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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.

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How to remove extra lines in ggplot2

I'm trying to create a graph of survival over time at a number of different sites. I have a fairly simple dataframe as below I have used the following code to make the plot: my_df <- data.frame(x = Survival$time, y = Survival$`% survival`, group =…
timeywimey
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Write wrapper function for `survival::Surv()` with default values

I've been working recently with CDISC data that is structured with pre-specified column names and certain expectations for the way survival data are coded. I want to write a wrapper for survival::Surv() that uses the structured data of the CDISC…
Daniel D. Sjoberg
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How to incorporate an offset variable while using coxphf()

library(coxphf) library(survival) im <- data.frame(X1 <- c(0.482, 0.283, 0.806, 0.510, 0.828, 0.675, 0.430, 0.743, 0.285, 0.954, 0.323, 0.349, 0.338, 0.818, 0.688), X2 <- c(0.750, 0.690, 0.604, 0.566,…
SaJa
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Plot pairwise_survdiff result table together with combined ggsurvplots

I am ploting two survival curves in combination using ggsurvplot_combine: one for the overall survival and another one for survival by a specific variable. I would like to also show the p-values for the survival comparison of each combination in the…
Eduardo Magalhaes
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How to predict risk scores with Cox models using lifelines package?

I have made multiple cox models with Lifelines package and I am trying to predict the risk score of each individual following information in CoxPhFitter page. predict_hazard is a suggested command in that page, but when I use it to predict risk…
Ali Fahmi
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Survival plot appearance

I am trying to recreate the following plot - I found this plot in other papers so I thought maybe there is some package I have skipped. I got a really close result using ggsurvplot function with this tutorial - but I failed to: Add the gap in the…
Daniel Ostrovsky
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Pooling Survreg Results Across Multiply Imputed Datasets - Error Message: log(1 - 2 * pnorm(width/2)) : NaNs produced

I am trying to run an interval regression using the survival r package (as described here https://stats.oarc.ucla.edu/r/dae/interval-regression/), but I am running into difficulties when trying to pool results across multiply imputed datasets.…
Rachel
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Confidence intervals on parameter estimates for an ATF model in R

UPDATED with dataset and code: dataset code I have a Cox regression and an ATF regression with the same covariates and dependent variables in R; that is, the only difference between the two is the modeling function. I'm trying to get the confidence…
MWolcott
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95% CI for survival linear combination (interaction) using vcov

i have this model Where TD is a binary variable, and Strata is a numeric variable equals to {1,2,3}. I need to get 95% CI for this two linear combinations: I have this function to construct confidence intervals pwp_gt_int <-…
JOSE ANTONIO RUIZ TAGLE MATURA
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Convert "survfit()" output to a matrix or dataframe

Example data below. My basic problem is that running "survfit" by itself gives a nice column with median lifespan for each category, which is the thing I want to extract from my survfit data. Ideally I'd like to export this "survfit" output as a…
Crawdaunt
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How to obtain expected time to death from ranger survival predictions?

I am trying to obtain the expected time to death from ranger predictions. Given the code below, how do I estimate the time to death from the survival probability in predictions$survival? library(survival) library(ranger) data <- pbc data <-…
Luca_brasi
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What is the output of predict.coxph() using type = "survival"?

I am trying to learn what the various outputs of predict.coxph() mean. I am currently attempting to fit a cox model on a training set then use the resulting coefficients from the training set to make predictions in a test set (new set of data). I…
Mao Pineda
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Using tidy selection together with the survival package - "Error: promise already under evaluation"

I am writing an R function that allows the user to specify an individual time variable when creating a survival::survfit object. The survival package has a "string-free" syntax, which means that the name of the time variable (in my case "dtime")…
Lukas D. Sauer
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Creating survival curve from summary plot

The software that I am using gives the summary output of the survfit function. What is the easiest way to take this information and use the ggsurvplot function? I understand that this summary data is in a different format from the traditional data…
davidk
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R Survminer Pairwise Survival difference Variable length error

Hello I am using the survival package and the survminer package to do some analysis. I am having trouble with pairwise_survdiff from the survminer package. Here is some simulated data that mimics my…
Victor Feagins
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