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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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gestate::event_prediction for predicting events for a study with enrollment completed

Is it possible to use gestate::event_prediction to predict event timing for a study with enrollment completed? event_prediction has a parameter for rcurve, which I am not sure how to input for a enrollment completed study. Here's is the example from…
user2272972
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What is the maximum follow-up time to use when comparing several cohorts in a survival analysis?

It has been a long time since I last performed a survival analysis, and I have a basic question about it. I have three cohorts, each with a different median follow-up time value that I have calculated using the reverse Kaplan-Meier estimator. The R…
EI_Stats
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How to generate a smoothed hazard plot in R?

I am trying to replicate some analyses that someone performed in Stata. They used a function (or program as they are called in Stata?) called "stexpect3" to generate a "smoothed hazard plot" like this. Wondering if anyone can point me in the…
krtbris
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How can I transform my data to be used by tmerge and a multistate survival model?

I am currently trying to model a multi-state survival problem. Subjects can be in one of 1 states (A through C). All states are sequentially entered and there is no reversal or jumping (i.e You must go from A-> B -> C in order, you can't go from…
Demetri Pananos
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Editing Axis Title in Schoenfeld Residuals Plot

I'd like to edit the y-axis titles of my Schoenfeld residuals plot, which currently say, "Beta(t) for [variable name]" where [variable name] is the variable's data entry name rather than its label name. For instance, I'd like to change "Beta(t) for…
Bren
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How to change the decimal separator in a ggsurvplot?

I would like to change the decimal separator of all the numbers (risk table, x and y axis, as well as p-value) in a Kaplan Meier curve from "." to "," (e.g. from 3.1415 to 3,1415). For the graph I use ggsurvplot from the survival package in R. I…
kobue1
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RMST2 covariates do not produce confidence intervals

I am using the rmst2 package on R. When i run the model without covariates, I get this result: Restricted Mean Survival Time (RMST) by arm Est. se lower .95 upper .95 RMST (arm=1) 9.788 0.279 9.241 10.334 RMST (arm=0)…
Sim Grewal
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RMS vs SURVIVAL package - Cox model - different wald value

I want to study the pvalue of the variables included in my Cox model. I compare this two results : library(survival) library(rms) n <- 1000 set.seed(731) age <- 50 + 12*rnorm(n) label(age) <- "Age" sex <- factor(sample(c('Male','Female'), n, …
Sle R.
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Problems with the reproduction in R of survival analysis results originally generated in Stata?

I am attempting to reproduce some survival analysis results published in a journal. The original results were produced in Stata. Here is the code: * COUPS gen c_coup=c replace c_coup=0 if exit!="coup" stset time, id(leadid) failure(c_coup) * REVOLT…
w5698
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Loop/iterate over many columns in R for Cox proportional hazards regression

I have a great number of events to analyse, all in separate columns as shown in my example below. I would like to create a model for each column labeled IDXX, through a FOR loop, in R. However, the code always returns the error Time and status are…
pyyyour
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How to build a Cox PH model manually (from coefficient found in coxph function)?

I built a cox PH model with the following code: library(rms) cox1 <- cph(Surv(survival_time, event) ~ var1 + var2 + var3 + var4, data = myDataBase) summary(cox1) Now I want to predict a survival probability at 12/24/36 months for a new…
B_slash_
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Mortality table | Extrapolation of rates to older ages

I am currently working on the construction of an experience mortality table. My problem is with the methods of extrapolation of the smoothed rates that I have obtained. I'm really struggling to implement an R code that will allow me to extrapolate…
Philippe BROU
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Overall survival plots of two cohorts and probability at specific time points

I want to calculate the overall survival of two cohorts. "dat" is the dataframe containing the data. The follow-up time of the patients is recorded in "follow_up_TIME" and "EXITUS" is a categorical variable where 0 = alive and 1 = death. I need to…
EI_Stats
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R survminer::ggsurvplot can't combine due to "atomic vector"?

Reproducible example: require(Survival) require(survminer) require(ggplot2) set.seed(42) a <- c(32,291,545, 44,3,792,352, 20,615,169, 61,156, 88,863,255, 33,132,5, 63,8,964,831, 55,133, 12, 54,261,867, 17, 12,699,233,251,446, 43,223, …
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Rshiny with Xgboost error: xgb.DMatrix does not support construction from closure

I am creating an Rshiny app to run a an xgboost survival model. To do this, the categorical variables in the UI need to be entered into the model as one hot encoded variables. I created a blank dataframe and then used reactive values to adjust the…
yussel60
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