Questions tagged [cox-model]

Cox proportional hazards regression is a semi-parametric method for survival analysis. No distributional form needs to be assumed, only that the effect of one-unit increase in a covariate is a constant multiple.

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Fisher Information for Cox Model

Actually, I'm working on a Statistical Genetics Article (Schaid and al,2010) in a retrospective likelihood context. In the article, authors present some result about conditional likelihood but I can't ...
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Survival analysis with two events

Suppose we have a cohort of subjects that have 0 disease complications at baseline we have followed them up over a period of 10 years and several subjects develop either of two complications of ...
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Why univariate Cox does not have its own survival curve and has to use KM curve as approximation?

I am aware that KM-estimator and Cox model use different method. However, I am under the impression that we show KM curve as approximation of univariate Cox model. My question is why univariate Cox ...
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33 views

Relationship between KM-estimator and Cox model

What is the relationship between KM-estimator and Cox model? What I am aware is that Cox model allow us to adjust covariates. If I build a Cox model and draw a KM curve (using survdiff function). ...
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Cox PH - R 'rms' package - Concordance (Train, CV & Test)

Please could someone verify if my methodology for calculating these three versions of concordance are correct when using the rms package? I have really struggled to ...
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Joint distribution of log hazard ratio estimates for two outcomes

I have a study where individuals are randomized to a treatment or control group, and there are two time-to-event outcomes $S_i$ and $T_i$ measured for each individual $i$. The two outcomes have some ...
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25 views

Variable selection for Cox regression repeated for multiple covariates of interest

I am doing a retrospective analysis of the effect of various measures of haemodynamics in sepsis on mortality. I will separately look at the effect of 5 independent variables: 1) shock index 2) blood ...
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20 views

Checking PH assumption using scaled Schoenfeld residual tests

My cox model violates the PH assumption (according to cox.zph test), and I'm trying to interpret the scaled Schoenfeld residual plot, but I've never seen a plot with points lying in such a flat manner....
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32 views

Does anyone know what is beta in Cox-nnet paper?

I was going through the methods in this paper: Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data [1] There they define (Equation 4) $$\theta_i=\...
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32 views

Plot of probability of 1-year survival event vs. variable value? Would be derived from a Cox model

I am hoping to plot the probability of a patient surviving to 1 year without progression (status==0) vs. the value of a continuous variable (...
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Advantages of using Cox model versus logistic GEE?

What are the advantages of using Cox proportional hazards model versus logistic GEE? Can one generate Kaplan-Meier remainder estimator curves using logistic GEE?
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Cox plot “spline fit is singular” warning

Hi I get a warning "spline fit is singular, try a small degrees of freedom" when I try to plot the Schoenfeld residuals. ...
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Cox Proportional Hazards - Survival Function Estimation (on new data)?

I understand that the relationship between the hazard function, the baseline hazard function and the covariates is the following: $$ ln(\frac{h(T)}{h_0(T)}) = \beta_1 x_1 + \beta_2 x_2 + \dots + \...
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Kaplan-Meier and Cox in R give different results

Please, can you explain, why these two formulas give different answers? Is this because Cox is a semi-parametric method and KM is non-parametric one? I marked the differences with asterisks. Kaplan-...
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Null hypothesis in Cox regression with a conflict between confidence intervals and P-values

Apologise for the simple question, I would just like to sanity check the interpretation of two results before I discuss them with a group of biologists. I have two results from Cox regression: ...
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Defining an applicable score index for patient survival prediction

Say I want to devise a score index for predicting patient overall survival (OS) based on a handful of co-variates, what would be the best way to do it? Briefly, I have performed a Cox regression ...
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I've been asked to add a Bonferroni correction to a multivariate Cox proportional hazards analysis (for overall survival)

I've been asked to add a Bonferroni correction to a multivariate Cox proportional hazards analysis (for overall survival). I believe this is unnecessary as long as you verify the assumption of ...
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Check if PH or AFT model should be fit

It is unclear to me when it is appropriate to fit an accelerated failure time (AFT) model rather than a proportional hazard (PH) model. I've tried googling and it appears as though PH models are ...
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How to conduct stratified Cox regression with Lasso regularization and k-fold cross validation in glmnet in R?

I have been conducting Cox PH survival analysis and I am new to this. I am following the steps below: Create surv object and predictor model matrix for variables I am interested in. Since my data is ...
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What is the relationship between the Harrel's C and the AUC?

I model survival outcomes using a Cox proportional hazards model and want to evaluate model fit. Harrel's concordance index C is defined as the proportion of observations that the model can order ...
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Survival analysis: Frailty vs Sandwich variance estimators

Question Can someone answer (in as non-technical terms as possible) whether or not frailty models and robust sandwich variance estimators are trying to solve the same problem in different contexts? ...
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How make distinct predictions for every observation using survreg for AFT models?

I have a life dataset where I have a few machines tested using the same parameter settings but results in different survival days. As an example below: ...
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Left-Truncated Right-Censored Cox Proportional Hazard Regression

If I have a left-truncated (remove everyone who has disease at baseline) and right-censored (1 if the person develops disease, 0 else). Time to event = min(age censored, age at disease diagnosis) ...
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Survival Analysis/Customer Attrition Model for Balances

I’m looking to model balance, meaning dollars, decay(attrition). In brief, I have time series customer data, which is aggregated to get customer’s balances for a specific product. Over time, the ...
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R coxph vs. coxme: Vastly different Coefficients of Determination

Comparing comparably defined models in R's coxph() and coxme() I experienced hugely different results when calculation the Coefficient of Determination using MuMIns r.squaredLR. For the coxme()-fit ...
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How to test interaction when loglinearity is violated in Cox model?

