Vegemite Function is Cowardly refusing - R-help

Thu, Apr 21, 2016 4:49 PM #

R version 3.2.2.
library(vegan)

I was to look at community tables from my dendrograms and am trying out the
vegemite command.  This is the error I get:

Error in vegemite(apst, apst.clusters) :
  Cowardly refusing to use longer than 1 char symbols:
Use scale

I thought the problem was that I was using the log transformed data, but I
tried it on the raw (which is single digit numbers), and still no luck.
Any suggestions would be appreciated.

Ansley Silva


*"The clearest way into the Universe is through a forest wilderness." John
Muir*


*Graduate Research Assistant*

*University of Georgia*

*D.B. Warnell School of Forestry and Natural Resources*

*180 East Green Street*

*Athens, GA 30602*
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data<-structure(list(necsur = c(1L, 4L, 0L, 8L, 0L, 1L), necame = c(4L, 
5L, 9L, 9L, 4L, 7L), niccar = c(1L, 1L, 1L, 2L, 1L, 4L), nicorb = c(2L, 
20L, 23L, 26L, 3L, 12L), nicpus = c(0L, 0L, 1L, 0L, 0L, 0L), 
    nictor = c(0L, 2L, 1L, 3L, 2L, 1L), oicina = c(0L, 0L, 0L, 
    0L, 0L, 0L), delgib = c(10L, 31L, 47L, 48L, 15L, 55L), cancha = c(5L, 
    6L, 4L, 4L, 1L, 6L), melbis = c(3L, 0L, 1L, 3L, 0L, 1L), 
    atelec = c(4L, 6L, 28L, 22L, 8L, 52L), copmin = c(0L, 0L, 
    1L, 1L, 0L, 1L), ontcon = c(3L, 3L, 11L, 7L, 1L, 2L), ontdep = c(2L, 
    0L, 0L, 0L, 0L, 0L), onthec = c(17L, 15L, 9L, 6L, 6L, 2L), 
    ontstr = c(0L, 0L, 0L, 1L, 1L, 0L), onttau = c(20L, 13L, 
    6L, 2L, 0L, 2L), ontpen = c(2L, 3L, 5L, 3L, 2L, 4L), onttub = c(2L, 
    3L, 4L, 1L, 1L, 0L), ontsub = c(0L, 0L, 0L, 0L, 0L, 0L), 
    phaign = c(0L, 0L, 0L, 0L, 0L, 0L), phavin = c(1L, 0L, 0L, 
    0L, 0L, 1L), Phyili = c(0L, 0L, 0L, 0L, 0L, 1L), canvir = c(0L, 
    1L, 0L, 0L, 0L, 0L), hybill = c(1L, 0L, 0L, 0L, 0L, 0L), 
    chlema = c(0L, 0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L, 
    0L, 1L, 1L), dicdil = c(0L, 0L, 0L, 0L, 0L, 0L), galjan = c(0L, 
    0L, 1L, 1L, 0L, 0L), cyclosig = c(0L, 0L, 0L, 0L, 1L, 0L), 
    omomon = c(1L, 2L, 4L, 10L, 1L, 6L), trofov = c(1L, 2L, 3L, 
    1L, 0L, 1L), trouni = c(1L, 0L, 0L, 1L, 0L, 0L), troter = c(0L, 
    1L, 1L, 0L, 0L, 0L), eusass = c(9L, 8L, 23L, 14L, 11L, 28L
    ), hiscoe = c(2L, 1L, 10L, 4L, 2L, 4L), hisabb = c(0L, 0L, 
    0L, 0L, 2L, 0L), sappen = c(0L, 0L, 0L, 0L, 0L, 0L), dercan = c(0L, 
    0L, 0L, 0L, 0L, 0L), cremax = c(4L, 7L, 1L, 2L, 2L, 5L), 
    plamac = c(1L, 0L, 3L, 2L, 2L, 2L), plafem = c(0L, 0L, 0L, 
    0L, 0L, 0L), plafos = c(1L, 1L, 3L, 2L, 1L, 2L), placom = c(6L, 
    3L, 3L, 10L, 13L, 7L), tacfim = c(0L, 0L, 1L, 0L, 0L, 0L), 
    cicsex = c(0L, 0L, 0L, 0L, 0L, 0L), spsK = c(0L, 0L, 0L, 
    0L, 0L, 0L)), .Names = c("necsur", "necame", "niccar", "nicorb", 
"nicpus", "nictor", "oicina", "delgib", "cancha", "melbis", "atelec", 
"copmin", "ontcon", "ontdep", "onthec", "ontstr", "onttau", "ontpen", 
"onttub", "ontsub", "phaign", "phavin", "Phyili", "canvir", "hybill", 
"chlema", "cyclev", "dicdil", "galjan", "cyclosig", "omomon", 
"trofov", "trouni", "troter", "eusass", "hiscoe", "hisabb", "sappen", 
"dercan", "cremax", "plamac", "plafem", "plafos", "placom", "tacfim", 
"cicsex", "spsK"), row.names = c("AP-0", "AP-100", "AP-200", 
"AP-300", "ST-0", "ST-100"), class = "data.frame")

apst.log <- decostand(apst, "log")
apst.bray <- vegdist(apst.log)
apst.clusters <- hclust(apst.bray, method = "average")
vegemite(apst, apst.clusters)