rarefy function in vegan, exporting to spreadsheet - R-SIG-ecology

Sun, May 29, 2016 11:45 AM #

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*
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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)