~400 subjects and 10 covariates trying to fit a Cox ph model for predicting survival in AML patients. To evaluate the models I am using a bootstrapping procedure of 50 ...
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How to construct a design matrix for coxph with pspline term?

I am wondering how to reconstruct the design matrix for a coxph() model with a pspline() term. For example, if I fit the ...
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106 views

The right way to report random effects in a Cox survival model

I have a data set (patients (15000) nested in hospitals (50)), with a number of covariates. I built a proportional hazards model in Stata, and entered site as a frailty term. I would like to report ...
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396 views

How to get the p-value for the full model from R's coxph?

In a coxph model with 2 variables (let's say age and sex), how can I get the p-values for LR, Wald and score tests which I see in the summary(coxphobject) as below? ...
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2answers
109 views

Interaction terms in Cox PH model

I am wondering if there is a way to interpret an interaction term from the coefficients rather than just looking at the survival curves? The factors involved are A, B, and C, which are all binary ...
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87 views

Predicting new data using a Case-cohort Proportional Hazards Model

I am fitting a Case-Cohort Proportional Harzards (CCH) model using the Survival (version 2.37-4) package in R 2.15.3. Normally with a Cox Proportional Harzards (coxPH) model, I can use the survfit ...
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Variable effect in Weibull and Cox models

Is it possible to compare effect of variable on the survival time in the Cox model and in the Weibull regression model?
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How would you visualize the difference between Cox/Weibull regression?

I'm trying to figure a way of properly displaying the difference\resemblance between various regression values on the same data set, using cox ph, weibull regression and log-normal regression. ...