[R] Missing variable in new dataframe for prediction
Hi,
I'm using a loop to evaluate several models by taking adjacent variables from
my dataframe.
When i try to get predictions for new values, i get an error message about a
missing variable in my new dataframe.
Below is an example adapted from ?gam in mgcv package
library(mgcv)
set.seed(0)
n-400
sig-2
x0 - runif(n, 0, 1)
x1 - runif(n, 0, 1)
x2 - runif(n, 0, 1)
x3 - runif(n, 0, 1)
f0 - function(x) 2 * sin(pi * x)
f1 - function(x) exp(2 * x)
f2 - function(x) 0.2*x^11*(10*(1-x))^6+10*(10*x)^3*(1-x)^10
f3 - function(x) 0*x
f - f0(x0) + f1(x1) + f2(x2)
e - rnorm(n, 0, sig)
y - f + e
Mydata-data.frame(y=y,x0=x0,x1=x1,x2=x2,x3=x3)
remove(list=c(y,x0,x1,x2,x3))
# Note below the syntax of the 3rd variable required for my loop
for (i in 4:5){
b-gam(y~s(x0)+ s(x1)+ ns(Mydata[,i], 3), data=Mydata)
newd - data.frame(x0=(0:399)/30,x1=(0:399)/30,x2=(0:399)/30,x3=(0:399)/30)
pred - predict.gam(b,newd)
}
Erreur dans model.frame(formula, rownames, variables, varnames, extras,
extranames, :
type (list) incorrect pour la variable 'Mydata'
De plus : Warning message:
not all required variables have been supplied in newdata!
in: predict.gam(b, newd)
#Defining the name for the variable as in the gam function doesn't solve the
problem
newd -
data.frame(x0=(0:399)/30,x1=(0:399)/30,x2=(0:399)/30,Mydata[,i]=(0:399)/30)
Erreur dans model.frame(formula, rownames, variables, varnames, extras,
extranames, :
type (list) incorrect pour la variable 'Mydata'
De plus : Warning message:
not all required variables have been supplied in newdata!
in: predict.gam(b, newd)
How should i define my new dataset to be able to get my predictions ?
Thanks in advance
O__ Alain Le Tertre
c/ /'_ --- Institut de Veille Sanitaire (InVS)/ Département Santé Environnement
(*) \(*) -- Responsable de l'unité Systèmes d'Information Statistiques
~~ - 12 rue du val d'Osne
94415 Saint Maurice cedex FRANCE
Voice: 33 1 41 79 68 76 Fax: 33 1 41 79 67 68
email: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Missing variable in new dataframe for prediction
The call to library(splines) is missing and also try replacing the
line b - ... with
fo - as.formula(sprintf(y ~ s(x0) + s(x1) + ns(%s, 3), names(Mydata)[i]))
b - do.call(gam, list(fo, data = Mydata))
to dynamically recreate the formula on each iteration of the loop
with the correct name, x2 or x3, inserted.
On 2/13/07, LE TERTRE Alain [EMAIL PROTECTED] wrote:
Hi,
I'm using a loop to evaluate several models by taking adjacent variables from
my dataframe.
When i try to get predictions for new values, i get an error message about a
missing variable in my new dataframe.
Below is an example adapted from ?gam in mgcv package
library(mgcv)
set.seed(0)
n-400
sig-2
x0 - runif(n, 0, 1)
x1 - runif(n, 0, 1)
x2 - runif(n, 0, 1)
x3 - runif(n, 0, 1)
f0 - function(x) 2 * sin(pi * x)
f1 - function(x) exp(2 * x)
f2 - function(x) 0.2*x^11*(10*(1-x))^6+10*(10*x)^3*(1-x)^10
f3 - function(x) 0*x
f - f0(x0) + f1(x1) + f2(x2)
e - rnorm(n, 0, sig)
y - f + e
Mydata-data.frame(y=y,x0=x0,x1=x1,x2=x2,x3=x3)
remove(list=c(y,x0,x1,x2,x3))
# Note below the syntax of the 3rd variable required for my loop
for (i in 4:5){
b-gam(y~s(x0)+ s(x1)+ ns(Mydata[,i], 3), data=Mydata)
newd - data.frame(x0=(0:399)/30,x1=(0:399)/30,x2=(0:399)/30,x3=(0:399)/30)
pred - predict.gam(b,newd)
}
Erreur dans model.frame(formula, rownames, variables, varnames, extras,
extranames, :
type (list) incorrect pour la variable 'Mydata'
De plus : Warning message:
not all required variables have been supplied in newdata!
