Draw a nomogram after glm
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 _S?n?gal
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
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
----- 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.