[R-sig-eco] rarefy function in vegan, exporting to spreadsheet
Dorothea Hug Peter
Dorothea.HugPeter at unige.ch
Mon May 30 13:22:23 CEST 2016
Dear Ansley
I just run the code you provided and it works fine for me. As a result I get:
AP1-1 AP1-2 AP1-3 AP1-4 AP2-1 AP2-2
S 8 7.757679 8.154923 10.164525 6.1662977 10.252731
se 0 1.376587 1.428898 1.450643 0.6982331 1.630957
attr(,"Subsample")
[1] 33
Have you tried the rarefy function on some model data?
Is your raremax in the correct format when you run the code for your entire dataset?
Regards
Dorothea Hug Peter
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Today's Topics:
1. rarefy function in vegan, exporting to spreadsheet (Ansley Silva)
----------------------------------------------------------------------
Message: 1
Date: Sun, 29 May 2016 14:45:50 -0400
From: Ansley Silva <daily.puja at gmail.com>
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] rarefy function in vegan, exporting to
spreadsheet
Message-ID:
<CAK2Sg-0M2V4izVvkALhre+2a_QDRJcae-V0rwWqTCY5rBsLt5w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
I have just joined the list and I hope I am submitting a question in the
correct format.
I have species data that I used to make rarefaction curves. I made my
rarefaction curves based on a dataset where I averaged my traps based on a
predictor variable. This worked fine, however, now I would like to get the
specific rarefied values and SE so I can use it for my diversity index in a
model.
With my uncollapsed dataset, I get the error:
Error in if (any(sample > minsample)) warning(gettextf("Requested 'sample'
was larger than smallest site maximum (%d)", :
missing value where TRUE/FALSE needed
I think I understand the error itself, but I do not know how to correct for
it. Essentially I would like to get rarefied values to use in a linear
model, but I am having difficulty extracting these values. Help is greatly
appreciated.
Thanks,
--
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 --------------
data<-structure(list(necsur = c(3L, 0L, 0L, 2L, 2L, 1L), necame = c(3L,
1L, 12L, 12L, 9L, 20L), niccar = c(0L, 0L, 0L, 1L, 0L, 0L), nicorb = c(0L,
30L, 31L, 3L, 0L, 48L), nicpus = c(0L, 0L, 0L, 0L, 0L, 0L), nictor = c(0L,
0L, 1L, 0L, 0L, 0L), oicina = c(0L, 0L, 0L, 0L, 0L, 0L), delgib = c(5L,
11L, 126L, 16L, 16L, 68L), cancha = c(0L, 0L, 1L, 2L, 2L, 4L),
melbis = c(1L, 0L, 0L, 0L, 0L, 0L), atelec = c(0L, 0L, 0L,
32L, 14L, 1L), copmin = c(0L, 0L, 0L, 0L, 0L, 0L), ontcon = c(0L,
1L, 3L, 0L, 0L, 6L), ontdep = c(0L, 0L, 0L, 0L, 0L, 0L),
onthec = c(1L, 28L, 7L, 14L, 0L, 29L), ontstr = c(0L, 1L,
0L, 2L, 0L, 0L), onttau = c(0L, 0L, 8L, 4L, 0L, 8L), ontpen = c(0L,
0L, 2L, 6L, 0L, 4L), onttub = c(0L, 0L, 3L, 2L, 0L, 6L),
ontsub = c(0L, 0L, 0L, 0L, 0L, 0L), ontorp = c(0L, 0L, 0L,
0L, 0L, 0L), phatri = c(0L, 0L, 0L, 0L, 0L, 1L), phaign = c(0L,
0L, 0L, 0L, 0L, 0L), phavin = c(0L, 0L, 0L, 0L, 0L, 0L),
phival = c(0L, 0L, 0L, 0L, 0L, 0L), diccar = c(0L, 0L, 0L,
0L, 0L, 0L), diggaz = c(0L, 0L, 0L, 0L, 0L, 0L), Phyili = c(0L,
0L, 0L, 0L, 0L, 0L), phyfor = c(0L, 0L, 0L, 0L, 0L, 0L),
physps = c(0L, 0L, 0L, 0L, 0L, 0L), dippun = c(0L, 0L, 0L,
0L, 0L, 0L), diplib = c(0L, 0L, 0L, 0L, 0L, 0L), euehum = c(0L,
