No, you do not need to be worried about that warning. You have rarefaction up to the observed community, and that is always constant, hence you get the warning of zero standard deviation. That should be fixed, but I’m too lazy. Contributions welcome in vegan at https://github.com/vegandevs/vegan/.
cheers, Jari Oksanen On 11 Jan 2019, at 20:09, Charlotte Reemts <cree...@tnc.org<mailto:cree...@tnc.org>> wrote: 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 [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org<mailto:R-sig-ecology@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
