All Questions
52 questions
0
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19
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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
32
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
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
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
1
vote
1
answer
519
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Using multiple genes building gene signature and survival analysis
This is the paper which is kind of I'm trying to implement based on my set of genes which i have narrowed down from WGCNA analysis.
Its a both conceptual and R related question[How to do it in R] my ...
- 235
1
vote
1
answer
144
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Difference between family = gaussian() and family = cox.ph(link='identity') in GAM and family = binomial(link="logit")
I wonder how do u decide if family = gaussian() or family = cox.ph(link='identity') or ...
- 165
2
votes
1
answer
119
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Is it possible to generate a scatterplot of relative hazard for participants superimposed on Cox regression line?
I have been using the rms package in R to perform Cox regression on time-to-event data. I have used the ...
0
votes
1
answer
349
views
Cox time-varying coefficient memory allocation issue
I'm trying to add time-varying coefficients using the tt() function with coxph to solve the problem of PH violations in my Cox ...
- 409
1
vote
1
answer
383
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Hazard ratio from Royston-Parmar model (flexsurv::flexsurvspline)
I have a covariate with time-varying coefficient with two categories (lets call it T), which I have modeled using the Royston-Parmar model from flexsurv package as following.
...
- 397
3
votes
2
answers
3k
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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
1
vote
0
answers
49
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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
1
answer
552
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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 ...
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0
votes
1
answer
1k
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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
0
votes
1
answer
658
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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
150
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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
4
votes
1
answer
2k
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Cox PH model and regression with log-log link function: is there a connection?
In this post: interpreting estimates of cloglog logistic regression, I read that when interpreting the results of a regression with a log-log link function, the exponent of the estimated coefficient ...
1
vote
1
answer
1k
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Evaluating Functional Form in Cox Regression using rcs
I was approaching Cox regression and need to evaluate whether is more suitable to model my independent variable as a non-linear prediction of the outcome.
Main questions is:
How do I check whether or ...
- 706
2
votes
1
answer
2k
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Estimating survival curves from Cox regression results
I can understand that it is possible to estimate survival curves directly from the results of a Cox regression.
The way it can be done, mathematically, is furthermore very nicely explained in this ...
- 21
0
votes
3
answers
4k
views
Cox regression with multiple factors [R]
I'm running a Cox regression with three different groups...
...
- 105
0
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0
answers
20
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In cox model, can the hemoglobin and homoglobin group be put in the same model?
fit.tdc <-
coxph(Surv(t1,t2,status) ~ Hemoglobingroup + hemoglobin + sex +
diabet + cluster(id), data)
fit.tdc
Can the hemoglobin and hemoglobin group be put ...
- 11
1
vote
1
answer
143
views
Presentation of a 3x3 categorical interaction for Cox proportional hazards regression using RMS package
I wanted to verify my presentation of a 3x3 interaction of two categorical variables var1 (exposure of interest) and var2 (effect modifier of interest) using the rms...
- 11
0
votes
2
answers
1k
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Calculating the Hazard Ratio for a Cox-regression model stratified by a variable (R)
I have built a Cox-regression model for 6 month mortality. When I created the original Kaplan–Meier curve, grouped by my variable of interest (hospital-acquired infection, Present vs Absent) the ...
- 41
2
votes
1
answer
304
views
Cox proportional hazards with left-censored time-dependent covariates
I'm doing statistical analysis on a cancer study. My specific dataset contains id, various co-variates such as age, sex, metastatic burden, etc. and time to event data for overall survival
I want to ...
- 55
3
votes
2
answers
186
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Should I use Cox model?
In a study of crowdfunding, I am investigating the relationship between the reputation of a person seeking funding for a project (a continuous variable) and the proportion of funding target received (...
- 715
2
votes
1
answer
2k
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Cox PH - R 'rms' package - Concordance (Train, CV & Test)
Please could someone verify if my methodology for calculating these three versions of concordance are correct when using the rms package? I have really struggled to ...
- 479
5
votes
0
answers
4k
views
How to better understand when to use Weibull AFT versus Cox Model for Failure Data
I am struggling to understand when I should consider using a Cox regression model versus using a Weibull AFT model to predict the end of life of mechanical components.
I have tried to apply the Cox ...
- 95
1
vote
1
answer
771
views
Interaction not significant in Cox regression model?
I ran a cox model with an interaction between two categorical variables (sex and treatment group) included like:
...
- 381
1
vote
1
answer
1k
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Baseline hazard function is the hazard function obtained when all covariates are set to zero
I am trying to learn Cox proportional hazard model but I have hit a wall with the basehaz function.
Lets suppose for example I have some data that I want to use ...
- 33
2
votes
2
answers
5k
views
How to choose the best combination of covariates in Cox multiple regression?
I am performing a multivariate Cox regression analysis, and would like to find what combination of those covariates best predict my outcome.
Say I have a list of candidate genes whose expressions ...
