All Questions
493 questions
0
votes
1
answer
575
views
Martingale residuals in Cox PH model for categorical variable
I understand that for continuous data, martingale residuals can be used to assess the linearity of the variable, but if it's a categorical variable (2 levels) is there any interpretation that comes ...
- 1
2
votes
1
answer
559
views
Assessing violations of the Cox proportional hazards assumptions
Cox models assume proportionality. These assumptions can often be formally tested (an example in R is cox.zph from the ...
- 363
1
vote
1
answer
1k
views
How to interpret the Wald Chi-square test for the frailty term in a mixed-effects Cox survival model?
Background
I'm fitting a Cox model to assess the relationship between treatment (binary) and time-to-event (event is also binary) while also controlling for 3 or 4 covariates. Because I want to ...
- 739
0
votes
1
answer
504
views
1
vote
1
answer
317
views
How to fit parametric distribution to baseline hazard in cox PH model
I develop Cox PH model with time-varying covariates to predict marginal probability of some event. The time frequency is measured in months and I have observations since 3 months to more than 160 ...
- 35
1
vote
1
answer
257
views
Cox PH controlling for multiple events
I'm working on a cox proportional hazard analysis in R using the survival package.
I´m analysing covariate effects on fish movement within a study area. The study area is divided into two zones ("...
- 11
1
vote
1
answer
2k
views
How to deal with left truncation in cox model in R
I have a longitudinal data with 8 follow-ups. My aim is to see the effect of a disease on ability decline at old age. In my study, I have sibling pairs, one with disease (1) and one without disease (0)...
- 139
2
votes
1
answer
313
views
Calculate time at risk using cox proportional hazards
Can you calculate the time at set risk from proportional hazard models?
Say I've got my model built for the whole population. The risk of developing an event in one year is 5%. After stratification, ...
- 155
0
votes
1
answer
698
views
How to test overlapping confidence intervals to see a significant difference between groups in a COX propotional model
Cox proportional models have been done with this result.
The two groups (C, B) had overlapping confidence intervals, while the p-value was significant at p<0.001. I have used this code to get the ...
- 103
0
votes
0
answers
338
views
Why R survAUC::AUC functions require both training and test data?
I am familiar with binary classification models, where the AUC is the metric from the area under the specificity-sensitivity curve, it indicates the performance on a dataset.
Now, I'd like to assess ...
- 21
3
votes
2
answers
3k
views
IPTW in Cox Regression model using the WeightIt package - Question on ATT vs. ATE interpretation
I am currently trying to perform some IPTW adjustment in the context of Cox Regression models.
I was interested in expanding my understanding of the differences between ATE vs. ATT estimation. I've ...
- 706
0
votes
1
answer
716
views
What is the meaning of the flexsurvreg plot and its res.t?
I use the flexsurverg to estimate the a Weibull survival model with a time varied covariate, where “utility” is a continuous function, and the result is shown as follows:
I plot the fit function and ...
- 57
1
vote
1
answer
4k
views
coxph() ran out of iterations and did not converge
Am relatively new in conducting survival analyses in R. I wanted to perform an univariate cox regression on my data set. For some of my variables this worked, but for the variable “white blood cell ...
- 11
1
vote
0
answers
49
views
IPTW and adjustment in Cox Regression Analysis [duplicate]
A question on how to deal with inverse probability of treatment weighted-Cox regression analysis.
Basically, I am evaluating how to use IPTW in the context of survival (and specifically, Cox ...
- 706
1
vote
2
answers
374
views
Why is the survival probability decreasing the more variables I use?
I'm using coxph in combination with survfit and I observed that, e.g., when I use the following syntax
...
- 3,493
2
votes
1
answer
1k
views
How to understand Aalen additive regression model?
How to understand these plots with fits from an Aalen’s additive regression model for censored data?
I simply wonder why the curves change between plus and minus. Do they have to understand such that ...
