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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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Getting cumulative risk values

Consider the following toy example: use https://data.princeton.edu/pop509/justices2.dta, clear stset tenure, fail(event == 1) stcrreg age year, compete (event == 2) stcurve, cif I want to plot a cumulative incidence curve as done above but then I…
bvowe
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How many bootstraps does rfsrc in the R package randomforestsrc peform?

Does anyone know how many bootstraps or subsamples a standard call to rfsrc performs? rf1<-rfsrc(Surv(time,status)~., data=myTable) Also rf1$err.rate which is described as "cumulative OOB error rate" for me at the above settings is a vector of…
StanW
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add pointwise confidence interval to prediction of survival curve plot

I have a data set of patients on a waiting list for an organ transplant. Event is death time. The set containts the following variables: patientID, time, status , age, gender, bmi, disease. I made a model of the survival time of a patient on the…
Dries De Witte
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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 censored at 5 years, event status and 38…
Faiz Yusufi
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How to add arrows to forest plot in survminer (ggforest)

I was wondering if there was a way to add two arrows to the x-axis of a forest plot, similar to what is shown in this example: How to add arrows to a forest plot? (this code does not work on ggforest) Here is the sample…
Megan
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Why does survey weight change R SQUARED?

library(survival) library(survminer) library(dplyr) ovarian=ovarian ovarian$weighting = sample(1:100,26,replace=T) fitWEIGHT <- coxph(Surv(futime, fustat) ~ age + rx,data=ovarian,weight=weighting) fitNOWEIGHT <- coxph(Surv(futime, fustat) ~ age +…
bvowe
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How can I visualize an interaction in cox model in r?

I fitted a model and had a significant interaction effect. How can I plot this in a graphic? It follows a toy example (only for illustration purposes): library(survival) # includes bladder data set library(survminer) fit2 <- coxph(Surv(stop, event)…
Guilherme Parreira
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Reshape Data based on Different columns

I need to reshape my data, to get it in a proper format for Survival Analysis. My current Dataset looks like this: Product_Number Date Status A 2018-01-01 0 A 2018-01-02 …
R overflow
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Coxph long format issues errors

I have my data in long format correctly yet when I run the coxph function: tryu <- coxph(Surv(entry,exit,dead==1) ~ age, na.action=na.omit,data=finalmerge) I get the following error: Warning message: In Surv(entry, exit, dead == 1) : Stop time…
user5298556
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How can I plot standard distributions fit with survreg()?

I can not plot logistic or gaussian distributions fit to my data. I load my data and create a survreg object gbcs <- read.csv("https://ryanwomack.com/data/gbcs.csv") recsurv <- Surv(rectime,censrec, gbcs) If I try to fit a exponential distribution,…
Fidel Alencar
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Feature selection in mlr using univariate.model.score filter on censored data

I am trying to perform feature selection in R using mlr and the univariate.model.score filter. In the documentation it says that surv.rpart is the default learner for this filter. My dataset contains censored survival data and I would like to use a…
panda
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Proc Phreg Baseline Statement Equivalent in R

Is there a way to generate a table similar to the output of the baseline statement in SAS' proc phreg. Specifically, I want baseline harzards and survival probabilities at several time points for all combinations of the covariate set.
user1916067
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Creating a function passing its arguments to the Surv function (or any other)

Please consider the following: To create a survival curve one can make use of the survfit function of the survival package. My aim is to write a function that (amongst other things) creates such a curve, but the function should work with different…
Frederick
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Extimate prediction accuracy of cox ph

i would like to develop a cox proportional hazard model with r, use it to predict input and evaluate the accuracy of the model. For the evaluation I would like to use the Brior score. # import various packages, needed at some point of the…
User12547645
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Formatting data for survival analysis - time variable in long form data

I'm new to survival analysis, and am unsure if I'm formatting my data correctly. Using this dummy data: id <- c(rep("1", 10), rep("2", 10), rep("3", 10), rep("4", 10), rep("5", 10)) age <- c((15:24), (35:44), (45:54), (55:64), (40:49)) event <-…
T.P.
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