R help - Feb 2010 - Error in mvpart example

Dear all,

I'm getting an error in one of the stock examples in the 'mvpart'
package. I tried:

require(mvpart)
data(spider)
fit3 <-
rpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method="dist")
#directly from ?rpart
summary(fit3)

...which returned the following:

Error in apply(formatg(yval, digits - 3), 1, paste, collapse = ",",
sep = "") :
  dim(X) must have a positive length

This seems to be a problem with the cross-validation, since the
"xerror" and "xstd" columns are missing from the summary
table as well.

Using the mpart() wrapper results in the same error:

fit4<-mvpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method="dist")
summary(fit4)

Note, changing the 'method' argument to ="mrt" seems,
superficially, to solve the problem. However, when the dependent variable is a
dissimilarity matrix, shouldn't method="dist" be used (as per the
examples)?

Thanks, in advance, for any help on this error.

Oliver

These functions (rpart, the mvpart wrapper, and summary.rpart) are
fairly complex doing many things.

For contributed packages you'd be best served by contacting the
author/maintainer. I've CC'd Glenn (the maintainer) here.

HTH

G

On Fri, 2010-02-26 at 13:55 +0000, Wearn, Oliver wrote:
> Dear all,
> 
> I'm getting an error in one of the stock examples in the
'mvpart'
> package. I tried:
> 
> require(mvpart)
> data(spider)
> fit3 <-
rpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water
> +twigs+reft+herbs+moss+sand,spider,method="dist") #directly
> from ?rpart
> summary(fit3)
> 
> ...which returned the following:
> 
> Error in apply(formatg(yval, digits - 3), 1, paste, collapse =
",",
> sep = "") : 
>   dim(X) must have a positive length
> 
> This seems to be a problem with the cross-validation, since the
> "xerror" and "xstd" columns are missing from the
summary table as
> well.
> 
> Using the mpart() wrapper results in the same error:
> 
>
fit4<-mvpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water
> +twigs+reft+herbs+moss+sand,spider,method="dist")
> summary(fit4)
> 
> Note, changing the 'method' argument to ="mrt" seems,
superficially,
> to solve the problem. However, when the dependent variable is a
> dissimilarity matrix, shouldn't method="dist" be used (as per
the
> examples)?
> 
> Thanks, in advance, for any help on this error.
> 
> Oliver
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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On 2010-02-26 6:55, Wearn, Oliver wrote:
> Dear all,
>
> I'm getting an error in one of the stock examples in the
'mvpart' package. I tried:
>
> require(mvpart)
> data(spider)
> fit3<-
rpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method="dist")
#directly from ?rpart
> summary(fit3)
>
> ...which returned the following:
>
> Error in apply(formatg(yval, digits - 3), 1, paste, collapse =
",", sep = "") :
>    dim(X) must have a positive length
>
> This seems to be a problem with the cross-validation, since the
"xerror" and "xstd" columns are missing from the summary
table as well.
>
> Using the mpart() wrapper results in the same error:
>
>
fit4<-mvpart(gdist(spider[,1:12],meth="bray",full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method="dist")
> summary(fit4)
>
> Note, changing the 'method' argument to ="mrt" seems,
superficially, to solve the problem. However, when the dependent variable is a
dissimilarity matrix, shouldn't method="dist" be used (as per the
examples)?
>
> Thanks, in advance, for any help on this error.
>
> Oliver
The cross-validation idea is a red herring; the documentation clearly
states:
   Weights and cross-validation are currently not implemented for
   method="dist".

The error message provides a clue: apply() is not happy with what it's
being fed. Since it mentions "dim", we can guess that the problem is
with the X in apply(X, .....).
This in turn suggests that formatg() may not be returning an array
and indeed in your example it returns a vector. I don't know what will
be broken if the last line in formatg() is changed to force the
returned value to be a matrix, but this will work for your example:


formatg <-
function(x, digits= unlist(options('digits')),
                  format= paste("%.", digits, "g",
sep='')) {
     if (!is.numeric(x)) stop("x must be a numeric vector")

     n <- length(x)
     #
     # the resultant strings could be up to 8 characters longer,
     #   assume that digits =4,  -0.dddde+104 is a worst case, where
     #   dddd are the 4 significant digits.
     dummy  <- paste(rep(" ", digits+8), collapse='')
     temp <- .C("formatg", as.integer(n),
                       as.double(x),
                           rep(format,n),
                           out= rep(dummy, n), NAOK=TRUE,
                                    PACKAGE="mvpart")$out
     if (is.matrix(x)) matrix(temp, nrow=nrow(x))
#    else temp
     else matrix(temp, nrow=1)
     }

Source this and

   summary(fit3)

seem to return reasonable values.

   -Peter Ehlers