Questions tagged [survival]

Survival analysis models time to event data, typically time to death or failure time. Censored data are a common problem for survival analyses.

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Book suggestions for survival analysis

I'm trying to learn more about survival analysis and I could really use some suggestions for good texts on the topic. I have a fairly strong background in applied statistical analyses (quantitative ...
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1answer
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Probabilistic models applied in survival analysis

I am trying to fit some probabilistic models for a survival analysis, that is, considering a parametric approach (I tried to fit the cox regression model, but the proportional hazards assumption was ...
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Adding a variable's effect (from literature) to an estimated Cox model

I have a Cox model (estimated with coxph), built using "some" variables. There is an extra variable that I have not measured, so it is not in my dataset, but I do know the effect of that ...
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How to test censoring patterns of two samples agree?

I am not sure I even understood the book. I am reading Applied Survival Analysis by Hosmer, Lemeshow and May's pg 58. The book says "Problems in study design and data collection can lead to ...
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59 views

How to calculate confidence intervals for the scale parameter of a parametric survival model?

I use R code to create the following AFT model survregLogNormal <- survreg(Surv(futime, fustat) ~ ecog.ps + rx, ovarian, dist = "loglogistic") Next, I ...
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Joint Model, Time-Dependent Endogenous Covariate in Longitudinal Submodel

Let us say we have a joint model whose hazard function (survival submodel) at a given time point $t$ is given by: $$ h_{i}\left(t \mid \mathcal{M}_{i}(t), w_{i}\right) = h_{0}(t) \exp \left\{\gamma^{\...
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When to use smoothing of the predictor in a time dependent incident dynamic ROC analysis, and is there any arguments not to use smoothing?

In the article “Estimation of incident dynamic AUC in practice”, Geloven et al. 2020 (https://www.sciencedirect.com/science/article/pii/S0167947320301869#b10) they describe: “In recent years, several ...
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1answer
43 views

Can one compare Hazard Ratio and Average Hazard Ratio?

I would like to compare three predictors of survival by comparing three cox regression models. One model violates the PH assumption which brought me to weighted cox regression as implemented by ...
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Regression analysis in interval censoring with time-varying covariates

This question is a follow up to the other one asked by someone else (Right censored survival analysis with interval data in R) and this one by me Left censoring with time-varying covariates I have ...
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Why are the survival curves different for the Kaplan Meier method and cox regression for the same categorical variable?

I have 1 categorical variable called group (1 = treatment, 2 = placebo). If I create the survival curves with the Kaplan Meier method in SPSS I see that the survival is better for the treatment group ...
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Cox-snell method for weibull proportional hazard survival analysis

I am a new in survival analysis, and I am considering using the Weibull proportional hazard function to fit my data, and after using the MLE to estimate the parameters, I hope to diagnose it with cox-...
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1answer
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AFT models in Stata with time-varying covariates

The AFT models from Stata's streg can handle time-varying covaraites. In particular, the manual states that streg is suitable ...
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How to sample non-event data for survival analysis

I am building a model to predict customer churn using survival analysis, COX regression in particular. While it is pretty straight forward to collect churn events, it is a little tricky to sample for ...
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deviance residual plot abnormal for cox proportional model

Hi, is the cox proportion hazard model violated? I'm not sure whether the problem is censored data or wrong prediction? But, there is only few significant variables can fit the hazard model adequately....
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Joint (or multivariate) model to predict two correlated time-to-event outcomes

this is a general question. Say you want to predict two time-to-event outcomes, the time until chronic heart disease, and time until diabetes. You think these outcomes are likely to be correlated, i.e....
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Right censored data

I have some data that is right censored. A study has recorded data for several years and some units have failed and some units have not failed (right censored). Now, some of the units observe a minor ...
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Survival analysis: How to deal with new information as time progresses?

Imagine we want to know the survival function for hotel guests getting into the pool, given a few controls: Each guest stays exactly 24 hours at the hotel Guests always apply sunscreen just before ...
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R Cox regression with cumulative time dependent covariate - variable coding

I would be grateful for your help regarding the correct coding of cumulative time dependent covariates in cox regression. I am exploring the association of injections (exposure, same dose for all ...
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1answer
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If we say "Survival difference adjusted for covariates" do we mean just additive adjustment, or allow also the interactions?

Let's make it independent from any statistical package, so I will provide just numbers for the illustration. Maybe this give you some clues. I want to compare two survival curves, for group A and B. ...
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Left censoring with time-varying covariates

I have a data with some participants entering the study with a disease of interest already present. For others, I have several points of observation where different factors were measured (such as ...
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Survival Analysis: samples with starting times before the data started being recorded

Summarize the problem: I'm working on a problem to estimate customer life time for our subscription-based business model. My data contains all purchase transactions between 2015-01-01 and 2020-12-31. ...
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1answer
39 views

Constructing hazard for x-year survival in cox models

If a person wants to assess the 1,5, or 10 year survival of a group of patients how should they consider right censoring for the patients? Between these 2 options what would be best for this 5 year ...
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Verification and visualization of survival analysis

I performed some experiment with two clones of cells CloneType red and green. The task was ...
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Log-rank test: should I run it once for the whole follow-up or also test for shorter time periods?

