[R-sig-eco] raremax value >2, cannot run rarefy

[Ansley Silva]

Hello,

R version 3.2.2, using the vegan package.

I am using the rarefy function to get rarefied values for my rarefaction
curves.
​Please see the attached data and code.
Instead of getting an output from rarefy function of values for S and SE, I
am getting the following message:
"There were 20 warnings (use warnings() to see them)"
It seems that the issue might be that my raremax value for this dataset is
equal to 1.  When I ran the same code on a dataset with a raremax of 5,
everything is okay.  When I ran the same code on a dataset with a raremax
of 0, my output of S and SE were all 0.
I am looking for an explanation for this.  Is there a way to get better
values for the output?  Would PC-ORD do the same thing?

Thanks much,
​

-- 
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(braalt = c(8L, 0L, 0L, 0L, 0L, 0L), dicfur = c(0L, 
0L, 3L, 2L, 0L, 0L), dicpur = c(0L, 0L, 0L, 1L, 0L, 0L), carvin = c(1L, 
0L, 0L, 0L, 0L, 0L), carsyl = c(0L, 0L, 1L, 0L, 0L, 0L), cargor = c(1L, 
0L, 0L, 0L, 0L, 0L), cyclosig = c(1L, 0L, 0L, 0L, 0L, 0L), helnig = c(0L, 
0L, 0L, 0L, 0L, 0L), helcla = c(0L, 0L, 0L, 0L, 0L, 0L), passub = c(0L, 
0L, 0L, 0L, 1L, 0L), anirus = c(0L, 0L, 0L, 0L, 0L, 0L), calopa = c(0L, 
0L, 0L, 0L, 0L, 0L), eusass = c(0L, 13L, 12L, 14L, 5L, 17L), 
    hiscoe = c(4L, 2L, 0L, 0L, 2L, 1L), hisfun = c(0L, 0L, 0L, 
    0L, 0L, 0L), saplug = c(0L, 0L, 0L, 0L, 0L, 0L), ontnod = c(0L, 
    0L, 0L, 0L, 0L, 0L), cremax = c(2L, 3L, 0L, 7L, 3L, 0L), 
    plamac = c(0L, 0L, 0L, 0L, 1L, 0L), placom = c(0L, 1L, 0L, 
    0L, 0L, 0L), plapra = c(0L, 0L, 0L, 2L, 0L, 0L), tacfim = c(0L, 
    1L, 0L, 2L, 0L, 7L), alesps = c(0L, 0L, 0L, 0L, 0L, 0L), 
    tetcar = 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), spsE = c(0L, 0L, 0L, 0L, 0L, 0L), spsF = c(0L, 
    0L, 0L, 0L, 0L, 0L), spsH = c(0L, 0L, 0L, 0L, 0L, 0L)), .Names = c("braalt", 
"dicfur", "dicpur", "carvin", "carsyl", "cargor", "cyclosig", 
"helnig", "helcla", "passub", "anirus", "calopa", "eusass", "hiscoe", 
"hisfun", "saplug", "ontnod", "cremax", "plamac", "placom", "plapra", 
"tacfim", "alesps", "tetcar", "spsA", "spsB", "spsC", "spsE", 
"spsF", "spsH"), row.names = c("PA1-1", "PA1-2", "PA2-1", "PA2-2", 
"PA2-3", "PA2-4"), class = "data.frame")

patp<-read.csv(file="PredPATP.csv", header=TRUE, row.names=1, sep=",") #NA values have to be removed
raremax<-min(rowSums(patp))
patprare<-rarefy(patp, raremax, se=TRUE) 
write.csv(patprare, file="ExprtPATPrare.csv")