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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Differences between logistic regression parameter estimates and Cox-proportional hazard parameters

We have been working on a survival analysis. We are examining tree seedling survival over a decade with annual to biannual census intervals. We have been using the package coxme in R for a mixed ...
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8k 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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How to simplify coxme survival models?

I have some questions about specifying a coxme (mixed-effects Cox proportional hazards) model in R and then simplifying it after reading the ...
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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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343 views

Visually Comparing the Kaplan-Meier Curve to the Cox PH Model Curve

I am conducting a survival analysis and have a few questions regarding it's interpretation with respect to the Cox Proportional Hazards Model: Why does the inclusion of different covariates change ...
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167 views

Is missing outcome in survival analysis a problem?

I would like to look at survival in time to event data. So individuals either have an event, or are censored. My problem is the sensitivity for detecting an event differs between arms. I.e. in the ...
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103 views

Cox interactions and co-linearity

I am interested in developing a model to predict survival based on a few predictors: age, sex, and two lab values, albumin and globulin. I have approximately 14,000 deaths in the data. I initially ...
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1k views

using caret and glmnet for variable selection

Im using the caret and glmnet package for variable selection. I only want to find the best model and the coefficients and use ...
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252 views

Interval Censored Survival Analysis

I am conducting a study on neurological diseased patients. I am looking into possible factors related to time-to-dementia. Costs associated with neurological testing allow us to assess all patients in ...
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425 views

Median survival time for stratified Cox model

I have a dataset of 30,000 patients who are matched by surgical procedure. My main exposure of interest is if the patient got regional anesthesia during surgery or did not. I have 27 different ...
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957 views

Cox proportional hazards with time-dependent covariates: predict in R

I would like to use the predict function (or something similar) in R to generate expected values from a Cox proportional hazards model with time-dependent covariates. The model takes the form ...
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566 views

How are absolute risks estimated by the cox model?

According to my modest understanding, the cox model is all about estimating hazard ratios, relative measures of risk. However, it is possible (in R using e.g. the packages pec or peperr) to estimate ...
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39 views

Analyzing uncensored time-to-event data with no risk of events after a certain period

I'm trying to investigate several independents on a dataset with time-to-event data for a treatment. I'm measuring time-to-treatment effect (where treatment effect is a binary parameter). Treatment ...
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70 views

How can I compare parametric and semiparametric survival models?

On a given dataset, I am running a semiprametric Cox proportional hazards model, together with a series of parametric models (Weibul, gamma, lognormal, exponential, etc.). How can I know which is ...
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Modelling recurrent events using Cox regression (in R)

I would appreciate a sanity check of whether I am using Cox PH regression in R correctly to analyse recurrent events. My work has used the instructions proposed in "Modelling recurrent events: a ...
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377 views

Cumulative hazard in the setting of Cox regression of repeated events

Cox regression is commonly extended to estimate repeated events processes (for a quick review see [ 1 ] and [ 2 ]). In Clark et al's first article in their excellent review series of survival ...
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545 views

Interpretation of scaled Schoenfeld residual for time dependent coefficient

https://cran.r-project.org/web/packages/survival/vignettes/timedep.pdf I've been following the vignette on implementing time dependent coefficient in addressing non proportional hazards in a cox ...
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330 views

How can the Cox proportional hazard model be formatted into a generalized linear model?

Is the Cox proportional hazard model a generalized linear model and how is formulated?
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505 views

Right-censored independent variable in Cox/logistic regression

I have a right-censored continuous independent variable that I want to include in a Cox regression. The variable is a physiologic test which is capped at a certain time, say 120 seconds, due to safety ...
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418 views

Handling Informative Censoring in Survival Analysis

In a survival study with informative censoring (for example, studying the effects of cigarettes on mortality and smokers are more likely to be Lost to Follow Up). This causes the censored data to be ...
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How is the hazard ratio in Cox proportional hazard models affected by the case sampling?

I'm trying to conduct survival analysis using Cox proportional hazard models, looking at a biomarker for heart disease. Age is a major risk factor, so I'm modeling the age as the time scale (counting ...
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Validate predictive power of Cox proportional hazards for individual observations

Note I've edited the example to be more intuitive and closer to my real data Intro I've got data on customers purchases and with it am trying to predict which customers are more likely to make next ...
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932 views

Is there a way to model left truncated and interval censored data in R or SAS?

We have a study where our participant underwent some surgery at time = 0, but at various ages. Our follow-up is based only on Medicare age-eligible people, so we have to wait until they reach the age ...
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378 views

heteroskedasticity in logit/cox

I am using a logit and a cox proportional hazard model for my analysis, and the newest version of Stata. I have found that there are no tests to check for heteroskedasticity for logit/probit models, ...
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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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800 views

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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434 views

How to use Cox proportional hazards model in interval-censored data with time-dependent variables?

