# Tagged Questions

Survival analysis is concerned with modelling the time before subjects change state, typically time until death or failure. One key feature of such data is that they can be censored, that is, some subjects will not have changed state before the study ends.

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### Nelson-Aalen estimator in discrete time

I was wondering whether the Nelson-Aalen estimator can be applied to discrete-time multi-state data (in months). I ask this because it seems that literature tends to present it only in the ...
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### Comparing means of two simple time series

I'm trying to look for difference in timing (ie. earlier/later) in a variable measured at regular intervals between two groups. This seems like a simple experimental design, and working in R, I'm ...
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### Obtaining a log-normal waiting time via sequential exponential or gamma distributions - is it possible?

Assume you've use a accelerated failure time model to find that the transition of subjects from State A to State B is log-normally distributed with parameters $\mu$ = X and $\sigma$ = Y. This now ...
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### Expected Value of Integral of Stochastic Process

Suppose we have a continuous-time stochastic process $X(t)$, which consists of a sequence of delta functions that, at each time $t$, have a probability $p(t)$ of taking a non-zero value. $p(t)$ lies ...
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### Propensity score weighting in Cox PH analysis and covariate selection

Regarding propensity score weighting (IPTW) when doing Cox proportional hazard modeling of time-to-event survival data: I have prospective registry data where we're interested in looking at treatment ...
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### Using propensity scores from twang in coxph

I've used the twang package to calculate propensity score weights in my observational data set. The twang vignette uses the ...
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### Best method to validate a multiply imputed Cox model with R?

This question is with regards to using a test data set to validate an imputed Cox model using R. With a non-imputed data set I would use val.surv() from ...
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### Interval censored current status data Cox proportional hazards model in R

Given interval censored survival times, how do I perform a current status data (case1 interval censored survival time) Cox PH model in R? I found the R package intocox, but the output is not ...
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### Survival analysis for event prediction

For each record in my datasets I have the following information $$(X_1 \ , \dots \ , X_m \ , \delta \ , T \ )$$ where $X_i$ are features, $\delta$ is 1 if the target event occurs and 0 otherwise, ...
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### Combined variance following multiple imputation with survival model

I have created 5 imputations of a dataset and have fit a survival model to them all in R. I want to combine the estimates of the coefficients and the standard errors of the coefficients. To do this I ...
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### How to calculate the population survival probability in a two stage randomized clinical trial?

I am trying to reproduce a paper on two stage randomized clinical trials. In these clinical trials, a patient is randomized to either of the maintenance therapies $B_1$ or $B_2$ upon their remission ...
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### Mean survival time of a Weibull distribution

I'm trying to calculate the mean survival time of a Weibull distribution, and am getting what feels like an errant estimate of the mean--and each source I look up for how to calculate the mean gives a ...
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### How to change the data structure from “group” to “individual” form for logrank test in R?

I'm working on mortality test by using fish exposing some chemicals. At the end got the data like this (a~g represent group, number represent no. of dead fish, each group n=40): ...
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### Visualize survival analysis with time dependent covariates

As a follow-up to Model suggestion for a Cox regression with time dependent covariates is the Kaplan Meier plot accounting for the time dependent nature of pregnancies. In other words the dataset is ...
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### Interpretation of sas output of survival Frailty model using Proc NLMIXED

I am new to the site, I am trying to fit a Weibull gamma frailty model in SAS for multiple event times per subject, using proc nlmixed procedure. Please how do I ...
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### Using multiple imputation for Cox proportional hazards, then validating with rms package?

I've been researching the mice package, and I haven't yet discovered a way to use the multiple imputations to make a Cox model, then validate that model with the rms package's ...
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### EM algorithm R code on Cox PH model with frailty

Let say I have a 'kidney catheter' data set. Data are about the recurrence times to infection, at the point of insertion of the catheter, for kidney patients using portable dialysis equipment. ...
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### Discrete time survival analysis with varying length event windows

I have data that appears very well-suited to discrete-time survival analysis, in that each subject has a consecutive sequence of observations from its entry into the system until its exit, and I'm ...
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### What's the name of this discrete distribution (recursive difference equation) I derived?

I came across this distribution in a computer game and wanted to learn more about its behaviour. It comes from the decision as to whether a certain event should occur after a given number of player ...
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### Can Cox regression be used to assess the difference between two treatments

In this project our objective was to compare the revision rates between two surgical techniques. We have time to revision (time between two surgeries), demographics, and other variables we are ...
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### Interval censored Cox proportional hazards model in R

Given interval censored survival times, how do I perform an interval censored Cox PH model in R? An rseek search turns up the package ...
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### Remove data starting before defined start date for survival analysis

I want to do survival analysis with a big data set. The data collection started on 1997-01-01 and is still continuing yet. However, episodes that started before ...
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### Appropriate Application of Survival Analysis

I have an experiment that will produce observations of the time until an event occurs. Some basic properties are that We count the number of events that have occurred at some point $t_1,...,t_n$. ...
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### Question on Survival Analysis

I'm working on a survival analysis project. In part of the project, I'm asked to "identify factors that may contribute to an increased risk of death". I have difficult time understanding what I'm ...
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### Best predictive Cox regression model using c-index and cross-validation

I want to explain the problem I have in this moment to know what do you think about the implementation I am designing. I have a set of 40 genes expression data as binary variables (overexpressed yes ...
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### How to generate predicted survivor curves from frailty models (using R coxph)?

