[R] Indicator Species analysis; trouble with multipatt
Ansley Silva
daily.puja at gmail.com
Tue Apr 19 14:16:54 CEST 2016
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 <jrkrideau at 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.puja at gmail.com
> > Sent: Mon, 18 Apr 2016 16:33:54 -0400
> > To: r-help at 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 at 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!
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>
--
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*
-------------- next part --------------
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"), nicpus = structure(c(1L, 1L, 1L, 1L,
1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
nictor = structure(c(1L, 1L, 2L, 1L, 1L, 1L), .Label = c("0",
"1", "10", "11", "16", "18", "2", "22", "3", "4", "5", "6",
"7", "8", "9", "PA"), class = "factor"), oicina = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "15", "2", "3",
"PA"), class = "factor"), delgib = structure(c(37L, 5L, 7L,
11L, 11L, 43L), .Label = c("0", "1", "10", "104", "11", "12",
"126", "13", "14", "15", "16", "18", "19", "2", "20", "21",
"22", "23", "24", "25", "26", "27", "28", "29", "3", "30",
"31", "32", "33", "34", "35", "37", "39", "4", "40", "43",
"5", "50", "6", "61", "63", "65", "68", "7", "72", "8", "81",
"82", "97", "PA"), class = "factor"), cancha = structure(c(1L,
1L, 2L, 7L, 7L, 10L), .Label = c("0", "1", "11", "12", "16",
"17", "2", "27", "3", "4", "5", "6", "7", "8", "9", "PA"), class = "factor"),
melbis = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "11", "17", "18", "2", "3", "4", "5", "6", "8", "9",
"PA"), class = "factor"), atelec = structure(c(1L, 1L, 1L,
22L, 7L, 2L), .Label = c("0", "1", "10", "11", "12", "13",
"14", "15", "17", "174", "18", "19", "2", "20", "21", "23",
"24", "27", "3", "30", "31", "32", "34", "37", "39", "41",
"42", "5", "51", "6", "61", "66", "7", "72", "76", "77",
"79", "8", "81", "83", "9", "97", "PA"), class = "factor"),
copmin = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "10", "11", "12", "2", "3", "33", "4", "5", "6", "7",
"8", "PA"), class = "factor"), ontcon = structure(c(1L, 2L,
8L, 1L, 1L, 12L), .Label = c("0", "1", "10", "11", "13",
"14", "2", "3", "33", "4", "5", "6", "7", "8", "PA"), class = "factor"),
ontdep = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "10", "2", "PA"), class = "factor"), onthec = structure(c(2L,
18L, 29L, 7L, 1L, 19L), .Label = c("0", "1", "10", "11",
"12", "13", "14", "141", "143", "16", "17", "18", "19", "2",
"20", "21", "24", "28", "29", "3", "30", "4", "48", "5",
"50", "54", "55", "6", "7", "70", "8", "9", "PA"), class = "factor"),
ontstr = structure(c(1L, 2L, 1L, 3L, 1L, 1L), .Label = c("0",
"1", "2", "3", "4", "5", "6", "7", "8", "PA"), class = "factor"),
onttau = structure(c(1L, 1L, 12L, 8L, 1L, 12L), .Label = c("0",
"1", "10", "104", "2", "24", "3", "4", "5", "6", "66", "8",
"PA"), class = "factor"), ontpen = structure(c(1L, 1L, 8L,
13L, 1L, 11L), .Label = c("0", "1", "11", "12", "13", "14",
"15", "2", "3", "34", "4", "5", "6", "7", "8", "9", "PA"), class = "factor"),
onttub = structure(c(1L, 1L, 7L, 5L, 1L, 10L), .Label = c("0",
"1", "11", "12", "2", "20", "3", "4", "5", "6", "7", "PA"
), class = "factor"), ontsub = structure(c(1L, 1L, 1L, 1L,
1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
ontorp = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), phatri = structure(c(1L, 1L,
1L, 1L, 1L, 2L), .Label = c("0", "1", "3", "PA"), class = "factor"),
phaign = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "2", "PA"), class = "factor"), phavin = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "2", "3", "5", "PA"), class = "factor"),
phival = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), diccar = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
diggaz = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), Phyili = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "3", "PA"), class = "factor"),
phyfor = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), physps = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
dippun = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), diplib = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
euehum = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), canvir = structure(c(1L, 3L,
3L, 1L, 1L, 2L), .Label = c("0", "1", "2", "3", "PA"), class = "factor"),
phycle = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"2", "PA"), class = "factor"), pseper = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
aphrus = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), hybill = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
geobla = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), geoege = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
boltho = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), braalt = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "3", "8", "PA"
), class = "factor"), chlery = structure(c(1L, 1L, 1L, 1L,
1L, 1L), .Label = c("0", "1", "3", "PA"), class = "factor"),
chlema = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "2", "PA"), class = "factor"), cyclae = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
cyclev = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "2", "5", "6", "PA"), class = "factor"), dicdil = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "3", "PA"), class = "factor"),
dicfur = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "2", "3", "PA"), class = "factor"), dicpur = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
galjan = structure(c(1L, 1L, 1L, 1L, 1L, 2L), .Label = c("0",
"1", "2", "3", "4", "5", "PA"), class = "factor"), carvin = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
carsyl = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), cargor = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
cyclosig = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "3", "5", "PA"), class = "factor"), helnig = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
helcla = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), scaqua = structure(c(1L, 1L,
1L, 1L, 1L, 2L), .Label = c("0", "1", "2", "PA"), class = "factor"),
scasub = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"2", "PA"), class = "factor"), oodama = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