- 21
1
vote
1
answer
106
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Cox Regression and Linkage Disequilibrium
I'm trying to figure out the best way to account for linkage disequilibrium in a cox regression, and would really appreciate your advice. I'm testing the effect of a particular allele on overall ...
- 41
2
votes
2
answers
547
views
How can I visualize fitting survival data to a proportional hazards model with a continuous variable?
I have (censored) survival data that I am fitting with a proportional hazards model with a continuous covariate, X (for my purposes, X ranges from 0 to 1). After fitting the model, I get a ...
- 121
0
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1
answer
2k
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How to interpret Coxnet in R?
I am using Coxnet package for a dataset of 457 observations and 180 variables and also for another dataset of 457 observations and 25000 variables.
...
7
votes
1
answer
11k
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How to interpret concordance index in Cox models?
I'm new using the survival package in R. Consider an example provided with the package:
...
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4
votes
1
answer
2k
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Cox survival data with time-varying continuous variable and time fixed covariate
I am interested in the paper entitled "Generating survival times to simulate Cox proportional hazards models with time-varying covariates " (Stat Med. 2012 Dec 20;31(29):3946-58.),and want to simulate ...
- 183
2
votes
1
answer
1k
views
What if linearity doesn't hold in a cox model?
I have built a multivariable cox model with coxph(). However, I am unable to run ggcoxfunctional() on some of the variables because of missing data.
...
- 165
3
votes
1
answer
691
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Cox Proportional-Hazards Regression vs. Regression modeling of competing risk using Fine and Gray
30000 patients all have one diagnosis in common, 3000 of them have been exposed to a potential risk factor before the common diagnosis. 1500 patients develop a malignancy after the common diagnosis.
...
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1
vote
1
answer
6k
views
Why are SPSS and R producing different results for a cox regression on the same data, with the same model specification?
I've performed a cox regression in rstudio (version 1.0.136) using the coxph function in the package "OIsurv". I've also performed the same analysis on SPSS using the same dataset, but i keep on ...
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0
votes
1
answer
2k
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How to use survival model to predict when there are time dependent continuous covariates
In my practical projects, I usually track a group of people for a few months, then I run a model based on the first few months behavior. Hopefully I can predict both overall and individual level's ...
- 21
5
votes
1
answer
7k
views
Can a Cox Proportional-Hazards Model be built only with continuous predictors
The literature on Survival Analysis is mainly from the Medical science where tipically the researcher want to evaluate the effect of a treatment to that of another one. So far, all the example I read ...
- 349
1
vote
1
answer
817
views
How to get Cox p-value for 20,000 genes?
If you run the following code, you will have a data frame real.dat which has 1063 samples for 20531 genes. There are 2 extra columns named ...
- 101
7
votes
1
answer
5k
views
Relative importance of variables in Cox regression
I've understood that relative importance of predictors is a tricky question. Suggested methods range from very complex models to very simple variable transformations. I've understood that the ...
- 2,403
1
vote
1
answer
391
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Comparing regression models with different coding of the same linear predictor
How can I determine whether one coding of a linear predictor leads to a better fit of the corresponding regression model than the other?
In the following example, the restricted cubic spline coding of ...
- 575
7
votes
1
answer
1k
views
Time varying coefficient in Cox model
I have a model for survival after an injury that is borderline passing the Schoenfeld test for the proportional hazards assumption (cox.zph() in R).
However, ...
- 1,333
7
votes
1
answer
4k
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Interpretation of coefficients of glmnet - LASSO/Cox model?
I have done a LASSO / Cox model run for a large dataset of 10K observations which has 1200 Variables.
...
- 85
2
votes
1
answer
108
views
R adds unexpected variable to interaction model
Not sure if this is more of a programming question (in which case please move to stack overflow) or a statistical model question (in which case, please read on!)
I'm exploring a data set and doing ...
- 10.2k
7
votes
1
answer
6k
views
Difference in chi-squared calculated by anova from cph and coxph
Is there a difference between chi-squared (from coxph -> anova) and Wald chi-squared (from ...
- 575
8
votes
2
answers
2k
views
Cumulative Hazard Function where "status" is dependent on "time"
This question is in relation to a dataset I've previously discussed here.
I'm trying to determine whether a treatment affects not only the number of visits a patient has to the doctor, but also how ...
- 458
5
votes
1
answer
5k
views
Using the calibrate function in rms package for Cox model: use 'hare' method or 'KM'?
I'm creating a calibration plot for my breast cancer prognostic Cox model, which doesn't include any fancy transformations, using the calibrate() function in the <...
- 927
2
votes
1
answer
1k
views
Simulation Analysis of a Cox Survival Model with Change Point.
I wish to simulate survival data for the following probabilistic model which will be analyzed using a Cox model:
An exposure $X$ is modeled as binary having $X \sim_{iid} \mbox{Bernoulli}(p)$ where $...
- 401
9
votes
3
answers
17k
views
Computing c-index for an external validation of a Cox PH model with R
First off, I'll state that I'm aware many questions get asked about the c-index. I've searched this site and others, and I haven't found an answer for my situation. I can successfully use ...
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