All Questions
493 questions
0
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0
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18
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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 ...
- 857
0
votes
0
answers
31
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 ...
- 857
1
vote
1
answer
43
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
0
votes
1
answer
35
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Time-dependent area under the precision recall
How to compare the time-dependent precision recall (PR) receiver operating curve (ROC) values for two cox regression models at multiple time points?
To compare two time-dependent AUC values, I would ...
- 101
1
vote
1
answer
47
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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
1
answer
39
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`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
132
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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
1
vote
2
answers
49
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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
0
votes
0
answers
26
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Interpretation of coxPH model with and without splines for non-linearity
I am fitting Cox Proportional Hazard Models to investigate the impact of external, military support (my covariate) on the "risk" of a peace agreement (my event of interest) after civil war.
...
- 11
3
votes
1
answer
90
views
Understanding survival curves with time-dependent covariates
In an observational cohort study, I want to assess the impact of exposure to a given prescription drug on mortality. Out of 841,161 patients, 150,279 (17.9%) died during follow-up. Exposure is a time-...
- 209
0
votes
0
answers
33
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Counting process approach in survival analysis with non-contiguous intervals?
I am setting up a Cox Proportional Hazards model in R to analyze survival time until a recurrence event occurs. Each case can experience multiple recurrence events, therefore I decided to emply the ...
- 11
2
votes
1
answer
365
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Dealing with non-proportional hazards in a Cox model with many variables and a large dataset
Summary: I am trying deal with non-proportional hazards in a Cox model on a large dataset. My question is whether the proportional hazards assumption really does not hold? If no, is the second model ...
- 209
1
vote
0
answers
20
views
penalized package [closed]
Has anyone used penalized package? I was using it for lasso in Cox regression, with time-varying coefficients.
The problem is when I made a plot with ...
- 11
0
votes
0
answers
19
views
Time-varying coefficients based on binary variables
I am doing a survival analysis, and for each individual i have one event occuring (the one of interest), then i have baseline events (inc1 & ...
- 143
5
votes
1
answer
261
views
Interpretation of R output for stratified cox-ph model
For the following model:
model <- coxph(formula = Surv(time, status) ~ treatment * sex + strata(sex), data = data)
this is (part of) the model summary in R:
...
- 61
0
votes
1
answer
47
views
In which cases should the time be transformed when plotting the smoothed scaled Schoenfeld residual plot?
I previously asked this question but didn't get any answers, so I'm reposting it now.
I aim to address the argument transform = '' in R, particularly concerning the ...
- 333
0
votes
0
answers
33
views
Sample size for a discrete-time survival model with a time-dependent covariate
How can I calculate the sample size for a prediction model (Cox regression) when the survival time is discrete (up to 6 points) and there is also a time dependent variable (with three categories) in ...
- 107
7
votes
1
answer
422
views
Diagnosing an unexpected pattern in a survival curve plot
I am conducting a survival analysis (using Cox proportional hazards regression) in R. My overall sample has a ~10% mortality rate, but the Kaplan-Meier survival curves that are derived from my ...
- 97
1
vote
1
answer
80
views
Should the curve be around zero when assessing the smoothed scaled Schoenfeld residual plot for proportional hazard assumption?
I'm using the smoothed scaled Schoenfeld residual plot to assess the proportional hazard assumption. I have a decent understanding of what a smoothed scaled Schoenfeld residual plot shows, but I'm ...
- 333
0
votes
1
answer
48
views
Does it make sense to convert the Y-axis by exp() on the smooth scaled schoenfeld residual plot?
I posted a question on Stack Overflow. But the question got closed as the person who closed it wrote that it should belong here in Stack Exchange. I'm not sure why but here is the link for the post. I'...
- 333
0
votes
0
answers
46
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Constructing nomogram from approximate model in Regression Modelling Strategies
In section 19.5 in Regression Modelling Strategies by Frank Harrell we make an approximate model using linear regression with ols. Since this is an ols object we have to calculate survival quantities ...
- 101
0
votes
0
answers
34
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Why would independences tests show significant correlation between variables while VIF shows no multicollinearity?
When conducting independence tests among the variables, some exhibit significant correlations, yet the VIF analysis indicates no multicollinearity. Is this common, and what implications does it hold ...
- 31
0
votes
0
answers
45
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Fitting a Discrete-time survival analysis
I am trying to fit a discrete-time survival analysis using R. My overall goal is to check if the variable pain impacts smoking. Every time I include the variable ...
3
votes
1
answer
600
views
How should I be interpreting martingale residuals and zph?
I'm new to survival analysis and am practicing on the AIDS Clinical Trials Group Study 175 Data from the UCI Machine Learning Repository. After using R to fit the Cox PH model, I made a plot to look ...
- 31
2
votes
1
answer
121
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When should the robust error function in R be used in Cox proportional hazard regressions?
Let's consider a scenario where I compute a HR that appears to violate the proportional hazard assumption according to the cox.zph test, but when plotting the ...
- 333
1
vote
1
answer
143
views
How do I interpret the HRs for each time interval computed by survSplit in R?
I’m testing the association between an exposure and outcome. I have performed a Cox proportional hazard model in R and estimated a HR. Both the exposure and the outcome are binary variables, where 1 = ...
- 333
11
votes
1
answer
768
views
SAS and R produced different results for the same cox ph model on the same data
I have fitted a Cox ph model using both R 4.3.1 and SAS 9.4 with the same data. In SAS, I used Proc phreg, while coxph function ...
- 123
0
votes
1
answer
112
views
Cox regression with two-way interaction and interaction p value
Hi I am using Cox regression to do some survival analysis.
I have one continous predictor variable called "biomarker" and two binary categorical variables sex and diabetes.