stemex = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"3", "PA"), class = "factor"), agoalb = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
moctet = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), pasmar = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
passub = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), apesin = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
anirus = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), calopa = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
harsps = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), copgly = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
omomon = structure(c(1L, 1L, 11L, 8L, 1L, 8L), .Label = c("0",
"1", "11", "12", "13", "15", "19", "2", "3", "32", "4", "5",
"6", "7", "8", "9", "PA"), class = "factor"), omosub = structure(c(1L,
2L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
trofov = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "14", "15", "16", "2", "22", "3", "31", "4", "5", "6",
"7", "PA"), class = "factor"), trouni = structure(c(3L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "4", "6", "8",
"PA"), class = "factor"), trotub = structure(c(1L, 1L, 1L,
1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
troaeq = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), troter = structure(c(1L, 2L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "3", "6", "8",
"PA"), class = "factor"), eusass = structure(c(3L, 19L, 63L,
15L, 14L, 63L), .Label = c("0", "1", "10", "107", "11", "12",
"126", "13", "130", "133", "14", "143", "15", "16", "17",
"18", "186", "19", "2", "20", "21", "22", "24", "25", "26",
"27", "28", "29", "3", "30", "31", "32", "33", "34", "37",
"38", "39", "4", "42", "43", "44", "45", "48", "49", "5",
"51", "53", "54", "56", "57", "6", "64", "65", "7", "70",
"71", "78", "79", "8", "82", "88", "89", "9", "93", "98",
"99", "PA"), class = "factor"), hiscoe = structure(c(1L,
2L, 15L, 1L, 1L, 2L), .Label = c("0", "1", "10", "11", "13",
"14", "17", "19", "2", "23", "27", "3", "30", "4", "43",
"5", "6", "7", "8", "9", "PA"), class = "factor"), hisabb = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "3", "4", "9",
"PA"), class = "factor"), hisfun = structure(c(1L, 1L, 1L,
1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
sappen = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), saplug = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
ontnod = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), dercan = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
cremax = structure(c(23L, 1L, 1L, 1L, 1L, 18L), .Label = c("0",
"1", "10", "11", "12", "13", "17", "18", "2", "23", "24",
"25", "28", "3", "30", "31", "33", "4", "5", "54", "6", "7",
"8", "PA"), class = "factor"), plamac = structure(c(1L, 2L,
7L, 2L, 1L, 1L), .Label = c("0", "1", "13", "2", "3", "4",
"5", "6", "8", "PA"), class = "factor"), ontcin = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
plafem = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "6", "PA"), class = "factor"), plafos = structure(c(1L,
1L, 1L, 2L, 1L, 2L), .Label = c("0", "1", "11", "2", "3",
"4", "9", "PA"), class = "factor"), placom = structure(c(1L,
3L, 1L, 12L, 9L, 10L), .Label = c("0", "1", "10", "14", "2",
"23", "3", "30", "33", "4", "40", "45", "5", "54", "6", "7",
"8", "PA"), class = "factor"), placin = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
plapra = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"2", "PA"), class = "factor"), phiumb = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "2", "PA"), class = "factor"),
tacfim = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "2", "4", "6", "7", "8", "PA"), class = "factor"), alesps = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "PA"), class = "factor"),
tetcar = structure(c(1L, 1L, 1L, 1L, 1L, 2L), .Label = c("0",
"1", "3", "4", "PA"), class = "factor"), tetvir = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("0", "1", "2", "5", "PA"), class = "factor"),
cicsex = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsA = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "2", "PA"), class = "factor"),
spsB = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsC = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
spsD = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsE = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
spsF = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsG = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
spsH = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsI = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
spsJ = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsK = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
spsL = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), spsM = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("0", "1", "PA"), class = "factor"),
spsN = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("0",
"1", "PA"), class = "factor"), X = c(NA, NA, NA, NA, NA,
NA)), .Names = c("necsur", "necame", "niccar", "nicorb",
"nicpus", "nictor", "oicina", "delgib", "cancha", "melbis", "atelec",
"copmin", "ontcon", "ontdep", "onthec", "ontstr", "onttau", "ontpen",
"onttub", "ontsub", "ontorp", "phatri", "phaign", "phavin", "phival",
"diccar", "diggaz", "Phyili", "phyfor", "physps", "dippun", "diplib",
"euehum", "canvir", "phycle", "pseper", "aphrus", "hybill", "geobla",
"geoege", "boltho", "braalt", "chlery", "chlema", "cyclae", "cyclev",
"dicdil", "dicfur", "dicpur", "galjan", "carvin", "carsyl", "cargor",
"cyclosig", "helnig", "helcla", "scaqua", "scasub", "oodama",
"stemex", "agoalb", "moctet", "pasmar", "passub", "apesin", "anirus",
"calopa", "harsps", "copgly", "omomon", "omosub", "trofov", "trouni",
"trotub", "troaeq", "troter", "eusass", "hiscoe", "hisabb", "hisfun",
"sappen", "saplug", "ontnod", "dercan", "cremax", "plamac", "ontcin",
"plafem", "plafos", "placom", "placin", "plapra", "phiumb", "tacfim",
"alesps", "tetcar", "tetvir", "cicsex", "spsA", "spsB", "spsC",
"spsD", "spsE", "spsF", "spsG", "spsH", "spsI", "spsJ", "spsK",
"spsL", "spsM", "spsN", "X"), row.names = c("AP1-1", "AP1-2",
"AP1-3", "AP1-4", "AP2-1", "AP2-2"), class = "data.frame")
ap<-mydata[1:24, ]
groups<-c(rep(1:4,6))
indval1<- multipatt(ap, groups1, control = how(nperm=999))
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