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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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the constant of the Cox model

I have computed a prognostic model using the Cox model (coxph function in R). I provide the standardised regression coefficients in my paper. However, a reviewer ask me to give the constant of the Cox model. Is it the same than the baseline…
Joeloutre
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Age as a time scale in survival analysis

In survival analysis, you measure the time from some startpoint and right censor your data. The code thus usually looks like this: fit <- coxph(Surv(time, status) ~ outcome + x1 + x2, data=db) However, in epidemiological analysis, the startpoint…
Dan Chaltiel
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CoxPHFitter: The input must have at least 3 entries

I am trying to run lifelines' CoxPHFitter (python3) and i get this value error: The input must have at least 3 entries! i've read the function it connects to at stats but im not sure how to imply the error to the data i have so i could run it…
Asael Bar Ilan
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coxph in R, beta affected by value of factor?

I'm running a coxph right now. My setup: I have a reference (no treatment), and then three different treatments (A, B, and C). I also have the interactions of A, B, and C, (e.g. samples treated with both treatment A and B, or A and C, etc...). I…
Crawdaunt
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Fine & Gray regression error

fg1<- crr(fu, exitus1, gfr, tdm, failcode=1, cencode=0) summary(fg1) I obtain this error and I don't understand why and how to fix it: Error in tf(uft) : argument "tf" is missing, with no default Here are my data: > str(fu) num [1:87] 15 27…
ArTu
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Survival analysis with time varying covariates using coxph in R

This is a snapshot of the R data frame df1 that I have. NEW_UPC IRI_KEY WEEK UNITS DOLLARS F D PR 11820005991 1073521 1230 1 14.29 NONE 0 0 11820005991 1073521 1232 1 …
Rnovice
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Cox regression : Are we supposed to keep the status column for test?

From the examples that I have seen for cox-regression: http://www.sthda.com/english/wiki/cox-proportional-hazards-model , the data includes the status or event column as well. But if I wish to train the cox model on train data, and then use the…
rj dj
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What is the "linear.predictors" in the result of cox?

I analyzed cox proportional hazard regression with example data. My R code is below. install.packages("randomForestSRC") install.packages("survival") library(randomForestSRC) library(survival) data(pbc, package="randomForestSRC") pbc.na <-…
SJUNLEE
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Plot a quadratic relation for a predictor of a cox regression with R

I need to plot the relative risk for a quadratic effect in a cox regression. My model looks like this: cox_mod <- coxph(Surv(time, status) ~ ph.karno + pat.karno + meal.cal + meal.cal_q, data = lung) Where meal.cal_q is…
user9413061
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Extimate prediction accuracy of cox ph

i would like to develop a cox proportional hazard model with r, use it to predict input and evaluate the accuracy of the model. For the evaluation I would like to use the Brior score. # import various packages, needed at some point of the…
User12547645
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Formatting data for survival analysis - time variable in long form data

I'm new to survival analysis, and am unsure if I'm formatting my data correctly. Using this dummy data: id <- c(rep("1", 10), rep("2", 10), rep("3", 10), rep("4", 10), rep("5", 10)) age <- c((15:24), (35:44), (45:54), (55:64), (40:49)) event <-…
T.P.
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adjust axis and colours figure simPH package R

I'm using the simPH package to plot hazard ratio's. As my variable is time, I would rather change the ticks and intervals at the x-axis to 0,30,60,90 etc instead of 0,50,100,150 which is currently plotted based on my data (x ranges from 0 to 180).…
LHey
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effect modification from coxph in R

I am investigating effect modification in the context of a time-varying cox model in R. My model is as follows: fit1.1<- with (data, coxph(Surv(startdays, enddays, event) ~ age*strata(Region) + BMI.time.var + cluster(id), ties="breslow")) I get the…
Trenton Honda
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How do I extract an individual graph from ggcoxdiagnostics dfBeta output in R?

Running ggcoxdiagnostics to produce dfBeta plots for a multivariate coxph regression model. require(survival) require(survminer) # Dummy data set.seed(100) permth_int <- seq(10) mortstat <- c(rep(1,9),0) age <- runif(10,50,70) sex …
Duncan McGregor
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IDI.INF function to compare the performance of two Cox regression models

I would like to use the IDI.INF function from the survIDINRI package to the performance of two Cox regression models. For this purpose, I have used the following script: > D=subset(Dataset, select=c("time","status","Var1","Var2","Var3", "Var4",…
Triade
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