I want to compute predicted survivor function for a Cox proportional hazards model with frailty terms [using survival package]. It appears that when frailty terms are in the model, the predicted ...
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### Starting point for survival analysis (overall survival and recurrence-free or progression-free survival)

In a RCT we would like to compare oncological outcome of two surgical 2-stage strategies, i.e. patients require to undergo both stages to become free of cancer. The problem is that strategy A ...
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### Nonhomogeneous Poisson Process Derivation of Survival Function

I would like to understand better the derivation of the inter-arrival time for a nonhomogeneous Poisson process. Can any one supply a link to a nice clear derivation? I'm only interested in the time ...
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### How to compare task completion times in a crossover study

Ten participants have completed a task using two different methods A and B. The first five participants completed the task first using method A then B. The remaining participants completed the same ...
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### “Ties” in Bayesian Survival Analysis

I have been reading about Bayesian methods for performing survival analysis. One of the things that strikes me is that in the three or so books that I have read, there has been no mention of handing ...
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### Calculating the Log Hazard Ratio with SE in R

In R, is there a predefined function that will give me the log hazard ratio and its standard error for a black male (as shown in the example below) given the output of coxph regression? ...
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### Using Stata for Survival Analysis with Exponential Model

Trying to: Plot survival function estimates (by arm or treatment) as well as associated point-wise confidence intervals based on the Exponential distribution Compare the Kaplan-Meier curves with ...
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### What are the differences between survival analysis and Poisson regression?

I'm working on a classical churn prediction problem using the number of visits of a given user to a site and I thought that Poisson Regression was the right tool for modelling the future engagement of ...
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### Combining several survival experiments

In four independent experiments, two strains (A and B) were compared in their respective survival curves. Two experiments show a clear-cut result (A survives at 100%, almost half B dies). Two further ...
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### Model suggestion for a Cox regression with time dependent covariates

I´m modeling the effect of pregnancy on the outcome of a disease (dead-alive). Approx 40% of the patients did become pregnant after the time of diagnosis-but at different points in time. So far I´ve ...
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### Level of uncertainty when measuring a period of time?

I need to create a raw data table for my science experiment, but I'm unsure what the level of uncertainty would be when measuring days. How would I determine the level of uncertainty when measuring a ...
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### Average of ongoing durations

Suppose I run a community center and I want to find the average length of time that someone is a rec center member. It is straightforward to do this with people who have already cancelled their ...
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### Compare two survival curves for paired data

I want to compare two different methods for detecting status change in a survival analysis. A group of subjects is being followed for a longer period (many years), and two examination methods have ...
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### Creating formula object for coxph()

I am trying to create the formula object for coxph() manually, as I want to reproduce it in RSRuby. Note that the response variable needs to be a ...
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### Cox regression when reference group had zero events

I would appreciate some advise on an a problem I ran into. I use SPSS for statistical analysis of a study. The study look into how a blood test predicts mortality with patients followup of 1 year. ...
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### Survival Analysis with Multiple Events

Suppose we have a population $P$ that we are interested in. We want to track the onset of particular conditions (i.e. $A$, $B$ and $C$). Suppose that as blood pressure drops, these events occur. So ...
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### Integral of survival function

If X is a nonnegative random variable representing the life of a component having distribution function F, and S is the survival ...
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### Mean residual life

If X is a nonnegative random variable representing the life of a component having distribution function F,the mean residual life ...
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### Looking for ways to compare between coxph models

I'm running Cox proportional hazards regression in R, and would like to test the option of categorizing one of my continuous variables to factor (I'm aware of the loss of data issue, just checking). ...
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### Survival analysis w/ repeated observations of experimental and control units within periods of differing size & trends over the periods

I have an experiment called Fear Conditioning Acquisition Protocol. We expose mice to subsequent white sounds followed by short electric shocks through the floor. Our aim is to let them learn to ...
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### Is Cox regression analysis including demographic covariates required for observational studies instead of Kaplan-Meier?

I have been reading quite a few papers and recently have started analyzing some data on a review that I am doing. I am trying to examine the effect of two different treatment options on a group of ...
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### How to deal with death in disease-free survival analysis?

If I have disease free survival data (defined as whether or not a particular disease has been diagnosed or not along with the time to that event or loss to follow up) and also overall survival data, ...
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### EM for truncated/censored data, how do those CDF's cancel?

I am practicing basic EM problems for qualifying exams. I am having trouble with truncated/censored data problems. There is something I don't understand about the complete-data likelihood. Consider ...