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...@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
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