I want to get the ...
- 51
0
votes
1
answer
66
views
non-significant p value in a multivariable cox regression following exhaustive model selection
I run an exhaustive model selection for Cox proportional hazard in R using "glmulti" package. I used the best model for creating multivariable Cox regression. In the multivariable Cox hazard,...
0
votes
2
answers
69
views
how to deal with exposure measurements long before inclusion using cox model
I have a longitudinal data with exposure air pollution and outcome cardiovascular disease. The inclusion starts from 2010 to 2017 and then I followed until 2021. I have measurement of pollution from ...
- 139
1
vote
1
answer
54
views
coxph function gave a weird hazard ratio in my simulation case
I fit three Cox models. The three hazard ratios are 0.52, 1.02, and 0.514, respectively. The first hazard ratio is the hazard ratio between the treatment arm and the control arm. The second is the ...
- 11
4
votes
1
answer
183
views
smooth scaled Schoenfeld residual plot - how to interpret the plot which is based on a stratified cox model?
I understand what a Smoothed scaled Schoenfeld residual plot is, and what it shows.
Before I go into details with my question, I will provide an example.
I use R to code.
Here is a cox model:
...
- 333
3
votes
1
answer
118
views
smooth scaled Schoenfeld residual plot - covariates with levels
I'm working with cox proportional hazard (cox-PH) in R. I'm using the smoothed scaled Schoenfeld residual plot to assess the PH assumption.
Suppose I have this model in R, disease as outcome and ...
- 333
0
votes
0
answers
14
views
Disaster exposure as treatment in survival analysis - multiple "treatments" / pre-"treatment" trends (in R)
I am looking at using a cox proportional hazards model to look at migration after disasters. I have two disasters at T1 and T2 (which are two years apart). I created two models looking at the risk of ...
- 399
0
votes
1
answer
166
views
Interpreting a Schoenfeld plot for Cox PH univariate model and correcting for violation of PH assumption (R)
I am having trouble understanding how to interpret a Schoenfeld plot and how to correct for the violation of PH assumption in Cox PH model when using continuous numeric covariates.
Here is the code I ...
1
vote
1
answer
79
views
Calculating overall survival probability for being a part of a group in Cox regression
I have created a mixed-effects Cox regression in r:
This can be created in coxph:
...
- 37
0
votes
1
answer
85
views
How to deal with missing survival times using Cox PH model (R)?
I have been working with a dataset that I would like to analyze using the Cox PH model in R. The data I have includes:
a start measurement year
an estimated mortality year
survival time that is the ...
2
votes
2
answers
230
views
CoxPH with one ID contributing many comparator observations
UPDATE-----------------
I have data where one ID can serve as a comparator several times.
This is done by creating a variable to group the treated in variable GROUP....
- 171
1
vote
1
answer
1k
views
violation of cox proportional hazard assumption
I'm using cox regression to analyse my data. The explanatory variable is a congenital disease (X) and the outcome is an another disease (Y), which is a comorbidity of the congenital disease. I'm ...
- 333
6
votes
1
answer
218
views
Causal survival analysis in a large prospective cohort when treating incident events as the exposure
I'm currently working on a large prospective cohort with the basic demographic characteristics and various socioeconomic factors collected at baseline. This cohort was follow up since baseline entry ...
- 63
1
vote
0
answers
172
views
Cox model with ridge term: how to choose value of theta?
The coxph() function in R package "survival" is used to fit the Cox proportional hazards model. This function allows a ridge() term in the formula to penalise selected terms, which requires ...
- 923
0
votes
0
answers
43
views
Why is my Cox-regression bootstrapped p-value so different from the statistically derived p-value?
It's been years since I've looked at this or the R language, so I'd appreciate some help and simple explanations (I'm not a statistician).
Using bootstrap analysis, I'm trying to derive the p-value of ...
- 605
0
votes
1
answer
203
views
Reason for getting NA in a single category of a categorical variable in a Cox model
I have a Cox model with time dependent variables as follows, where ibd is a categorical variable with 3 levels.
However, I am not sure why there is a NA for regression coefficient in the last level of ...
- 13
0
votes
1
answer
90
views
(Cumulative) baseline hazard in cox models with time-dependent coefficients
I would like to know if there is an easy way to estimate the (cumulative) baseline hazard from a cox model with time-varying coefficients over different time intervals. After creating the time ...
0
votes
1
answer
30
views
Different results between Cox regression models when using Surv in different ways?
Why results are different between the two examples of Cox models where Surv was defined in different ways?
...
- 15
1
vote
1
answer
59
views
Multiple events in Cox PH with time varying data
I study coups d'etat. I would like to understand the relationship between leader/country characteristics and the likelihood of coup attempts.
I have a leader-country-year dataset with one entry for ...
- 173
3
votes
1
answer
1k
views
Schoenfeld residuals for factors with cox.zph
The cox.zph function of the survival package computes the Schoenfeld residuals for each variable and tests the porportionality assumption with a score test, but I ...
0
votes
1
answer
487
views
How to calculate score residual for cox ph model?
I try to understand the "score residual" from cox ph model in R.
There is one reference site I have used for it.
Can someone help me to get the score residual manually (I mean, using formula)...
0
votes
1
answer
75
views
Stratification vs. point estimates for a cox proportional hazards model?
I am fitting a cox proportional hazards model looking at mortality. I have a number of covariates and a specific predictor of interest (inflammation), and I am also looking at how the effect of ...
- 85
2
votes
1
answer
37
views
A survival model with multiple concomitant survival events
I would like to know if there is a statistical model to analyze my problem:
I want to test if the location of the tumor is related to the level of a particular biomarker
A patient may have multiple ...
- 633