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
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