[R] function gdist, dist and vegdist in mvpart
sina.muster at web.de
Wed Mar 8 19:12:11 CET 2006
Dear R community,
I am analyzing plant communities with the function mvpart, using a
dissimilarit matrix as input. The matrix is calculated with the funtion
fit <- mvpart(gdist (ba12[,18:29], meth="maximum", full=TRUE,
sq=F) ~ beers + slope_dem + elev_dem+ plc_dem + pr_curv+
This works fine. Now I would like to use other dissimilarity measures as
can be found in the function dist (STATS) or vegdist (VEGAN).
De'Ath notes that gdist should be interchangeable with dist - but I
receive following error message:
> fit21 <- mvpart(dist (ba12[,18:29], meth="minkowski", diag=T,
upper=T p=2) ~
beers + slope_dem + elev_dem+ plc_dem + pr_curv+
Error in model.frame(formula, rownames, variables, varnames, extras,
Variable lengths differ
When computing the matrices directly...
ba12.dist1 <- gdist (ba12[,18:29], method="maximum", full=T, sq=F)
ba12.dist2 <- vegdist (ba12[,18:29], method="jaccard", diag=T, upper=T)
ba12.dist3 <- dist (ba12[,18:29], method="minkowski", p=1, diag=T, upper=T)
and looking at them, there appears to be no difference though only
ba12.dist1 works with mvpart. With the other two I get the same error
message as above.
What I am missing? Where is the problem?
Thanks for helping.
University of Potsdam, Germany
Department of Geoecology
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