Let's assume we have a 5-year follow-up for survival for two groups, and I report their crude mortality rates for years 1, 2, 3, 4 and 5. After that, would it be reasonable to test the mortality ...
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69 views

Computing Chi-square values from Schoenfeld residuals

Based on page 164-165 of [Collett:Modelling Survival data in medical research (Third edition-2014)] the Schoenfeld for individual test and for global test can be obtained as follows[1]. However, ...
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If market opt-out is happening due to contacts through campaigns

I am relatively new to statistical analysis. I have a scenario. There are various campaigns through which the customers are contacted. Only customers with their marketing preference as 'Yes' are being ...
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a one sample size of median survival (time to event endpoint)

In my master thesis, I need to determine and calculate the number of cases for median time to event. The method is according to Brookmeyer & Crowley, 1982. My question is: How can I determine the ...
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131 views

How to calculate Schoenfeld Residuals in R

I am trying to manually calculate the schoenfeld residuals in Cox model. Please see the code below. Sresid gives the calculation in cox.zph function using schoenfeld residuals. Schoenfeld gives the ...
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How to validate or make predictions from a spatial Cox PH survival model built with R-INLA?

I'm trying to model deforestation as a survival analysis. I have a raster map where unaffected areas are zero and deforested pixels have values 1-20 depending on the year of deforestation (2001-20). I ...
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225 views

Step by step reference on machine learning for survival analysis?

I want to apply machine learning methods to survival analysis. This is, I have a sample of survival times $(t_1,...,t_m)$, censoring indicators $(\delta_1,...,\delta_m)$, and covariates ${\bf{x}_i}$, $...
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1answer
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Hazard function to PDF computation [closed]

I am trying to formulate the computation between the Hazard function and probability density function. Given an example: pdf_arr = [0.2, 0.2, 0.2, 0.2, 0.2]. My ...
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Conversion from hazard function to probability density function

While following this conversion follow: https://lifelines.readthedocs.io/en/latest/_images/map.png I am unable to convert from PDF to hazard function and vice versa. ...
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1answer
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95%CI for the difference in risk (Cox regression)

I have using following cox model to investigate the association between two exposures and a time to event outcome (0=no event, 1=event). ...
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Fitting a survival model to see if there is interaction between gender and age

hi I am new to survival analysis. I am trying to fit a cox regression model with age, sex, type of case(local vs imported cases), and regions(urban vs rural). I tries to fit two model ModelA ...
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1answer
64 views

Nelson-Aalen estimator for cumulative hazard

This is a question to help me understand how the Nelson-Aalen is computed in practice. There is probably something simple that I don't see... Let $\{T_j\}_{j=1}^n$ be survival times, and $\{T_j^*\}_{j=...
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Interpretation/ explanation for NA values produced by cox.zph

I have set up several Cox proportional hazards models in R, and am using cox.zph from the survival package to test the ...
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How to use a categorical covariates with high dimensionality in survival analysis

I am performing survival analysis on a dataset which contains mostly numerical variables, and binary categorical variables. However there is only one categorical variable which has up to 20 different ...
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1answer
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How to get adjusted logrank in the Cox model, if I have two covatiates?

Let's say I have a model (pseudolanguage): survival = My_Factor + sex + age. I do it to adjust the hazard ratio for sex and categorized age={<30yr; >=30yrs} (not my choice). I can get two p-...
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Meta-analysis of time-to-event data for single group design

I would like to perform a meta-analysis of time-to-event data for a single group (i.e. there is no comparison group). How do I do so, what are the statistics required? I understand that for 2-group ...
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1answer
138 views

Dealing with left-, right- and interval-censoring and left- and right-truncation

I have a survival data set with left-, right- and interval-censoring and left- and right-truncation. Now I want to fit a Cox proportional hazard and an AFT model to these data. What is the best way to ...
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How to get main effects (deviance table) on the censored quantile regression in R quantreg::crq?

I know it's about R, but it's anyway a statistical question. I want to calculate confidence intervals for the survival quantiles (median and the 1st quartile). I was asked to use namely the censored ...
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1answer
30 views

Bartholomew estimate of variance of median for exponential distributed RVs

Suppose, $X_1, X_2, \ldots X_n \sim \text{iid Exponential}(\theta)$. The median is given by $\log(2) \theta$. The MLE of the median is given by: $$ \hat{M} = \log(2) \sum_{i=1}^n X_i / n $$ And the ...
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How to compare the effect size of one exposure on different outcomes?

I am modeling the effect of a risk factor on two types of disease by using subdistribution hazard mode (so death is a competing factor for the diseases), when I analyzed for two types of disease ...
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why is hazard function tending to infinity

How to prove that if h(t) hazard function is failure rate function then integration of h(t) from 0 to infinity is infinity .
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133 views

Test for proportional hazards assumption in coxme model - Error and abortion of R session

I'm trying to do a survival analysis using a mixed-effects cox proportional hazards model in R with coxme. My data is - actually - fairly simple. I followed the survival of insect that were kept in ...
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1answer
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Are arguments for regularization/penalties applied by default to the coxph() function in the 'survival' package in R?

I'm reading through the documentation for the 'survival' package in R, pdf link, and as I understand it, there are three methods for applying penalty to the basic Cox regression function: ridge, p-...
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How to deal with participants that don't last through a treatment?

My study involves repeated measures to compare the effectiveness of two distinct drug formulations at reducing the volume of an abscess, measured at three time-points (one baseline and two follow-ups),...
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1answer
57 views

Restricted mean survival time per patient

Apologies for the basic question (I have a clinical training background therefore am not so experienced on the stats front). Is it possible to calculate the restricted mean survival time for each ...
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1answer
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Can I put variables correlated to time in a Cox proportional hazard model? (Bird migration)

I use the Cox PH model in an ecology study in order to estimate the risk of "migration departure" of a bird species according to different variables. In this way I can put forward the ...

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