in: predict.gam(b, newd)
#Defining the name for the variable as in the gam function doesn't solve the
problem
newd -
data.frame(x0=(0:399)/30,x1=(0:399)/30,x2=(0:399)/30,Mydata[,i]=(0:399)/30)
Erreur dans model.frame(formula, rownames, variables, varnames, extras,
extranames, :
type (list) incorrect pour la variable 'Mydata'
De plus : Warning message:
not all required variables have been supplied in newdata!
in: predict.gam(b, newd)
How should i define my new dataset to be able to get my predictions ?
Thanks in advance
O__ Alain Le Tertre
c/ /'_ --- Institut de Veille Sanitaire (InVS)/ Département Santé
Environnement
(*) \(*) -- Responsable de l'unité Systèmes d'Information Statistiques
~~ - 12 rue du val d'Osne
94415 Saint Maurice cedex FRANCE
Voice: 33 1 41 79 68 76 Fax: 33 1 41 79 67 68
email: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch 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.
Re: [R] Missing variable in new dataframe for prediction
Actually this simpler replacement for the b - ... line would work just as well:
fo - as.formula(sprintf(y ~ s(x0) + s(x1) + ns(%s, 3), names(Mydata)[i]))
b - gam(fo, data = Mydata)
On 2/13/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
The call to library(splines) is missing and also try replacing the
line b - ... with
fo - as.formula(sprintf(y ~ s(x0) + s(x1) + ns(%s, 3), names(Mydata)[i]))
b - do.call(gam, list(fo, data = Mydata))
to dynamically recreate the formula on each iteration of the loop
with the correct name, x2 or x3, inserted.
On 2/13/07, LE TERTRE Alain [EMAIL PROTECTED] wrote:
Hi,
I'm using a loop to evaluate several models by taking adjacent variables
from my dataframe.
When i try to get predictions for new values, i get an error message about
a missing variable in my new dataframe.
Below is an example adapted from ?gam in mgcv package
library(mgcv)
set.seed(0)
n-400
sig-2
x0 - runif(n, 0, 1)
x1 - runif(n, 0, 1)
x2 - runif(n, 0, 1)
x3 - runif(n, 0, 1)
f0 - function(x) 2 * sin(pi * x)
f1 - function(x) exp(2 * x)
f2 - function(x) 0.2*x^11*(10*(1-x))^6+10*(10*x)^3*(1-x)^10
f3 - function(x) 0*x
f - f0(x0) + f1(x1) + f2(x2)
e - rnorm(n, 0, sig)
y - f + e
Mydata-data.frame(y=y,x0=x0,x1=x1,x2=x2,x3=x3)
remove(list=c(y,x0,x1,x2,x3))
# Note below the syntax of the 3rd variable required for my loop
for (i in 4:5){
b-gam(y~s(x0)+ s(x1)+ ns(Mydata[,i], 3), data=Mydata)
newd - data.frame(x0=(0:399)/30,x1=(0:399)/30,x2=(0:399)/30,x3=(0:399)/30)
pred - predict.gam(b,newd)
}
Erreur dans model.frame(formula, rownames, variables, varnames, extras,
extranames, :
type (list) incorrect pour la variable 'Mydata'
De plus : Warning message:
not all required variables have been supplied in newdata!
in: predict.gam(b, newd)
#Defining the name for the variable as in the gam function doesn't solve
the problem
newd -
data.frame(x0=(0:399)/30,x1=(0:399)/30,x2=(0:399)/30,Mydata[,i]=(0:399)/30)
Erreur dans model.frame(formula, rownames, variables, varnames, extras,
extranames, :
type (list) incorrect pour la variable 'Mydata'
De plus : Warning message:
not all required variables have been supplied in newdata!
in: predict.gam(b, newd)
How should i define my new dataset to be able to get my predictions ?
Thanks in advance
O__ Alain Le Tertre
c/ /'_ --- Institut de Veille Sanitaire (InVS)/ Département Santé
Environnement
(*) \(*) -- Responsable de l'unité Systèmes d'Information Statistiques
~~ - 12 rue du val d'Osne
94415 Saint Maurice cedex FRANCE
Voice: 33 1 41 79 68 76 Fax: 33 1 41 79 67 68
email: [EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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.
__
R-help@stat.math.ethz.ch 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.
