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.
Questions tagged [survival]
445 questions
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Mean beta hat does not equal to true beta by sim.survdata
I recently use the R "sim.survdata" function in "coxed" package to simulate survival data. I did 2k simulations with one covariate and coefficient = 1. Each time I fitted a Cox regression and recorded the estimated beta and 95% CI. However the…
Weiyu Qiu
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unexpected symbol in "tt" function for categorical variable
I have a dataset with time, event and 4 predictor variables of which "Q.V4" is a categorical variable which needs to be transformed using tt function. This variable has 4 levels - Q1, Q2, Q3, Q4
F1 <- data.frame(
time=c(102,48,84,72,66,90),
…
Biostats
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1 answer
Shiny scatterplot with real-time Kaplan-Meier
I have constructed an interactive scatterplot in Shiny. Using plotly, I can select groups of points and render the annotations for this group in a table next to the plot.
library(survival)
library(survminer)
mtcars <-…
Matt
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plot specific groups within strata in ggsurvplot
I wonder how I can plot only specific groups within a predefined strata. For instance in the examples below, how can I for instance plot only sex:0,rx:Obs against sex:1,rx:Obs as one specific survival-plot (not faceted), ignoring the other…
user2300940
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How do I specify the layout of plots in ggcompetingrisks?
Below is a sample code:
set.seed(2)
failure_time <- rexp(100)
status <- factor(sample(0:3, 100, replace=TRUE), 0:3,
c('no event', 'death', 'progression','other'))
disease <- factor(sample(1:6, 100,replace=TRUE), 1:6,
…
kna123
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Stratified Fisher and Wilcoxon test
I would like to perform a stratified fisher test.
I've tried with tabulate without success.
These are my data:
> db$site
[1] 2 2 2 3 1 1 1 1 1 1 1 1 1 1 2 3 1 1 1 1 1 1 1 1 2 2 3 3 1 1 3 1 2 1 1 2 1 1 1 1 1 3 1 1 1 1 1 3 1
[50] 2 1 1 3 3 3 1 1…
ArTu
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Actuarial vs. predicted survival comparison
I have a set of patients and their actuarial 1- and 5-years survival. I have also used their data with a certain commonly utilised medical score, that calcualtes survival probability for 1- and 5-years (for example 75% and 55% respectively). I'd…
opir
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1 answer
Cox PH time-dependent covariate formatting in R
I am trying to perform a Cox proportional hazards analysis with a time-dependent covariate in R. I have read the relevant documentation (Therneau et al.) and several tutorials but am struggling to format my data properly given how the covariate is…
panbear
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votes
2 answers
In cox regression categorical levels not shown in my output
In my data, Hemoglobin_group is a categorical variable with 6 levels. When I run the below code, I can't see Hemoglobin_group levels in the output. How can I solve this problem?
fit <- coxph(Surv(Time,Status)~Hemoglobin_group, data)
fit
My output:
…
Cgdmm
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How to interpret PySurvival's predict_survival output?
I've built a model using PySurvival's CoxPH model and then ran the predict_survival function to check its output. Here's a sample of the output it provides when printing the result of the predict_survival function after calling it with the following…
Zach Goodman
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1 answer
How to use use predict() for survreg models?
This is my model:
library(eha)
fit.aft <- aftreg(formula = Surv(time, status) ~ age + sex, data = kidney,
dist = "lognormal")
however this is what I see if I want to use predict:
predict(fit.aft)
Error in UseMethod("predict")…
David
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1 answer
How to know if the data is censored in a survival analysis using r
I have a data set that looks like this (a nonsense example):
id <- c(1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3)
year <- c(1990, 1991, 1992, 1989, 1990, 1991, 1992, 1993, 1989, 1990, 1992, 1993)
event<- c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1)
df <-…
johnny
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Survival anaylsis: parameters for concordance_index_censored (scikit-survival)
I want to implement concordance_index_censored on my test set, using the model I trained.
I don't understand which should be my input into the estimate parameter in concordance_index_censored().
Is it somewhere in coxnet_pred? If not, where should I…
DoreenBZ
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R Error in grid.Call with survminer :: ggsurvplot with new packages versions
I use the ggsurvplot from survminer package in R to plot Kaplan-Meir curves. Here is the code and the following error:
library(ggplot2)
library(survival)
library(survminer)
km_fit_2cohorts <- survival::survfit(Surv(time_event_M, indic_Death) ~…
Clem
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1 answer
What is the R code for making a Kaplan Meier plot for how many people develop diabetes during 10 years when the data set includes info up to 25 years?
I struggle with R ....How do I cut out the observations from 10- 25 years to make a Kaplan meier plot for up to 10 years:
what would I add to this line of code? Or would I Need to make separate groups for 0-1 year, 1-2 years and so on?
km.model <-…
Murphy
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