0L, 0L, 0L, 0L, 0L), canvir = c(0L, 2L, 2L, 0L, 0L, 1L),
phycle = c(0L, 0L, 0L, 0L, 0L, 0L), pseper = c(0L, 0L, 0L,
0L, 0L, 0L), aphrus = c(0L, 0L, 0L, 0L, 0L, 0L), hybill = c(0L,
0L, 0L, 0L, 0L, 0L), geobla = c(0L, 0L, 0L, 0L, 0L, 0L),
geoege = c(0L, 0L, 0L, 0L, 0L, 0L), boltho = c(0L, 0L, 0L,
0L, 0L, 0L), braalt = c(0L, 0L, 0L, 0L, 0L, 0L), chlery = c(0L,
0L, 0L, 0L, 0L, 0L), chlema = c(0L, 0L, 0L, 0L, 0L, 0L),
cyclae = c(0L, 0L, 0L, 0L, 0L, 0L), cyclev = c(0L, 0L, 0L,
0L, 0L, 0L), dicdil = c(0L, 0L, 0L, 0L, 0L, 0L), dicfur = c(0L,
0L, 0L, 0L, 0L, 0L), dicpur = c(0L, 0L, 0L, 0L, 0L, 0L),
galjan = c(0L, 0L, 0L, 0L, 0L, 1L), carvin = c(0L, 0L, 0L,
0L, 0L, 0L), carsyl = c(0L, 0L, 0L, 0L, 0L, 0L), cargor = c(0L,
0L, 0L, 0L, 0L, 0L), cyclosig = c(0L, 0L, 0L, 0L, 0L, 0L),
helnig = c(0L, 0L, 0L, 0L, 0L, 0L), helcla = c(0L, 0L, 0L,
0L, 0L, 0L), scaqua = c(0L, 0L, 0L, 0L, 0L, 1L), scasub = c(0L,
0L, 0L, 0L, 0L, 0L), oodama = c(0L, 0L, 0L, 0L, 0L, 0L),
stemex = c(0L, 0L, 0L, 0L, 0L, 0L), agoalb = c(0L, 0L, 0L,
0L, 0L, 0L), moctet = c(0L, 0L, 0L, 0L, 0L, 0L), pasmar = c(0L,
0L, 0L, 0L, 0L, 0L), passub = c(0L, 0L, 0L, 0L, 0L, 0L),
apesin = c(0L, 0L, 0L, 0L, 0L, 0L), anirus = c(0L, 0L, 0L,
0L, 0L, 0L), calopa = c(0L, 0L, 0L, 0L, 0L, 0L), harsps = c(0L,
0L, 0L, 0L, 0L, 0L), copgly = c(0L, 0L, 0L, 0L, 0L, 0L),
omomon = c(0L, 0L, 4L, 2L, 0L, 2L), omosub = c(0L, 1L, 0L,
0L, 0L, 0L), trofov = c(0L, 0L, 0L, 0L, 0L, 0L), trouni = c(2L,
0L, 0L, 0L, 0L, 0L), trotub = c(0L, 0L, 0L, 0L, 0L, 0L),
troaeq = c(0L, 0L, 0L, 0L, 0L, 0L), troter = c(0L, 1L, 0L,
0L, 0L, 0L), eusass = c(10L, 2L, 9L, 17L, 16L, 9L), hiscoe = c(0L,
1L, 43L, 0L, 0L, 1L), hisabb = c(0L, 0L, 0L, 0L, 0L, 0L),
hisfun = c(0L, 0L, 0L, 0L, 0L, 0L), sappen = c(0L, 0L, 0L,
0L, 0L, 0L), saplug = c(0L, 0L, 0L, 0L, 0L, 0L), ontnod = c(0L,
0L, 0L, 0L, 0L, 0L), dercan = c(0L, 0L, 0L, 0L, 0L, 0L),
cremax = c(8L, 0L, 0L, 0L, 0L, 4L), plamac = c(0L, 1L, 5L,
1L, 0L, 0L), ontcin = c(0L, 0L, 0L, 0L, 0L, 0L), plafem = c(0L,
0L, 0L, 0L, 0L, 0L), plafos = c(0L, 0L, 0L, 1L, 0L, 1L),
placom = c(0L, 10L, 0L, 45L, 33L, 4L), placin = c(0L, 0L,
0L, 0L, 0L, 0L), plapra = c(0L, 0L, 0L, 0L, 0L, 0L), phiumb = c(0L,
0L, 0L, 0L, 0L, 0L), tacfim = c(0L, 0L, 0L, 0L, 0L, 0L),
alesps = c(0L, 0L, 0L, 0L, 0L, 0L), tetcar = c(0L, 0L, 0L,
0L, 0L, 1L), tetvir = c(0L, 0L, 0L, 0L, 0L, 0L), cicsex = c(0L,
0L, 0L, 0L, 0L, 0L), spsA = c(0L, 0L, 0L, 0L, 0L, 0L), spsB = c(0L,
0L, 0L, 0L, 0L, 0L), spsC = c(0L, 0L, 0L, 0L, 0L, 0L), spsD = c(0L,
0L, 0L, 0L, 0L, 0L), spsE = c(0L, 0L, 0L, 0L, 0L, 0L), spsF = c(0L,
0L, 0L, 0L, 0L, 0L), spsG = c(0L, 0L, 0L, 0L, 0L, 0L), spsH = c(0L,
0L, 0L, 0L, 0L, 0L), spsI = c(0L, 0L, 0L, 0L, 0L, 0L), spsJ = c(0L,
0L, 0L, 0L, 0L, 0L), spsK = c(0L, 0L, 0L, 0L, 0L, 0L), spsL = c(0L,
0L, 0L, 0L, 0L, 0L), spsM = c(0L, 0L, 0L, 0L, 0L, 0L), spsN = 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", "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"), row.names = c("AP1-1", "AP1-2",
"AP1-3", "AP1-4", "AP2-1", "AP2-2"), class = "data.frame")
raremax<-min(rowSums(apst))
apstrare<-rarefy(apst, raremax, se=TRUE)
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