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
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