Questions tagged [survival]
Survival analysis models time to event data, typically time to death or failure time. Censored data are a common problem for survival analyses.
3,447 questions
0
votes
0
answers
14
views
creating synthetic data for iv+survival ipdma [closed]
I am attempting to create a synthetic dataset to show the benefit(?) of an IV+survival method in an IPDMA. This has required detailed examination of the IV relationship to not violate the assumptions, ...
- 1
0
votes
0
answers
13
views
Survival curves cross on survival analysis with time-dependent predictor variable
I'm running an extended Cox proportional hazard model for a time-dependent predictor variable. Basically I'm interested in learning if there were any changes to the duration of sickness absence ...
- 1
2
votes
0
answers
49
views
Martingale and Deviance residuals in parametric recurrent event analysis?
I'm developing a nonlinear joint model in which the survival part consists of a parametric time-to-event model that describes a recurrent event process. In this parametric RTTE part I'm directly ...
- 21
0
votes
2
answers
41
views
Cox regression assumptions
I am analyzing the association between a plasma biomarker and disease incidence, self-reported via yearly questionnaires. The total sample size is 824 of which 65 reported at least one event (I am not ...
- 11
0
votes
1
answer
28
views
What are the differences between PS-match and adjusted Cox regression?
This is more like an extension of the following question: Propensity Score Matching with Cox Regression
I am wondering what are the differences between these:
matching patients with PS and running ...
- 581
2
votes
1
answer
42
views
Are there any advantages of survival analysis over regression for prediction?
I came across survival analysis recently, and it seems quite useful for modeling the time that an event occurs and/or handling censoring. The motivating examples in the literature make sense, for ...
- 500
0
votes
0
answers
22
views
How to plot hazard ratio from coxph model with tt() term [closed]
This question is related to another that I posted here:
How to visually assess tt() suitability in coxph
If we have a time-varying HR that arises from a time-dependent coefficient because we have ...
- 867
0
votes
0
answers
34
views
How to visually assess tt() suitability in coxph? [closed]
For this example, I am taking cues from the time-dependent survival vignette.
I am interested in understanding how to assess the suitability of a covariate-time interaction using ...
- 867
0
votes
0
answers
24
views
Not computed tests in gofstat in R
I am working on a survival analysis project. For this project, I use this dataset:
https://archive.ics.uci.edu/dataset/519/heart+failure+clinical+records
I began by importing these libraries :
...
- 1
3
votes
1
answer
23
views
Can I use age as a time varying covariate in a Cox PH?
I am studying how long a rebel group leader remains in charge of a rebel group until they are forced to step down. I have leader-year data with the following variables:
...
- 183
1
vote
2
answers
35
views
"Impossible" crossing of Kaplan-Meier curves
Here is a picture from a small set of lung cancer patients. The blue curve represent overall survival: time from radiotherapy to death of any cause. The red line represents disease free survival: time ...
- 892
2
votes
1
answer
43
views
Is it possible to perform a survival analysis in a patient population only, using their age of onset as time-to-event data?
We have data on the age of onset of a certain disease in a patient population of 1,000 cases. The average age of onset is 60 years. The data were obtained by recruiting patients who visited either of ...
- 87
0
votes
0
answers
11
views
How to Split a Small Dataset for Survival Analysis: Train/Validation or Include a Test Set?
I am working on survival analysis for pancreatic cancer with a small dataset of 140 samples. The dataset includes WSI and mask data along with survival information.
1. Current Approach
I use 5-fold ...
2
votes
1
answer
41
views
probability that the failure is on the individual as observed
In his paper Regression Models and Life Tables, where he introduced the proportional hazard model, David Cox states that:
For the particular failure at time $t_{(i)}$, conditionally on the risk set $\...
- 103
0
votes
0
answers
17
views
Calculating net survival: should one use the relsurv or popEpi package?
The Pohar Perme estimator was proposed in 2012 as an unbiased estimator of net survival, initially in cancer studies. Net survival estimates the survival compared to the background mortality expected ...
5
votes
1
answer
160
views
Inverse of hazard function
I want to know $t$ based on the output of the hazard function $\lambda(t)$. Is it possible to numerically solve the inverse of the hazard function as defined as:
$\lambda(t)=\frac{f(t)}{S(t)}$
where $...
