Quantcast

Competing-risks nomogram

classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Competing-risks nomogram

Firas Abdollah
Hi R users,

I'd like to draw a nomogram using a competing-risks regression (crr function in R), rather than a cox regression. However, the nomogram function provided in the Design package is not good for this purpose.
Do you have any suggestion.
I really appreciate your help

Many thanks

F.Abdollah, MD
San-Raffele hospital
Milan, Italy
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Competing-risks nomogram

Frank Harrell
Replace the Design package with the rms package.  Use the ordinary linear regression trick to predict the linear predictor from the competing risk regression, then use nomogram on this new model (that merely represents the fit of interest).
Frank
Firas Abdollah wrote
Hi R users,

I'd like to draw a nomogram using a competing-risks regression (crr function in R), rather than a cox regression. However, the nomogram function provided in the Design package is not good for this purpose.
Do you have any suggestion.
I really appreciate your help

Many thanks

F.Abdollah, MD
San-Raffele hospital
Milan, Italy
Frank Harrell
Department of Biostatistics, Vanderbilt University
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Competing-risks nomogram

Firas Abdollah
Many thanks for the prompt response.
However, I am afraid that it is not completely clear for me. I
apologize, I am not a statistician.
Sorry, may be what I will say make totally non sense, but what I
understood is the following:
Let's suppose that I need to predict cancer-specific survival using
the variables X and Y. What I need to do is to develop a model that
include these variables and predict cancer-specific survival using the
competing-risks regression. Then, I shall calculate the "predictions"
of this model at a certain time point, then I shall use these
prediction as an "endpoint", and predict it using a linear regression
model that include the same variables, i.e X and Y. Finally, I use the
coefficients of this final model to develop a nomogram. Is that
correct?

Many thanks again




Should I calculate the "prediction" of the competing-risks regression
model, and then use this "prediction" as an "endpoint" and predict it
using a linear regression by including the same variables as
predictors?

On Fri, Jun 24, 2011 at 1:27 PM, Frank Harrell [via R]
<[hidden email]> wrote:

> Replace the Design package with the rms package.  Use the ordinary linear
> regression trick to predict the linear predictor from the competing risk
> regression, then use nomogram on this new model (that merely represents the
> fit of interest).
> Frank
>
> Firas Abdollah wrote:
> Hi R users,
>
> I'd like to draw a nomogram using a competing-risks regression (crr function
> in R), rather than a cox regression. However, the nomogram function provided
> in the Design package is not good for this purpose.
> Do you have any suggestion.
> I really appreciate your help
>
> Many thanks
>
> F.Abdollah, MD
> San-Raffele hospital
> Milan, Italy
>
> Frank Harrell
> Department of Biostatistics, Vanderbilt University
>
> ________________________________
> If you reply to this email, your message will be added to the discussion
> below:
> http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3622291.html
> To unsubscribe from Competing-risks nomogram, click here.



--
Firas Abdollah, MD
Dept. of Urology
San Raffaele Hospital
Vita-Salute University,
Via Olgettina 60, 20132, Milan, Italy
Tel. +39 02 2643 7286
Fax. +39 02 2643 7298
E-mail: [hidden email]
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Competing-risks nomogram

Frank Harrell
Yes you use the linear predictor from your regression as the dependent variable in the rms package's ols function.  You will get an R^2 of 1.0.  You can depict the ols model with nomogram().  Note that there are so many statistical issues in competing risks that doing this without a statistician is risky.
Frank
Frank Harrell
Department of Biostatistics, Vanderbilt University
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Competing-risks nomogram

Firas Abdollah
Many thanks

On Sat, Jun 25, 2011 at 10:00 PM, Frank Harrell [via R]
<[hidden email]> wrote:

> Yes you use the linear predictor from your regression as the dependent
> variable in the rms package's ols function.  You will get an R^2 of 1.0.
>  You can depict the ols model with nomogram().  Note that there are so many
> statistical issues in competing risks that doing this without a statistician
> is risky.
> Frank
> Frank Harrell
> Department of Biostatistics, Vanderbilt University
>
> ________________________________
> If you reply to this email, your message will be added to the discussion
> below:
> http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3625011.html
> To unsubscribe from Competing-risks nomogram, click here.



--
Firas Abdollah, MD
Dept. of Urology
San Raffaele Hospital
Vita-Salute University,
Via Olgettina 60, 20132, Milan, Italy
Tel. +39 02 2643 7286
Fax. +39 02 2643 7298
E-mail: [hidden email]
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Competing-risks nomogram

rgeskus
In reply to this post by Firas Abdollah
Dear Firas,

Regression on the subdistribution hazard can be performed by fitting a weighted Cox model. See Geskus, Biometrics 67, p. 39-49, 2011. Hence, cph (and coxph) can be used directly; there is no need to use the crr function in cmprsk. The result from the weighted cph fit should allow you to obtain a nomogram for the cause-specific cumulative incidence.

with best regards,

Ronald Geskus
Academic Medical Center
Amsterdam
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Competing-risks nomogram

Firas Abdollah
I will try it out..Thanks a lot

On Mon, Jun 27, 2011 at 10:08 AM, rgeskus [via R]
<[hidden email]> wrote:

> Dear Firas,
>
> Regression on the subdistribution hazard can be performed by fitting a
> weighted Cox model. See Geskus, Biometrics 67, p. 39-49, 2011. Hence, cph
> (and coxph) can be used directly; there is no need to use the crr function
> in cmprsk. The result from the weighted cph fit should allow you to obtain a
> nomogram for the cause-specific cumulative incidence.
>
> with best regards,
>
> Ronald Geskus
> Academic Medical Center
> Amsterdam
>
> ________________________________
> If you reply to this email, your message will be added to the discussion
> below:
> http://r.789695.n4.nabble.com/Competing-risks-nomogram-tp3621907p3627184.html
> To unsubscribe from Competing-risks nomogram, click here.



--
Firas Abdollah, MD
Dept. of Urology
San Raffaele Hospital
Vita-Salute University,
Via Olgettina 60, 20132, Milan, Italy
Tel. +39 02 2643 7286
Fax. +39 02 2643 7298
E-mail: [hidden email]
Loading...