- 3,493
1
vote
1
answer
552
views
In data setup for Cox regression, how to handle a subject's time before treatment of interest (i.e. before time-zero)?
Background
I'm designing a study that models time-to-event for two groups of study subject: people who receive a treatment and those who do not. I'm fairly new to applied survival analysis, so I've ...
- 739
0
votes
1
answer
98
views
Reference in survival analysis is not 0
I am conducting survival analysis, investigating the association between a binary factor (TRUE/FALSE) and all cause mortality. I use the ...
- 355
1
vote
1
answer
3k
views
Does the weight option in coxph function fit the weighted cox regression model?
Suppose I have a survival data with the variables time: follow up time, event: event indicator(1 or 0) with 1 as an event and 0 ...
- 313
0
votes
1
answer
146
views
How to calculate 95% CI around the percentage attenuation using a bootstrap method
I am trying to repeat the statistical methods of an article in which Cox regressions were used to compute hazard ratios (HRs) for the association between life-course SES and death. The author created ...
0
votes
1
answer
92
views
Shorten survival analyses and curves
From my survival analyses, I get a survival curve showing a very large number of censures between 4000 and 4500 days, and then a considerable drop due to the decrease in numbers (mostly drop outs).
...
- 165
0
votes
1
answer
535
views
How do I color the points provided in cox.zph plot? [closed]
I'm trying to distinguish between the two groups in this scaled Schoenfeld residuals plot:
As you can see there are two groups for test temperature which I am hypothesizing are split based on 340 C ...
- 13
1
vote
1
answer
374
views
Can one use NRI and IDI in regularized cox-regression?
I have a dataset with 1500 patients for which I want to predict the outcome of death.
I wanted to utilize multivariate cox-regression in a model containing biomarkers and other covariates. I was told ...
- 51
1
vote
1
answer
1k
views
Survival analysis: How to code 'left censored' data?
I have data on the closure of brands of stores and I would like to model the factors that influence the risk of closure. I know all the stores that are open on a certain date, 1st January 2015 (but ...
- 227
0
votes
1
answer
372
views
Cox proportional hazards model with participants dropping out without event
In R, I analyse time-to-event data to explore the effect of a biomarker on an event risk. To do this, I work with data that looks like this toy dataset:
...
- 165
4
votes
1
answer
1k
views
Interpretation of coxph - rsq , cox.zhp, robust and concordance
I would like to get explained the following situations in coxph (library(survival))
The Concordance, what is a good Concordance?
What does it mean ...
- 270
1
vote
1
answer
1k
views
Cox regression in subgroups
I ran an analysis in which I used Cox regression to investigate the relationship between a number of predictor variables and time to death. I used R for that: ...
- 199
5
votes
1
answer
3k
views
0
votes
1
answer
1k
views
Testing the difference between 2 Cox regression models
I am running an ANOVA test on R comparing the results of 2 cox regression models. Model 1 has variableA (binary). Model 2 has the interaction term for variableA * variableB (3 categories).
I'm not ...
- 1
2
votes
1
answer
196
views
Correct way to add both time-varying and time-invariant predictors in coxph()
I have time-varying and time-invariant predictors in my cox model. What will be the correct way to add both of them using coxph()? In my model, income, development, ...
- 211
0
votes
1
answer
540
views
Three-way interaction cox hazard. (Testing the difference in impact of a two-way interaction for two groups)
Some background: For my dissertation I'm working on a survival analysis on the hazard of exiting a firm for men vs women. After doing the basic analysis I want to investigate if the control variables ...
- 11
2
votes
1
answer
693
views
Test/validate a random forest survival model
I have around 7,588 features for 100 subjects with time to event and status data. I have built 100 random forest survival models with 75/25 train-test splits using ...
- 163
0
votes
1
answer
415
views
Cox model with multiple measures does not recognize the number of IDs?
I am running a survival cox model with multiple measures, here is the code:
...
- 3
1
vote
1
answer
166
views
How to plot survival probabilities of cox regression with firth's penalized likelihood?