The question is self-explanatory. I have survival data (n=156) which, in about half of the observations, is right-censored or interval-censored. I'm am using R to do the analysis and I know I can use ...
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677 views

Interpretation of interaction term in Cox PH model when centering LP on mean values of predictors

Let's say I have a Cox PH model for predicting the risk of dying, that in a simplified form looks something like this: ...
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Interpretation AFT, Cox PH and discrete-time hazard model

I am struggling with the interpretation of the AFT model, Cox proportional hazard model and discrete-time hazard model. My question is: Can the coefficients in discrete-time hazard model also be ...
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326 views

What are the independence assumptions of Cox models with time varying covariates?

In longitudinal studies, you might be observing time-to-event endpoints with some covariate that changes as a function of time. When covariates are fixed at baseline, the only independence assumption ...
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277 views

Survival analysis - Using parameter estimates of a fully-parameterized PH model into an AFT model

I want to predict an event based on transactional data. I'm only interested in predicting either future hazard or time-to-event. My understanding is that to predict in the future I have to use a fully-...
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347 views

How do I compare 2 models?

I would like to show that a new biomarker (let's say percent tumor volume reduction at 3 weeks of treatment estimated with automatic methods) performs better than an old one (same measure, but based ...
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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 ...
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75 views

p trend for Hazard Ratios of a categorical independent variable

I ran an analysis using a Proportional Hazards Cox regression model. My variable of interest is exposure to pesticides (kg of pesticides applied within 500m of home). We do not expect a linear ...
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30 views

Homogeneity test in survival meta-analysis with adjusted HR

I was wondering what was the way to measure heterogeneity in a survival meta-analysis. I have for each study, an hazard ratio calculated with a penalized cox model (...
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135 views

How to calculate the survival function in R for a glmnet cox family?

I have a sample data of 583 type 2 diabetes patients and want to calculate the 5 year incidence probability of an event for every patient. Variables which were collected are time to an event variable ...
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1answer
106 views

Survival analysis with time dependent covariates and non-proportional hazards in R

I am attempting to do a survival analysis which will examine the effects of both rainfall (a time-dependant variable) and altitude on nest survival in a species of wasp found in NW Ecuador. I have ...
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1answer
123 views

propensity score matching by disease and cox PH regression.. am I right?

Normally I understood propensity score matching is the way to match the treated group and untreated group. But I noticed some studies that used propensity score matching to match disease and non-...
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71 views

Proportional hazards assumption for cox regression - global test or graphical assessment

I have run a cox regression with only a treatment in mind so far and have then tested the proportional hazards assumption along with a graphical assessment using the log-log survival plot. My global ...
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1answer
147 views

Piecewise survival analysis?

I am trying to analyze time-to-event data (time to completion of a task). Looking at the KM curves, there is a distinct behavioral change around 12 months. This makes sense, because at 12 months there ...
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45 views

Mix Effects Survival modeling (coxme)

I have some experimental data looking at arsenic toxicity in mice and I'm trying to screen for potential biomarkers that associate with survival. I sampled mouse microbiome communities at 2 time ...
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88 views

interpretation of cox HR under non-proportional hazard

When the true hazard ratio $\lambda(t)$ is time varying as shown below, I used a standard cox regression to get a hazard ratio. If the hazard ratio of $\lambda=0.78$, how can this value be interpreted?...
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1answer
45 views

Logistic vs Cox PH model : different hypothesis for a single case

Let's say I'm interested in comparing the apparition of an event in 2 groups. I could take the problem by 2 ways : consider the dates and compute a Cox PH model. consider only the proportion of ...
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78 views

What does the result of a fitted cox ph model tell me?

I am currently experimenting with survival analysis in R. One important Model is the Cox Proportional Hazard Model. Using the default lung data the R enviroment provides, I would like to play with the ...
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112 views

Implementation of time-varying coefficients model for Cox regression

I would like to implement the time-varying coefficients model (cf. Fan and Zhang, 1999) for a Cox proportional hazards model, as proposed by Cai and Sun (2003), and studied by Tian, Zucker and Wei (...
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155 views

multivariate cox regression - combining genotypes for each SNP

For 53 SNP I have coded genotypes as 0 for aa, 1 for ab, and 2 for bb for 29 samples and I have outcome and time to outcome. Here outcome is called "BCR" below. I am using the survival package in R ...
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121 views

What variant of interaction when the PH assumption is violated in a CoxPH Model?

When the assumption of proportional hazards is violated, the suggestion is to interact offending covariates with time (or a function of time). In this blog post, the author suggests to include only ...
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622 views

Why are baseline hazard functions after Cox PH regression different in Stata and R

I am a Stata user now teaching myself R. I have been trying to recapitulate analyses done in Stata using R but have got stuck. A multi-variable Cox regression with an offset in Stata and R give ...
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Approach to a complex survival analysis

Hello and thanks for reading! I'm a student who has unfortunately 'designed' quite a complicated experiment which I'm struggling to analyse statistically. I do like statistics but my experience is ...