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
[[alternative HTML version deleted]]
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
On Mon, 2013-06-24 at 19:33 +0800, Suparna Mitra wrote:> H > ello R-experts, > I want to do ordination plots using vegan metaMDS. > I have a where many cells have zero values. ><snip />> I am having two different kind of errors for these two data... > Error 1 > > ord1 <- metaMDS( > X > ="bray")That is fundamentally wrong - you are setting argument `X` to the character vector `"bray"`, that is not how you call metaMDS(). Hence I suspect you didn't bother to include the full code...! Let's assume you cal actually call metaMDS() correctly... The first set of warnings (not the error) come `vegdist()`. The first is from : if (method > 2 && any(rowSums(x, na.rm = TRUE) == 0)) and hence if you do which(rowSums(X, na.rm = TRUE) == 0) you'll see which rows (samples) have no counts at all. The second warning in the first set comes from if (any(is.na(d))) warning("missing values in results") hence by the time vegdist has computed the dissimilarity, those computation ended up generating one or more `NA` values. Things go downhill from there as the error generated from within metaMDS() is because we are comparing the distances with the smallest representable number and any comparison with `NA` yields `NA` and hence the first Error you see. We should probably catch that but I don't have a reproducible example to see why we don't...> 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 factorsLook at `str(data)` and if any of the columns are factors, change them to be numeric or find out why R thinks they are factors - it wouldn't normally convert numeric data to a factor when reading the data in. What is `data`? You only refer to `Genus_data`. Please try to be specific about exactly what you did - i.e. include the actual code. I suspect the things you try below are pointless as it is not zero distances that are the problem but sites for which no observations were recorded. G> 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Gavin Simpson, PhD [t] +1 306 337 8863 Adjunct Professor, Department of Biology [f] +1 306 337 2410 Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca 523 Research and Innovation Centre [tw] @ucfagls University of Regina Regina, SK S4S 0A2, Canada