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Questions tagged [survival]

Survival analysis compares the statistical strength of predictors for events encoded as occuring or censored in concert with a time variable. It can be parametric or non-parametric.

445 questions
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Change x-axis labels for ggsurvplot

library(survival) library(survminer) I am using the survminer package to plot unadjusted Kaplan Meier plots. I am calculating mortality comparing different exposures and I have a very specific problem: Is there a way to change the x axis labels of…
Pontus Hedberg
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How to model interaction of covariate with time when proportionality assumption is violated in survival analysis in R

In R, what is the best way to incorporate the interaction term between a covariate and time, when the proportionality test (with coxph) shows that the proportionality assumption in the Cox model is violated? I know that you can either use strata or…
B.Z.
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survreg with left truncated (delayed entry) data

I am trying to fit a delayed entry parametric regression model for a Poisson process with Weibull baseline rate. It doesn't appear that R's survreg function supports left truncated data (I get the error: start-stop type Surv objects are not…
Jake
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Xgboost for survival using mlr in R

I would like to use mlr to run xgboost on right-censored survival data in R. The xgboost code lists an objective function survival:cox which says: survival:cox: Cox regression for right censored survival time data (negative values are considered…
panda
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Plotting the Hazard Function in R using survminer?

We can use survminer to plot the survival function or cumulative hazard function, but I cannot see a way to use it to plot the hazard function. For example, library(survival) library(tidyverse) library(survminer) data(lung) # Run Kaplan-Meier on…
Lily Clements
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how to fix 'Error: variable lengths differ (found for 'input$s')' in R Shiny

I'm trying to make a simple shiny ap for creating kaplan-meier survival curves that are stratified by selection the user makes. When I code the KM calculation statically (with the column name thorTr) it works but the calculation and plot is static.…
R. Cantor
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Time-Dependent Cox Model

Consider the attached (dummy) sample csv file where two methods (i.e. Method A and Method B) are used to evaluate time to progression (PFS) in cancer patients. For each patient we also have the overall survival (OS). data available as CSV from…
user86533
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Why doesn't this survfit plot start at 100%

When I plot the survfit plot of data with two different censoring events, the overall plot (s0) doesnt start at time = 0, pstate = 100%, but jumps to 100% when the first cencoring event occurs. Here you can see in an example, where the jump occurs…
LittleLynx
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Does officer-package accept ggsurvplot-object?

I'm trying to export a ggsurvplot-object to powerpoint with officer-package with no success. I was able to find a lot of instructions on how to use now obsolute ReporterS-package for this and a few mentions that officer should work as well. There…
Lauri Pautola
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why do results of clogit and bife function (both in R) differ?

I like to calculate a logistic fixed effect panel regression (conditional maximum likelihood) in R and get predicted values and/or average marginal effects. I found two functions: bife and clogit from the survival packages Nevertheless, the…
k.r.
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Computing SE or CI for ggadjustedcurves

How can I compute index of variability (SE or CI) for ggadjustedcurves from survminer function? I am using the conditional method. Anyone have any input or resource?
mindhabits
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Nan and Inf in survreg model summary

I'm using survival analysis to evaluate the relative distance (instead of time, as it's usually the case with survival statistics) before a given event happened. As the dataset I'm working with is quite big, you can download the .rds file of my…
Ari Olivelli
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Xgboost cox survival time entry

In the new implementation of cox ph survival model in xgboost 0.81 how does one specify start and end time of an event? Thanks The R equivalent function would be for example : cph_mod = coxph(Surv(Start, Stop, Status) ~ Age + Sex + SBP, data=data)
aiedu
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cox model doesn't suppport "mright" survival data

Good morning, I have been trying to do a stratified logistic regression in R after matching for a Case/Control study and encountered a in my opinion unexpected mistake. I have reproduced the error using the mtcars data…
Member0815
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unable to plot kaplan-meier curve with survfit object from a list using ggsurvplot

I am trying to plot Kaplan-Meyer curve using ggsurvplot from survminer package. I'm unable to plot it when I pass a survfit object saved in a list. Let me use lung dataset as a example. Everything works…
zesla
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