I am using EcoTest.sample (rareNMtests package) to compare rarefaction curves
for 19 vegetation plots on two soil types (alluvial and canyon). The code below
produces the following warning (more than 50 times): "In cor(x > 0) : the
standard deviation is zero".
The test still produces all the expected output. I tried sorting the dataset by
SiteType, but still got the error. Curiously, sorting the data produced a
significant difference between the site types (p around 0.3), while there was
no difference between the unsorted data (p around 0.09).
Should I be concerned about the warnings? Why does sorting the dataset make a
difference?
Thanks,
Charlotte
rawdata<-read.table(text="Plot SiteType sp1 sp2 sp3 sp4 sp5 sp6 sp7 sp8 sp9
sp10 sp11 sp12 sp13 sp14 sp15 sp16 sp17 sp18 sp19
sp20 sp21 sp22 sp23 sp24 sp25 sp26 sp27 sp28 sp29
sp30 sp31 sp32 sp33 sp34 sp35
2 canyon 1 0 1 0 1 1 0 1 0 0 1 0 0 0 1 0 0
0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0
3 alluvial 1 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0
0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0
5 alluvial 1 0 0 0 0 0 0 1 1 0 0 0 0 1 1 0
0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0
6 alluvial 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0
0 0 1 0 1 1 0 0 0 1 0 0 0 0 0 0 1 0 0
7 alluvial 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0
8 alluvial 1 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0
0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0
10 alluvial 1 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0
0 0 1 0 0 1 0 0 0 0 0 0 1 0 1 1 1 0 0
11 canyon 1 1 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0
0 0 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 0
12 canyon 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
13 canyon 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0
0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0
14 canyon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
15 canyon 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0
16 canyon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
17 canyon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0
18 canyon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1
0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0
19 canyon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0
20 canyon 1 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1
22 alluvial 1 0 0 0 0 1 0 0 0 1 0 0 1 0 1 0
0 0 0 0 0 1 0 1 1 0 0 1 0 1 0 0 1 0 0
23 alluvial 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
0 0 1 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0
", header=T)
data<-rawdata[,-1]
rownames(data)<-rawdata[,1]
library(rareNMtests)
test.data<-EcoTest.sample(data[,-1], by=data$SiteType, MARGIN=1, trace=F)
#error message and no significant difference
data2<- data[do.call(order, data),]
test.data2<-EcoTest.sample(data2[,-1], by=data2$SiteType, MARGIN=1, trace=F)
#error message and significant difference
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