From: Frank Harrell <f.harrell_at_vanderbilt.edu>

Date: Fri, 06 May 2011 11:30:00 -0700 (PDT)

Frank Harrell

Department of Biostatistics, Vanderbilt University

Date: Fri, 06 May 2011 11:30:00 -0700 (PDT)

Don't attach the Design package. Use only rms. Please provide the output of lrm (print the f object). With such a strong model make sure you do not have a circularity somewhere. With nomogram you can specify ranges for the predictors; default is 10th smallest to 10th largest.

rms will not make customized nomograms such as the one you included.

Frank

Hi all R users,

Thanks Frank for your advices

In fact I posted all my script. In the R Help, the script for nomogram is
long and I took only the part what I think interesting in my case.
I use informations from( datadist {Design} and rms {rms}) in the help of R
software to do my code.

I see that I progress with my nomogram. Because with the following code
where I put my real variables names:

library(Design)

library(rms)

d <- datadist(Fire)

options(datadist='d')

f<-lrm(Ignition~FMC+Charge,data=Fire)

summary(f,FMC=c(0,506.40),Charge=c(45,646)) # min and max of FMC: 0 ,506.40
and the min and max of Charge: 45, 646

plot(Predict(f,FMC=0:506.40,Charge=646))
plot(nomogram(f, interact=list(Charge= c(.2,.7)))) # sorry, not understand
vector c(.2,.7) from R help

As result, I have the figure 1 then figure 2 but there is a problem. Because
the 3rd line of Figure 2 "Charge" must to go 0 until 650.
Also the linear predictor must to go 0 until 1.
http://r.789695.n4.nabble.com/file/n3503828/nomo.jpeg
http://r.789695.n4.nabble.com/file/n3503828/nomogram.jpeg
After, is it possible to draw my nomogram like the 3rd graph that I found in
Internet, it is easier to understand.

http://r.789695.n4.nabble.com/file/n3503828/nogramme.bmp
Nb: I Apologize for my bad english

Thanks for your help

Komine

PhD student

Dakar _Sénégal

West Africa

Komine wrote:

*>
*

> Hi all R users

*> I did a logistic regression with my binary variable Y (0/1) and 2
**> explanatory variables.
**> Now I try to draw my nomogram with predictive value. I visited the help of
**> R but I have problem to understand well the example. When I use glm
**> fonction, I have a problem, thus I use lrm. My code is:
**> modele<-lrm(Y~L+P,data=donnee)
**> fun<- function(x) plogis(x-modele$coef[1]+modele$coef[2])
**> f <- Newlabels(modele,c(L="poids",P="taille"))
**> nomogram(f, fun=list('Prob Y<=1'=plogis),
**> fun.at=c(seq(0,1,by=.1),.95,.99),
**> lmgp=.1, cex.axis=.6)
**> fun.at=c(.01,.05,seq(.1,.9,by=.1),.95,.99),
**> lmgp=.2, cex.axis=.6)
**> options(Fire=NULL)
**> Result is bad and I have this following error message:
**> Erreur dans value.chk(at, i, NA, -nint, Limval, type.range = "full") :
**> variable L does not have limits defined by datadist
**>
**> Could you help me on the code to draw nomogram.
**> Nb: my English is low, I apologize.
**> Thank for your help
**> Komine
**>
*

Komine wrote:

*>
*

> Hi all R users

*> I did a logistic regression with my binary variable Y (0/1) and 2
**> explanatory variables.
**> Now I try to draw my nomogram with predictive value. I visited the help of
**> R but I have problem to understand well the example. When I use glm
**> fonction, I have a problem, thus I use lrm. My code is:
**> modele<-lrm(Y~L+P,data=donnee)
**> fun<- function(x) plogis(x-modele$coef[1]+modele$coef[2])
**> f <- Newlabels(modele,c(L="poids",P="taille"))
**> nomogram(f, fun=list('Prob Y<=1'=plogis),
**> fun.at=c(seq(0,1,by=.1),.95,.99),
**> lmgp=.1, cex.axis=.6)
**> fun.at=c(.01,.05,seq(.1,.9,by=.1),.95,.99),
**> lmgp=.2, cex.axis=.6)
**> options(Fire=NULL)
**> Result is bad and I have this following error message:
**> Erreur dans value.chk(at, i, NA, -nint, Limval, type.range = "full") :
**> variable L does not have limits defined by datadist
**>
**> Could you help me on the code to draw nomogram.
**> Nb: my English is low, I apologize.
**> Thank for your help
**> Komine
**>
*

Komine wrote:

*>
*

> Hi all R users

*> I did a logistic regression with my binary variable Y (0/1) and 2
**> explanatory variables.
**> Now I try to draw my nomogram with predictive value. I visited the help of
**> R but I have problem to understand well the example. When I use glm
**> fonction, I have a problem, thus I use lrm. My code is:
**> modele<-lrm(Y~L+P,data=donnee)
**> fun<- function(x) plogis(x-modele$coef[1]+modele$coef[2])
**> f <- Newlabels(modele,c(L="poids",P="taille"))
**> nomogram(f, fun=list('Prob Y<=1'=plogis),
**> fun.at=c(seq(0,1,by=.1),.95,.99),
**> lmgp=.1, cex.axis=.6)
**> fun.at=c(.01,.05,seq(.1,.9,by=.1),.95,.99),
**> lmgp=.2, cex.axis=.6)
**> options(Fire=NULL)
**> Result is bad and I have this following error message:
**> Erreur dans value.chk(at, i, NA, -nint, Limval, type.range = "full") :
**> variable L does not have limits defined by datadist
**>
**> Could you help me on the code to draw nomogram.
**> Nb: my English is low, I apologize.
**> Thank for your help
**> Komine
**>
*

*>
*

> Hi all R users

*> I did a logistic regression with my binary variable Y (0/1) and 2
**> explanatory variables.
**> Now I try to draw my nomogram with predictive value. I visited the help of
**> R but I have problem to understand well the example. When I use glm
**> fonction, I have a problem, thus I use lrm. My code is:
**> modele<-lrm(Y~L+P,data=donnee)
**> fun<- function(x) plogis(x-modele$coef[1]+modele$coef[2])
**> f <- Newlabels(modele,c(L="poids",P="taille"))
**> nomogram(f, fun=list('Prob Y<=1'=plogis),
**> fun.at=c(seq(0,1,by=.1),.95,.99),
**> lmgp=.1, cex.axis=.6)
**> fun.at=c(.01,.05,seq(.1,.9,by=.1),.95,.99),
**> lmgp=.2, cex.axis=.6)
**> options(Fire=NULL)
**> Result is bad and I have this following error message:
**> Erreur dans value.chk(at, i, NA, -nint, Limval, type.range = "full") :
**> variable L does not have limits defined by datadist
**>
**> Could you help me on the code to draw nomogram.
**> Nb: my English is low, I apologize.
**> Thank for your help
**> Komine
**>
*

Frank Harrell

Department of Biostatistics, Vanderbilt University

-- View this message in context: http://r.789695.n4.nabble.com/Draw-a-nomogram-after-glm-tp3498144p3503857.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help_at_r-project.org mailing list 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.Received on Fri 06 May 2011 - 18:38:47 GMT

This quarter's messages: by month, or sorted: [ by date ] [ by thread ] [ by subject ] [ by author ]

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Fri 06 May 2011 - 18:40:05 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*