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Questions tagged [cox-regression]

The term Cox regression model (omitting proportional hazards) is sometimes used to describe the extension of the Cox model to include time-dependent factors. However, this usage is potentially ambiguous since the Cox proportional hazards model can itself be described as a regression model.

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R - model.frame() and non-standard evaluation

I am puzzled at a behaviour of a function that I am trying to write. My example comes from the survival package but I think that the question is more general than that. Basically, the following code library(survival) data(bladder) ## this will load…
Theodor
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Adding column of predicted Hazard Ratio to dataframe after Cox Regression in R

I need to add columns of predicted hazard ratio in the dataframe after running Cox PH regression in R. The dataframe is a panel data where numgvkey if firm identifier and age is time identifier. You can download a small section of the date from this…
Jairaj Gupta
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How can I add p-value to my concordance index plot in R?

In my survival analysis task, I have used cox proportional model to calculate concordance index (c-index) value in different groups of my dataset. I was wondering how can I add p-value to my c-index plot to compare different groups to look like this…
user3576287
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How to plot a Cox hazard model with splines

I have a following model: coxph(Surv(fulength, mortality == 1) ~ pspline(predictor)) where is fulength is a duration of follow-up (including mortality), predictor is a predictor of mortality. The output of the command above is this: …
Oposum
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Can I perform all subsets variable selection for a Cox Proportional Hazards Model in R?

I am trying to use a function similar to, if not actually, regsubsets in the leaps package in program R when selecting the top Cox Proportional Hazards models for my data. Is this possible? and if so does a function already exist?
marcellt
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Predicting and Plotting Survival Curve with the CoxPH

I am trying to predict and plot the (estimated) survival curve for a new observation in R. Using the "survival" library and the "lung" data set, I first fit a cox proportional hazards model to the data. Then, I tried to predict and plot the survival…
stats_noob
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Why coxph() results some of the coefficient as NA when using survSplit() in R?

I'm working with survival data, and using survSplit() to deal with non-proportionality with time-dependent coefficients. The model is based on the article by Terry Therneau et. al. (2020)…
Vilponk
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Computing SE or CI for ggadjustedcurves

How can I compute index of variability (SE or CI) for ggadjustedcurves from survminer function? I am using the conditional method. Anyone have any input or resource?
mindhabits
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Feature (Covariates) selection in CoxPHFitter, Lifelines Survival Analysis

i am using this implemented model in Python for the purpose of survival analysis: from lifelines import CoxPHFitter Unfortunately i am not able(i do not know how) to loop over all covariates (features) to run the regression individualy for the…
Antonio Dichev
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Create formula call from character string

I use a best subset selection package to determine the best independent variables from which to build my model (I do have a specific reason for doing this instead of using the best subset object directly). I want to programmatically extract the…
Todd Shannon
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Parameter estimates and variance for stratified variables in Cox regression (strata / survival package)

I have run Cox regression using the survival package to calculate mortality hazard ratio of an exposure A. I have found that the age variable violated the proportional hazard assumption (with cox.zph) and used strata(age)to stratify age in further…
jeanphikri
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Plotting predicted survival curves for continuous covariates in ggplot

How can I plot survival curves for representative values of a continuous covariate in a cox proportional hazards model? Specifically, I would like to do this in ggplot using a "survfit.cox" "survfit" object. This may seem like a question that has…
RNB
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Machine learning models for predicting when some event will occur

Consider the problem where I need to predict when a particular event is going to occur based on the past data (data available with time stamp) available. For example Assume a particular machine is running and we have the data collected from that…
B K
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How to predict survival time in Cox's Regression Model in R?

I have a modeled a problem using Cox's regression and now want to predict the estimated survival time for an individual. The model has a list of covariates on which the survival time depends. This tells us how to calculate P(T>t) which is basically…
statBeginner
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Negative event times encountered; not permitted for Cox family

I am running a coxph model using glmnet. The following is the code that I am using: data <- read.csv("CSM Tiers by Org.csv", stringsAsFactors = FALSE, na.strings = "?") x <- model.matrix(~ data$CSM + data$Exclude + data$Queue) y <- data$Time status…
EsBee
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