I am using the coxphf() function (in the coxphf package) in R and am not sure how to plot survival probabilities. Does anyone ...
- 11
5
votes
2
answers
3k
views
Plot of hazard ratio for primary endpoint and continuous covariate
I wonder if you could tell me the R code to use to obtain a graph similar to the one below. (from: https://www.nejm.org/doi/full/10.1056/NEJMoa1215740)
That is, I would like to graph the association ...
- 83
1
vote
1
answer
266
views
Time varying effect in time dependent cox model
In the case of Stanford heart transplant dataset (jasa), is it possible to check if the effect of the time dependent covariate of transplant is time varying as well ? If that's the case can we compute ...
- 15
0
votes
1
answer
658
views
How do you interpret outputs of Cox regression based on data type of an independent categorical variable?
I have the following data frame which consists of a grouping variable, as well as time ans status variables for survival analysis:
...
- 199
0
votes
1
answer
77
views
Time after time-dependent variable in Cox model
I am trying to create a time dependent (covariate) cox regression model for a survival analysis project I am interested in. A brief overview of my dataset:
I have a cohort starting from 2011-01-01, ...
- 15
0
votes
1
answer
67
views
PR estimation of a cross sectional study with a continuous variable possibly by Cox proportional hazard regression
I have a table of a simple cross sectional data:
...
- 101
1
vote
1
answer
835
views
Possible non-linearity pspline Cox model
Our working group ran a Cox regression with a p-spline to model the possible non-linearity of continuous variables. However, I'm a bit confused with the interpretation of the linearity or non-...
- 606
1
vote
2
answers
657
views
Multi-state Cox models: different formulas for different transitions?
I'm using coxph from Therneau et al's survival package to model a multi-state system. Transitions include:
Baseline -> ...
- 363
0
votes
0
answers
360
views
Cox Proportional Hazards Model for panel data
I want to get the same results of implementing cox-box by R for this SAS code,
...
- 31
1
vote
1
answer
256
views
Confirming the censoring state transition with a multi-state Cox model with recurrent events
I am working with data that contains information about the age at which each person enrolled in a study; zero or more hospitalization events for a disease (with age information); the age at which they ...
- 363
2
votes
1
answer
1k
views
Model diagnostics for multi-state models in survival::coxph in R
I am trying to fit a multi-state model using the coxph function from the survival package in R and I want to perform some model ...
0
votes
1
answer
150
views
What should I do if only 1 covariate violate the proportionality assumption in Cox PH?
Can I still use Cox PH model? or I will have to find a non-PH model? What are the available models that can be used here?
Schoenfeld residuals (using ...
- 227
0
votes
1
answer
70
views
Predict risk from pre-trained Cox PH model
I came accross this article about AMD (age-related macular degeneration, a kind of eye diseases) recently. The article fitted a Cox PH model to predict risk of disease advancing to advanced stage. The ...
0
votes
1
answer
790
views
How to compare two models with and without restricted cubic spline by likelihood test? #mice #survival # rms
I’m new to using multiple imputations and I would like an opinion on using it with survival analysis in R.
I would like to perform a multiple imputation on data with missing values (mice package) and ...
0
votes
1
answer
198
views
How to calculate a life table for different baseline groups (Cox survival analysis)
I wish to recreate a table from a study (DOI: 10.1097/MAO.0000000000001914).
The study includes survival analyses on whether or not patients loose their hearing. Hearing is described using two ...
- 13
1
vote
2
answers
579
views
Merging survival data with time varying covariates
In merging the data in R the censored observations are merged well but the observed subjects are not. For example, the second subject had an event at time 0.546. How can I merge the time varying ...
- 137
2
votes
1
answer
5k
views
Survival curve from time-dependent coefficients in the Cox model
I fitted a Cox Model that does not satisfy the proportional hazards assumption. Thus, I included time-dependent coefficients using the tt() function in the same way ...
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