indexing by empty string (was RE: Error in predict.randomForest ... subscript out of bounds with NULL name in X)

Hi Andy,
I'm not exactly sure if this is a problem with indexing by name; i.e., is
the following behavior by design?  The problem is that names or dimnames
that are empty seem to be treated differently, and one can't index by them:

R> junk = 1:3
R> names(junk) = c("a", "b", "")
R> junk
a b
1 2 3
R> junk[""]
<NA>
  NA
R> junk = matrix(1:4, 2, 2)
R> colnames(junk) = c("a", "")
R> junk[, ""]
Error: subscript out of bounds
You can index them by number, e.g.,
junk[, 2]

and you can use which() to find the numbers where the colname is empty.

junk[, which(colnames(junk) == "")]
I may need to find workaround...
Going back to the original issue with predict, I don't think you need a 
workaround. I think you need give your matrix some colnames.

Best,
Ista

-----Original Message-----
From: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of Czerminski, Ryszard
Sent: Wednesday, January 25, 2012 10:39 AM
To: r-help at r-project.org
Subject: [R] Error in predict.randomForest ... subscript out
of bounds with NULL name in X

RF trains fine with X, but fails on prediction

library(randomForest)
chirps <-
c(20,16.0,19.8,18.4,17.1,15.5,14.7,17.1,15.4,16.2,15,17.2,16,17,14.1)

temp <-
c(88.6,71.6,93.3,84.3,80.6,75.2,69.7,82,69.4,83.3,78.6,82.6,80
.6,83.5,76
.3)

X <- cbind(1,chirps)
rf <- randomForest(X, temp)
yp <- predict(rf, X)
Error in predict.randomForest(rf, X) : subscript out of bounds

BTW: Just find out that  apparently predict() does not like
NULL name in

X, because this works fine:
one <- rep(1, length(chirps))
X <- cbind(one,chirps)
rf <- randomForest(X, temp)
yp <- predict(rf, X)
Ryszard Czerminski
AstraZeneca Pharmaceuticals LP
35 Gatehouse Drive
Waltham, MA 02451
USA
781-839-4304
ryszard.czerminski at astrazeneca.com

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and provide commented, minimal, self-contained, reproducible code.
Hi Ista,

When you write a package, you have to anticipate what users will throw at the code.  I can insist that users only input matriices where none of the column names are empty, but that's not what I wish to impose on the users.  I can add the name if it's empty, but as a user I don't want a function to do that, either.  That's why I need to look for a workaround.

Using which() seems rather clumsy for the purpose, as I need to combine those with the non-empty ones, and preserving ordering would be a mess.

Andy
-----Original Message-----
From: r-help-bounces at r-project.org 
[mailto:r-help-bounces at r-project.org] On Behalf Of Ista Zahn
Sent: Wednesday, February 01, 2012 5:45 AM
To: r-help at r-project.org
Subject: Re: [R] indexing by empty string (was RE: Error in 
predict.randomForest ... subscript out of bounds with NULL name in X)

Hi Andy,

On Tuesday, January 31, 2012 08:44:13 AM Liaw, Andy wrote:
I'm not exactly sure if this is a problem with indexing by 
name; i.e., is
the following behavior by design?  The problem is that 
names or dimnames
that are empty seem to be treated differently, and one 
can't index by them:
R> junk = 1:3
R> names(junk) = c("a", "b", "")
R> junk
a b
1 2 3
R> junk[""]
<NA>
  NA
R> junk = matrix(1:4, 2, 2)
R> colnames(junk) = c("a", "")
R> junk[, ""]
Error: subscript out of bounds
You can index them by number, e.g.,
junk[, 2]

and you can use which() to find the numbers where the colname 
is empty.

junk[, which(colnames(junk) == "")]

I may need to find workaround...
Going back to the original issue with predict, I don't think 
you need a 
workaround. I think you need give your matrix some colnames.

Best,
Ista

-----Original Message-----
From: r-help-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of 
Czerminski, Ryszard
Sent: Wednesday, January 25, 2012 10:39 AM
To: r-help at r-project.org
Subject: [R] Error in predict.randomForest ... subscript out
of bounds with NULL name in X

RF trains fine with X, but fails on prediction

library(randomForest)
chirps <-

c(20,16.0,19.8,18.4,17.1,15.5,14.7,17.1,15.4,16.2,15,17.2,16,17,14.1)

temp <-
c(88.6,71.6,93.3,84.3,80.6,75.2,69.7,82,69.4,83.3,78.6,82.6,80
.6,83.5,76
.3)

X <- cbind(1,chirps)
rf <- randomForest(X, temp)
yp <- predict(rf, X)
Error in predict.randomForest(rf, X) : subscript out of bounds

BTW: Just find out that  apparently predict() does not like
NULL name in

X, because this works fine:
one <- rep(1, length(chirps))
X <- cbind(one,chirps)
rf <- randomForest(X, temp)
yp <- predict(rf, X)
Ryszard Czerminski
AstraZeneca Pharmaceuticals LP
35 Gatehouse Drive
Waltham, MA 02451
USA
781-839-4304
ryszard.czerminski at astrazeneca.com

--------------------------------------------------------------
------------
Confidentiality Notice: This message is private and may
...{{dropped:11}}

______________________________________________
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.
Notice:  This e-mail message, together with any 
attachme...{{dropped:11}}

______________________________________________
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.

Notice:  This e-mail message, together with any attachme...{{dropped:11}}