R help - Apr 2009 - Overlapping parameters "k" in different functions in "ipred"

Dear List,

I have a question regarding "ipred" package. Under 10-fold cv, for
different knn ( = 1,3,...25), I am getting same misclassification errors:
#############################################
library(ipred) 
data(iris) 
cv.k = 10 ## 10-fold cross-validation 
bwpredict.knn <- function(object, newdata) predict.ipredknn(object, newdata,
type="class")
for (i in seq(1,25,2)){
set.seed(19)
a<-errorest(Species ~ ., data=iris, model=ipredknn, estimator="cv",
est.para=control.errorest(k=cv.k), predict=bwpredict.knn, nk = i)$err
print(a)
}
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
[1] 0.02666667
#############################################
I think its is because in "ipredknn" and "control.errorest"
has the same variable "k" (I guess k=5 default in ipredknn is
returning). If I use

errorest(Species ~ ., data=iris, model=ipredknn, estimator="cv",
est.para=control.errorest(k=cv.k), predict=bwpredict.knn, k = 1)

the following message is generated:
Error in cv.factor(y, formula, data, model = model, predict = predict,  : 
  formal argument "k" matched by multiple actual arguments

I can't seem to change "k" to "nk" in
"ipredknn". If I try
ipred::ipredknn <- function (formula, data, subset, na.action, nk = 5,
...){.......}
I get the message-
Error in ipred::ipredknn <- function(formula, data, subset, na.action,  : 
  object "ipred" not found

How can I fix that? Any suggestion would be greatly appreciated.

Thanks in advance,


- mek

R.Version() $platform "i386-pc-mingw32" $arch "i386" $os
"mingw32" $system "i386, mingw32" $status ""
$major "2" $minor "8.1" $year "2008" $month
"12" $day "22" $`svn rev` "47281" $language
"R" $version.string "R version 2.8.1 (2008-12-22)"

WilDsc0p wrote:
> Dear List,
> 
> I have a question regarding "ipred" package. Under 10-fold cv,
for different knn ( = 1,3,...25), I am getting same misclassification errors:
> #############################################
> library(ipred) 
> data(iris) 
> cv.k = 10 ## 10-fold cross-validation 
> bwpredict.knn <- function(object, newdata) predict.ipredknn(object,
newdata, type="class")
> for (i in seq(1,25,2)){
> set.seed(19)
> a<-errorest(Species ~ ., data=iris, model=ipredknn,
estimator="cv", est.para=control.errorest(k=cv.k),
predict=bwpredict.knn, nk = i)$err
> print(a)
> }
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> [1] 0.02666667
> #############################################
> I think its is because in "ipredknn" and
"control.errorest" has the same variable "k" (I guess k=5
default in ipredknn is returning). If I use

No, but because you are resetting the seed of the random number 
generator to the same value in each iteration of your loop.



> 
> errorest(Species ~ ., data=iris, model=ipredknn, estimator="cv",
est.para=control.errorest(k=cv.k), predict=bwpredict.knn, k = 1)
> 
> the following message is generated:
> Error in cv.factor(y, formula, data, model = model, predict = predict,  : 
>   formal argument "k" matched by multiple actual arguments
> 
> I can't seem to change "k" to "nk" in
"ipredknn". If I try
> ipred::ipredknn <- function (formula, data, subset, na.action, nk = 5,
...){.......}
> I get the message-
> Error in ipred::ipredknn <- function(formula, data, subset, na.action, 
:
>   object "ipred" not found
> 
> How can I fix that? Any suggestion would be greatly appreciated.

You don't need (see above), but you can with assignInNamespace() and 
friends, see ?assignInNamespace.


Uwe Ligges



> Thanks in advance,
> 
> 
> - mek
> 
> R.Version() $platform "i386-pc-mingw32" $arch "i386"
$os "mingw32" $system "i386, mingw32" $status ""
$major "2" $minor "8.1" $year "2008" $month
"12" $day "22" $`svn rev` "47281" $language
"R" $version.string "R version 2.8.1 (2008-12-22)"
> 
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