Re: [R] Draw a nomogram after glm

From: Frank Harrell <f.harrell_at_vanderbilt.edu>
Date: Tue, 10 May 2011 05:56:45 -0700 (PDT)

by is not an argument to c( )
datadist needs to know the final coding of variables so run it after doing any re-codes.
You are using the wrong syntax for interact= Please take a while to read the full documentation before responding further, and read my earlier posts.
Frank

Komine wrote:
>
> Hi,
> I try always to do my nomogram. I change little my code in order to
> definite the range of my linear predictor.
> But I do not succeed to have 0 until 1. I tried this code.
> library(rms)
> d <- datadist(Fire)
> options(datadist='d')
> Fire$Ignition=c(0,1,by=0.1)
> f<-lrm(Ignition~FMC+Charge,data=Fire)
> print(f)
> summary(f,FMC=c(0,506.40),Charge=c(45,646))
> plot(nomogram(f, interact=list(FMC,Charge)))
>
> The result is:
>

>> print(f)

>
> Logistic Regression Model
>
> lrm(formula = Ignition ~ FMC + Charge, data = Fire)
>
> Model Likelihood Discrimination Rank Discrim.
> Ratio Test Indexes Indexes
>
> Obs 231 LR chi2 0.04 R2 0.000 C 0.501
> 0 77 d.f. 2 g 0.026 Dxy 0.002
> 0.1 77 Pr(> chi2) 0.9796 gr 1.026 gamma 0.003
> 1 77 gp 0.006 tau-a 0.002
> max |deriv| 7e-13 Brier 0.222
>
>
> Coef S.E. Wald Z Pr(>|Z|)
> y>=0.1 0.6832 0.3018 2.26 0.0236
> y>=1 -0.7033 0.3020 -2.33 0.0199
> FMC 0.0002 0.0011 0.18 0.8601
> Charge -0.0001 0.0009 -0.07 0.9424
>
>
>> summary(f,FMC=c(0,506.40),Charge=c(45,646)) 

> Effects Response : Ignition
>
> Factor Low High Diff. Effect S.E. Lower 0.95 Upper 0.95
> FMC 0 506.4 506.4 0.10 0.58 -1.04 1.24
> Odds Ratio 0 506.4 506.4 1.11 NA 0.36 3.45
> Charge 45 646.0 601.0 -0.04 0.55 -1.11 1.03
> Odds Ratio 45 646.0 601.0 0.96 NA 0.33 2.81
>> plot(nomogram(f, interact=list(FMC,Charge)))
> http://r.789695.n4.nabble.com/file/n3511218/nomogram_2.jpeg
> Please can I do to have linear predictor between 0 to 1.
> Thanks very much for your Help
> Komine
>


Frank Harrell
Department of Biostatistics, Vanderbilt University
--
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Received on Tue 10 May 2011 - 12:59:28 GMT

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