[R] Error with metaMDS

[Sarah Goslee]

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