- 51
0
votes
1
answer
27
views
Separate Test Set for Cross-Validation for Small Sample (n=140)
I’m working on a survival analysis model with a small internal dataset (n=140). An outside researcher suggests splitting the dataset into train/val and setting aside a separate test set (e.g., ~10%, ...
- 1
0
votes
0
answers
25
views
How to Interpret Concordance Index Below 0.5 in Cross-Cohort Survival Analysis
I am conducting a survival analysis where I use cross-cohort validation for performance estimation (CV strategy can't be changed, its an external requirement). My metric of choice is the concordance ...
- 1
1
vote
1
answer
39
views
Simulating machine maintenance occurrences using Weibull distributions
I have a set of machines and I am trying to simulate the occurrence of maintenance jobs for the set of machines. I have a fitted Weibull distribution for the time between occurrences of maintenance ...
- 11
0
votes
1
answer
34
views
Setting a reference in Cox regression with splines and interaction
I run a Cox regression with a continuous variable age and a categorical variable sex. The model includes splines for the continuous variable and an interaction between both. I want to choose the ...
- 343
3
votes
1
answer
41
views
Restricted time window for survival analysis using Kaplan Meier estimates
I am kinda new to statistics, so I have a question about survival analysis using Kaplan Meier estimates. In my samples (tumors), I think a certain feature has a positive prognostic impact (better ...
- 31
0
votes
0
answers
18
views
low AIC on Skew-Normal AFT
I am interested in making an AFT model based on the Skew-Normal distribution. For this I am basing myself on the following article. When running the model and comparing it with others such as Weibull, ...
- 281
0
votes
1
answer
58
views
Note on standard errors reported by `flexsurv` package as compared to `survival` package
My original question (which is below) was about converting standard errors reported by flexsurv to the standard errors reported by ...
- 63
0
votes
0
answers
27
views
Comparing different timepoints of measurements (1,2,3,4) for a group of individuals who survived vs. not survived
In most cases we have a time series based measurement (CD8T) for a group of individuals who survived or not survived (Survival) from a disease (repeated measurements). The timepoint based measurements ...
0
votes
0
answers
32
views
What distribution describes the duration until a first poisson event occurs?
Imagine you have 100 individuals observed for 100 days. Every day, each individual has a 10% chance of an event occurring. What is the distribution in duration until the first event?
Empirically it ...
- 605
0
votes
0
answers
26
views
Simulating bias comparing linear regression with Cox Proportional Hazard model for prediction on censored data
I wanted to show how censoring biases linear regression and how that could be resolved with survival regression using simulated data. My simulation now suggests, that survival regression (I tried a ...
- 281
1
vote
1
answer
44
views
Cox Proportionall Hazards compared to AFT and the proportional hazards assumption
I am dealing with survival analysis in R in big population datasets with millions of rows. My first option was a cox regression
...
- 33
3
votes
2
answers
119
views
Risk with censored covariates - which method should I use?
TL;DR - my data consists of:
Age of toddler visit to hospital due to household injury.
Record of age at which toddler crawls, walks and runs. Records are censored since some toddlers arrive at the ...
- 2,694
4
votes
2
answers
159
views
Concordance index in survival analysis (Gonen and Heller)
I am working on a project to externally validate a clinical prediction model. The original model coefficients were estimated using a Cox model. The model uses the baseline hazard and coefficients to ...
- 923
1
vote
1
answer
56
views
Time-dependent effects: tt function using nsk () in coxph()
I am using coxph() to compare tree seedling survival data between three treatments (Large, Small, Control). However, coxzph() showed that the coefficient for the Small treatment differed with time. To ...
- 13
0
votes
0
answers
29
views
Log-rank test statistic for multi-way splitting in survival trees
In survival trees, the log-rank test statistic is most often used for split selection. This involves selecting the binary split that produces the largest value of the log-rank test statistic.
This ...
- 23
3
votes
1
answer
87
views
Probability expression in Multi-Task Logistic Regression
I'm trying to understand how the authors of this paper (Learning Patient-Specific Cancer Survival Distributions as a Sequence of Dependent Regressors) obtain the general formula on page for the ...
- 103
0
votes
0
answers
15
views
How to Calculate Cumulative Incidence for Each Case ID in Competing Risks Analysis Using R?
I’m working with a dataset in R and trying to calculate the cumulative incidence for each case ID in the presence of competing risks. My dataset looks like this:
...
