[R] Vegemite Function is Cowardly refusing
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*
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)
__
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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.
Re: [R] Indicator Species analysis; trouble with multipatt
Thanks for the replies.
I have fixed the problem. I only need to reorganized my data. Now my
question is about asking questions correctly. I hope I've got it. Please
find the script attached here.
R Version 3.2.2
I am looking for indicator species with Indicspecies package. After
running the function multipatt, I get the following error:
Error in is.factor(x) : object 'groups1' not found
**Is this reproducibility satisfactory? I fixed the problem by
reorganizing my csv file. I was trying to be efficient when making my
groups and that was causing the trouble.
Thanks.
On Tue, Apr 19, 2016 at 6:47 AM, John Kane <jrkrid...@inbox.com> wrote:
> Hi Ansely,
> As Jim points out we really need some sample data to go with the code.
>
> Have a look at ?dput which is the best way to supply sample data here or
> have a look at
> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
> and/or http://adv-r.had.co.nz/Reproducibility.html for some general
> suggestions on asking questions here---including discussions of using dput()
>
> John Kane
> Kingston ON Canada
>
>
> > -Original Message-
> > From: daily.p...@gmail.com
> > Sent: Mon, 18 Apr 2016 16:33:54 -0400
> > To: r-help@r-project.org
> > Subject: [R] Indicator Species analysis; trouble with multipatt
> >
> > Hello,
> >
> > *Error in tx %*% comb : non-conformable arguments*
> >
> > Suggestions greatly appreciated. I am a beginner and this is my first
> > time
> > posting.
> >
> > I would like to get the summary for indicator species analysis, using
> > package indicspecies with multipatt. I am getting errors, I believe, do
> > to
> > my data organization. After reorganizing and reorganizing, nothing has
> > helped.
> >
> >> data<- read.csv(file="Data1.csv", header=TRUE, row.names=1, sep=",")
> >> ap<-data[c(1:24, 1:81)]
> >> groups<-c(rep(1:4,6))
> >> indval<- multipatt(ap, groups, control = how(nperm=999))
> > *Error in tx %*% comb : non-conformable arguments*
> >
> >
> >
> > --
> > Ansley Silva
> >
> >
> > *"The clearest way into the Universe is through a forest wilderness."
> > John
> > Muir*
> >
> >
> > *Graduate Research Assistant*
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
>
> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
> Check it out at http://www.inbox.com/earth
>
>
>
--
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*
install.packages("indicspecies")
library(indicspecies)
mydata<-
structure(list(necsur = structure(c(6L, 1L, 1L, 4L, 4L, 2L), .Label = c("0",
"1", "11", "2", "24", "3", "4", "42", "5", "8", "9", "PA"), class = "factor"),
necame = structure(c(11L, 2L, 5L, 5L, 17L, 9L), .Label = c("0",
"1", "10", "11", "12", "13", "15", "2", "20", "22", "3",
"4", "5", "6", "7", "8", "9", "PA"), class = "factor"), niccar =
structure(c(1L,
1L, 1L, 2L, 1L, 1L), .Label = c("0", "1", "19", "2", "3",
"4", "5", "6", "PA"), class = "factor"), nicorb = structure(c(1L,
18L, 19L, 17L, 1L, 27L), .Label = c("0", "1", "10", "11",
"12", "13", "15", "16", "18", "19", "2", "20", "21", "23",
"25", "29", "3", "30", "31", "32", "33", "36", "4", "40",
"42", "44", "48", "5", "50", "6", "61", "7", "8", "9", "PA"
), class = "factor"), ni
[R] Indicator Species analysis; trouble with multipatt
Hello, *Error in tx %*% comb : non-conformable arguments* Suggestions greatly appreciated. I am a beginner and this is my first time posting. I would like to get the summary for indicator species analysis, using package indicspecies with multipatt. I am getting errors, I believe, do to my data organization. After reorganizing and reorganizing, nothing has helped. > data<- read.csv(file="Data1.csv", header=TRUE, row.names=1, sep=",") > ap<-data[c(1:24, 1:81)] > groups<-c(rep(1:4,6)) > indval<- multipatt(ap, groups, control = how(nperm=999)) *Error in tx %*% comb : non-conformable arguments* -- Ansley Silva *"The clearest way into the Universe is through a forest wilderness." John Muir* *Graduate Research Assistant* __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
