selectFGR - variable selection in fine gray model for competing risks

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selectFGR - variable selection in fine gray model for competing risks

Raja, Dr. Edwin Amalraj
Dear All,

   I would like to use R function 'selectFGR' of fine gray model in competing risks model.  I used the 'Melanoma' data in 'riskRegression' package.  Some of the variables are factor.  I get solution for full model but not in variable selection model.  Any advice how to use factor variable in 'selectFGR' function.  The following R code is produced below for reproducibility.

library(riskRegression)
library(pec)
dat <-data(Melanoma,package="riskRegression")
Melanoma$logthick <- log(Melanoma$thick)
f1 <- Hist(time,status)~age+sex+epicel+ulcer
df1 <-FGR(f1,cause=1, data=Melanoma)
df1
df <-selectFGR(f1, data=Melanoma, rule ="BIC",  direction="backward")

Thanks in advice for your suggestion. Is there any alternative solution ?

Regards
Amalraj raja


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
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Re: selectFGR - variable selection in fine gray model for competing risks

Thomas Alexander Gerds
Dear Raja

the technical problem is that the function crrstep does not communicate
the selected variables in a proper way. the function pec::selectFGR uses
rownames(crrstep.fit$coefficients). the other problem is that I don't
like and never use backward elemination -- so, I am not motivated to fix
this. However, I copy this email to Rob van Kruijsdijk who wrote the
function ... maybe he wants to fix. you can always fix this yourself by
copying the functions selectFGR, predictEventProb.selectFGR.

Best Thomas


"Raja, Dr. Edwin Amalraj" <[hidden email]> writes:

> Dear All,
>
>    I would like to use R function 'selectFGR' of fine gray model in
> competing risks model.  I used the 'Melanoma' data in 'riskRegression'
> package.  Some of the variables are factor.  I get solution for full
> model but not in variable selection model.  Any advice how to use
> factor variable in 'selectFGR' function.  The following R code is
> produced below for reproducibility.
>
> library(riskRegression)
> library(pec)
> dat <-data(Melanoma,package="riskRegression")
> Melanoma$logthick <- log(Melanoma$thick)
> f1 <- Hist(time,status)~age+sex+epicel+ulcer
> df1 <-FGR(f1,cause=1, data=Melanoma)
> df1
> df <-selectFGR(f1, data=Melanoma, rule ="BIC",  direction="backward")
>
> Thanks in advice for your suggestion. Is there any alternative solution ?
>
> Regards
> Amalraj raja
>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

--
7LL-4 No one is the reason for your happiness except you yourself.

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[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.
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Re: selectFGR - variable selection in fine gray model for competing risks

rgeskus
In reply to this post by Raja, Dr. Edwin Amalraj
Dear Raja,

A Fine and Gray model can be fitted using the standard coxph function with
weights that correct for right censoring and left truncation. Hence I
guess any function that allows to perform stepwise regression with coxph
should work. See e.g. my article in Biometrics
https://doi.org/10.1111/j.1541-0420.2010.01420.x, or the vignette
"Multi-state models and competing risks" in the survival package.

best regards,

Ronald Geskus, PhD
head of biostatistics group
Oxford University Clinical Research unit
Ho Chi Minh city, Vietnam
associate professor University of Oxford
http://www.oucru.org/dr-ronald-b-geskus/

"Raja, Dr. Edwin Amalraj" <[hidden email]> writes:

> Dear All,
>
>    I would like to use R function 'selectFGR' of fine gray model in
> competing risks model.  I used the 'Melanoma' data in 'riskRegression'
> package.  Some of the variables are factor.  I get solution for full
> model but not in variable selection model.  Any advice how to use
> factor variable in 'selectFGR' function.  The following R code is
> produced below for reproducibility.
>
> library(riskRegression)
> library(pec)
> dat <-data(Melanoma,package="riskRegression")
> Melanoma$logthick <- log(Melanoma$thick)
> f1 <- Hist(time,status)~age+sex+epicel+ulcer
> df1 <-FGR(f1,cause=1, data=Melanoma)
> df1
> df <-selectFGR(f1, data=Melanoma, rule ="BIC",  direction="backward")
>
> Thanks in advice for your suggestion. Is there any alternative solution ?
>
> Regards
> Amalraj raja
>
>
> The University of Aberdeen is a charity registered in Scotland, No
SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir.
SC013683.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.