Error with metaMDS
Hi, On Mon, Jun 24, 2013 at 12:04 PM, Suparna Mitra
<suparna.mitra.sm at gmail.com> wrote:
Dear Sarah, Thanks for your reply. But I don't have any site where all the species are 0.
Well, that's what this says:
1: In distfun(comm, method = distance, ...) : you have empty rows: their dissimilarities may be meaningless in method ?bray?
Is there anyway to calculate the dissimilarity between sites where it computes only the non-zero species values. Excluding all the zero event will result a big loss in species data. I don't want to delete the cases where may be 5out of 8 sites have species info, only 3 don't have.
There's no reason to delete those. Bray-Curtis and similar metrics consider only joint presences, not joint absences. If you have a lot of sites with no species in common, it can also cause problems. That's what vegan::stepacross is intended to deal with.
Should I replace zero with a very small number. What is the best thing to do in such cases?
The best thing to do in such cases is to provide a reproducible example to R-help. At the very least, str(X) str(data) # called in metaMDS() but not described; also, don't call your data data and double-check to make sure you don't have any all-zero rows or NA values in your data. Sarah
On 24 June 2013 21:24, Sarah Goslee <sarah.goslee at gmail.com> wrote:
Hi, What do you expect the dissimilarity between a site with no species and a site with some species to be? If you want to use Bray-Curtis dissimilarity, you need to drop the sites with no species, as the error message suggests. But if you can answer my first question, you may be able to select a different dissimilarity metric that matches your expectations numerically. Sarah On Mon, Jun 24, 2013 at 7:33 AM, Suparna Mitra <suparna.mitra.sm at gmail.com> wrote:
H
ello R-experts,
I want to do ordination plots using vegan metaMDS.
I have a where many cells have zero values.
Data structure:
X[1:10,1:14]
Height.1 Height.2 Height.3 Height.4 Height.5 Height.6 Height.7
Height.8 Height.9 Height.10 Height.11 Height.12 Height.13
D30I1A 46 0 0 0 0 0 0
0 0 0 39 0 98
D30I1B 46 0 0 0 0 0 0
0 0 0 39 0 98
D30I1C 70 0 0 0 0 0 0
0 0 0 0 85 0
D30I2A 47 0 0 0 0 0 0
0 0 0 49 0 105
D30I2B 68 0 0 0 0 0 0
0 0 0 83 0 214
D30I2C 0 75 0 0 0 0 0
0 0 0 0 83 0
D30I3A 48 0 0 0 0 0 0
0 0 0 42 0 107
D30I3B 64 0 0 0 0 0 0
0 0 0 72 0 177
D30I3C 72 0 0 0 0 0 0
0 0 0 0 96 0
D30M1A 60 0 0 0 0 0 0
0 0 0 74 0 169
Another data structure
Genus_data[1:10,1:14]
Sample Acanthamoeba Acidianus Aegilops Alphapapillomavirus
Asfivirus
Brassica Buchnera Coprinellus Diaphorobacter Hartmannella Ignicoccus
1 HS1_S1 0 0 0 0
0
0 0 0 0 0 0
2 HS2_S2 0 1 1 0
0
0 0 0 0 1 0
3 HS3_S3 0 0 0 1
0
0 1 1 1 0 0
4 HS4_S4 0 0 0 0
1
0 0 0 0 0 0
5 HS13_S5 0 0 0 0
0
0 0 0 0 0 0
6 HS14_S6 0 0 0 0
0
1 0 0 0 0 0
7 HS15_S7 0 0 0 0
0
0 0 0 0 0 0
8 HS16_S8 0 0 0 0
0
0 0 0 0 0 1
9 HS25_S9 1 0 0 0
0
0 0 0 0 0 0
I am having two different kind of errors for these two data...
Error 1
ord1 <- metaMDS(
X
="bray")
Square root transformation
Wisconsin double standardization
Error in if (any(dist < -sqrt(.Machine$double.eps))) warning("some
dissimilarities are negative -- is this intentional?") :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In distfun(comm, method = distance, ...) :
you have empty rows: their dissimilarities may be meaningless in
method
?bray?
2: In distfun(comm, method = distance, ...) : missing values in results
Error 2
ord.data= metaMDS(data, distance="bray")
Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0))
{
:
missing value where TRUE/FALSE needed
In addition: Warning message:
In Ops.factor(left, right) : < not meaningful for factors
I searched all the details of metaMDS where it is suggested to avail the
argument 'zerodist'
So I tried both
X.dist1 <- metaMDSdist(X, method="bray",zerodist = "ignore")
X.dist2 <- metaMDSdist(X, method="bray",zerodist = "add")
Can Please help me with this.
Thanks,
Mitra
Sarah Goslee http://www.functionaldiversity.org