In a Cox PH regression, I would like to model an interaction between two variables. The problem is that one of the variables breaks the log-linearity assumption. Based on my previous questions (...
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Different results for Cox regression

I am trying to get my head around Cox regression. I found quite a good paper on the subject by R. Tibshirani: A plain man's guide to the proportional hazards model. On page 67 he gives a toy example, ...
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Why is the exponential function used in Cox regression?

I am trying to get my head around Cox regression. I found quite a good paper on the subject by R. Tibshirani: A plain man's guide to the proportional hazards model. On page 66 he states: For ...
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Assessing loss of different parsimony levels (Cox Model)

I have a Cox Proportional Hazard model with 6 covariates to determine OS. I am now trying to simplify this model by taking some of this covariates down. This is intended for a wide audience so I'm ...
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Survival Analysis and multiple observations

I am currently conducting a survival analysis for the first time and I am finding the conceptual aspects of the analysis a bit tricky. I have a hospitalization dataset that spans over a 20 year period ...
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Is it suitable to fit a Cox PH model for Life Data?

I have life data where experiments are conducted at different settings to observe machine degradation. A close example of how the data looks like is from this link: http://www.statvision.com/webinars/...
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Simulating survival data for a Cox model with a dichotomous time-varying covariate in R

I am interested in simulating non-proportional data following the formulation in Section 3.1 of the article: [Generating survival times to simulate Cox proportional hazards models with time‐varying ...
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Same results using time dependent covariates in Cox model as in unadjusted model?

I encountered a case where the coxph model result is exactly the same with and without time dependent covariate adjustment. I tested using the Stanford heart transplant dataset (jasa) as exampled in ...
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How to plot the area under curve and the calibration curve for cox regression model applied to a test sample?

How to plot the area under curve and the calibration curve for cox regression model applied to a test sample using rms package? please
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Simulate confidence intervals for the absolute difference between two hazard ratios

I am examining the time to an (recurrent) event in response to different medications between men and women. I am adopting a 'within-individual' design whereby each person's time spent on- and off- the ...
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Finding exposures given a risk set and an MLE

I'm tackling advanced use of a Cox proportional model and I've been given the exposure times for two risk sets shown below $ R_{_1}: 7,8,11,15,19 $ $ R_{_2}: 6,8,10,13,18 $ I've also been given the ...
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Expressing a hazard function with a Cox proportional hazards model

I'm trying to wrap my head around Cox models as well as how to express them in the form of hazard functions when you have both categorical AND numeric covariates. I need some assistance with this ...
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156 views

Including a baseline risk for each participant to consider having a different number of data points in Cox model

We used the Cox model to associate environmental exposures with time to heart failure using cohort data. The following question has been raised: When using the extended Cox model, did you include a ...
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How to better understand when to use Weibull AFT versus Cox Model for Failure Data

I am struggling to understand when I should consider using a Cox regression model versus using a Weibull AFT model to predict the end of life of mechanical components. I have tried to apply the Cox ...
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128 views

Simulation in R of data based on Cox proportional-hazards model for power analysis

I would like to fit data based on Cox proportional-hazards model and then simulate new data based on a fitted model. For instance, provided that the fit is ...
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How to obtain predicted time to event using survival analysis?

I have a dataset with right censored data and I have fitted a cox regression model on it but I realised that the output of the model is a hazard rate rather than a prediction of time to event. I have ...
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log values in coxph model?

I have a data frame of gene expression values (sequencing). When I do CPM-normalization without doing log2, I get much "better" (lower) p-values compared to when I do log2-CPM. What is the ...
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Attirbutable risk from competing risks

There are a number of ways to estimate attributable risk fractions from Cox regression and logistic regression. Does anyone know how to estimate attributable risk from a competing risks regression ...
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proportional hazards model with fixed interval censoring = cloglog GLM with fixed effect of time?

Consider a survival analysis with time-constant coefficients, interval-censored, where the observation intervals are consistent across all individuals (e.g. each individual is observed at the end of ...
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What does the output of a Cox Proportional Hazard model mean?

For a linear regression plugging different X values to the fitted model gives us the different predicted Y values, for a logistic regression we get the different log odds: what does the output of the ...
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Multiple cox regression with no events in one group of one variable — survival analysis

I am trying to run a multivariate Cox regression analysis but I have 1 value for 1 variable that has no events reached. This variable was treatment (values = treatment 1, treatment 2, treatment 3, and ...
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Cox regression and penalised spline

I am doing a time-to-event investigation and am using a Cox proportional hazards regression model. It is the first time I have worked with this technique. The time-to-event is the number of trials a ...
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Dealing/Interpretating confounding variables in cox regression (time-varying covariates using counting process notation)

I have 3 predictors which are correlated by approx. 0.57. One measures the intensity of a task. One measures the success (profitability above x) of a task and one the failure of a task (profitability ...
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'pspline ' or 'rms' in a Cox model?

I am quite new in the spline subject and I have a question! I am using a Cox model and I was afraid that some of the variables included in the model have a non-linear effect on survival. So I tested ...