- 103
3
votes
1
answer
52
views
Cumulative incidence function - compare time at which a specific cumulative incidence is reached
I have survival data and I've plotted cumulative incidence functions stratified by treatment status (with age as the time scale). I used Gray's test to compare the overall cumulative incidence ...
- 75
5
votes
2
answers
129
views
What does one do when the Hessian matrix is too sensitive?
I used the survival package in R to calculate the maximum likelihood estimates of Weibull regression co-efficients in R. I then tried to replicate the results by writing the log likelihood function ...
- 63
4
votes
1
answer
88
views
cloglog vs logistic regression survival analysis
I'm not looking for an explanation of the difference between hazards and odds here, what I am curious about is determining if, as is sometimes presented, a hazard model (cloglog link) is equivalent to ...
- 63
3
votes
1
answer
51
views
On self-consistent estimators of survival functions. How do they work?
I'm reading about how the estimation of the survival function is "self-consistent" because as Efron showed, we can estimate the survival function in the presence of right censoring as
$$
\...
- 33
0
votes
1
answer
40
views
`pspline()` terms and checking proportional hazards
I have fit a Cox model with pspline() terms for the continuous covariates. I am trying to better understand how pspline() terms ...
- 209
3
votes
1
answer
138
views
Understanding and reporting Cox models with spline terms
I have fit a Cox model with pspline() terms for the continuous covariates. I am trying to have a better understanding of what happens to report my results ...
- 209
0
votes
0
answers
15
views
Prove the monotone property of "discretized" failure rate
Let $F$ be a cumulative distribution function for a nonnegative continuous random variable and $f$ be the corresponding probability density function. The failure rate of $F$ is then $h(t)=f(t)/(1-F(t))...
- 73
0
votes
1
answer
32
views
CoxPHFitter and WeibullAFTFitter() lifelines implementation
I am trying to build a survival model to predict years of life lost; currently, I am running several different survival analysis methods to compare their results: AFT and Cox PH.
I am using the ...
- 1
0
votes
1
answer
107
views
How to get Hazard Ratios in subgroups by coxph?
How to get the Hazard Ratios in each level of the subgroup variable? For example, in my example below, I want to get HR/(95% CI) in male patients (treatment effect of arm1 to arm 2 in male patients) ...
- 529
1
vote
2
answers
51
views
Survival Analysis in R: Using Categorical vs. Continuous Gene Expression with survfit() and coxph()
I'm currently performing a survival analysis based on the expression of a single gene. Here's what I'm doing:
I standardized the gene expression data using scale().
...
- 11
4
votes
1
answer
51
views
Am I dealing with within-cluster dependence or independence? (Cox proportional hazards model/frailty model)
this is my first time asking a stats questions anywhere online. I'm a young female PhD student and quite anxious about this, so if possible, please be kind. I'll do my best to ask my questions clearly....
- 41
3
votes
2
answers
79
views
Predicting the Next Event's Timestamp Based on Historical Data with Possible Patterns?
I'm working on a personal project where I aim to predict the time of the next event based on a series of historical timestamps. The dataset I have consists of around 400k timestamps of past events.
...
- 131
2
votes
2
answers
81
views
Where should the $\leq$ go in the definition of the hazard function?
I have come across two definitions of the hazard function in several textbooks and online resource.
Definition 1. Here for example.
$$h(t) = \lim_{\epsilon \to 0+}\dfrac{P(t < T \leq t + \epsilon \...
- 23
0
votes
0
answers
14
views
Addressing endogeneity issue in Cox model
I’m working with panel data where the variables are group level indicators of performance. To put simply, the predictor is a group-level aggregated quantity (e.g., average reputation of members) which ...
4
votes
1
answer
66
views
Simulating time-fixed confounder in time-varying survival model
I am attempting to simulate a survival Cox PH setting with time-varying exposure in R. The goal is assess the effect of a time-fixed confounder in the relationship exposure-outcome.
What I am trying ...
- 794
0
votes
0
answers
20
views
Feature selection for Cox Model with low event number
I am interested in wether a set of 30 variables can predict OS in cancer. I have reduced my features to 15 after checking for multicollinearity. The problem is, I only have around 70 events in my data ...
- 1
0
votes
0
answers
15
views
Assessing for statistical significance of change in trend rate of events with survival analysis in R
I have data examining the date of an event following a particular procedure among different sampled individuals. I expect that within X days of the procedure, the rates of my event will increase and ...
- 1