[R-sig-eco] Missing species names in metaMDS object

hilasegre hilasegre at gmail.com
Thu Oct 24 15:07:47 CEST 2013 

Hello,
I'm trying to run a nMDS on presence/absence data.
I have a species over sites matrix with 450 sites and 186 species, in
similar structure to the matrix varespec shown in this tutorial
http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf.
The only difference is the data is 0/1 and not frequncy.

metaMDS runs fine and i am able to show the sites scores using ordiplot, but
as for species - i can plot the scores but not the labels. This might be
because the item spcies is missing these values. This is my metaMDS object
species item:
$ species   : num [1:186, 1:2] -0.0249 -0.11 -0.4334 -0.6566 0.4679 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:2] "MDS1" "MDS2"
  ..- attr(*, "shrinkage")= Named num [1:2] 0.413 0.24
  .. ..- attr(*, "names")= chr [1:2] "MDS1" "MDS2"
  ..- attr(*, "centre")= Named num [1:2] -0.1466 0.0388
  .. ..- attr(*, "names")= chr [1:2] "MDS1" "MDS2"

This is code i ran:
Sps.mds=metaMDS(spp_sites_mat, distance="jaccard", k=2,autotransform=F)

and this is the data matrix:
str(spp_sites_mat)
List of 186
 $ ADON.CUPA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ AEGI.GENI: num [1:450] 0 0 0 0 0 1 1 0 1 0 ...
 $ AINS.TRAC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ AJUG.CHAM: num [1:450] 0 1 0 0 0 0 0 0 0 0 ...
 $ ALCE.ACAU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ALKA.STRI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ALLI.STAM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ALOP.UTRI: num [1:450] 0 1 1 0 0 0 0 0 1 0 ...
 $ ALYS.MINU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ANAG.ARVE: num [1:450] 0 0 0 1 0 0 0 0 0 0 ...
 $ ANCH.AEGY: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ANDR.TELE: num [1:450] 1 1 0 0 0 0 0 0 1 0 ...
 $ ANEM.CORO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ANTH.HEBR: num [1:450] 1 0 0 1 1 0 0 0 0 0 ...
 $ ANTH.PSEU: num [1:450] 0 1 1 0 0 0 0 0 0 0 ...
 $ ANTI.ORON: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ AREN.LEPT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ARTE.SQUA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASPH.RAMO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASTR.ASTE: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASTR.CALL: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASTR.HAMO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASTR.PELE: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASTR.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ASTR.TRIB: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ATRA.CANC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ AVEN.BARB: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ AVEN.STER: num [1:450] 1 1 1 1 0 0 0 0 0 1 ...
 $ BELL.FLEX: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ BISC.DIDY: num [1:450] 0 0 0 0 0 0 0 0 0 1 ...
 $ BORA.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ BROM.ALOP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ BROM.FASC: num [1:450] 0 0 0 0 1 1 1 1 1 0 ...
 $ BROM.LANC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ BROM.SCOP: num [1:450] 0 1 0 1 1 0 0 0 0 0 ...
 $ CALE.ARVE: num [1:450] 0 0 1 1 0 0 0 0 0 0 ...
 $ CALE.PALA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CAMP.ERIN: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CAMP.HIER: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CAMP.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CART.TENU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CATA.LUTE: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CATA.RIGI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CENT.CROC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CHAE.TRIC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CHIL.IPHI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CHRY.CORO: num [1:450] 0 0 0 0 0 0 0 1 0 0 ...
 $ CLYP.JONT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ COMP.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CONV.ALTH: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CORO.SCOR: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CRAS.ALAT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CREP.ASPE: num [1:450] 1 0 0 1 1 0 0 0 0 0 ...
 $ CREP.SANC: num [1:450] 0 1 1 0 0 0 0 0 0 0 ...
 $ CRUP.CRUP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CUSC.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ CYNO.DACT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ DAUC.CARO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ DIAN.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ECHI.ADEN: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ECHI.JUDA: num [1:450] 0 0 0 0 0 1 0 1 0 1 ...
 $ EROD.GRUI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ EROD.MALA: num [1:450] 0 0 0 0 0 1 0 0 0 0 ...
 $ EROD.MOSC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ERUC.HISP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ERYN.CRET: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ EUPH.AULA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ EUPH.CHAM: num [1:450] 0 1 0 0 0 0 0 0 1 0 ...
 $ EUPH.HELI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ EUPH.OXYO: num [1:450] 0 0 0 1 0 1 0 0 0 0 ...
 $ EUPH.PEPL: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ FACT.ASCH: num [1:450] 0 0 0 0 0 0 1 0 0 0 ...
 $ FERU.COMM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ FILA.CONT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ FILA.PALA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ FILA.PYRA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GAGE.COMM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GALI.DIVA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GALI.JUDA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GALI.SETA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GERA.MOLL: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GERA.ROTU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ GERO.HYBR: num [1:450] 0 1 0 1 1 0 0 0 0 0 ...
 $ HEDY.RHAG: num [1:450] 1 0 0 0 0 0 0 0 0 0 ...
 $ HELI.ROTU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ HELI.SALI: num [1:450] 0 0 0 0 1 1 0 0 1 0 ...
 $ HIPP.UNIS: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ HIRS.INCA: num [1:450] 0 0 0 1 0 0 0 0 1 1 ...
 $ HORD.BULB: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ HORD.SPON: num [1:450] 0 0 0 1 1 0 0 0 0 0 ...
 $ HYME.CIRC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ HYPA.HIRT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ IRIS.PALA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ ISAT.LUSI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ LAGO.CUMI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ LATH.APHA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ LATH.BLEP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ LATH.HIER: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
 $ LATH.MARM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
  [list output truncated]
 - attr(*, "row.names")= int [1:450] 1 2 3 4 5 6 7 8 9 10 ...

I have no idea why are the species names missing, there are no warning. I
only found questions regarding missing species scores, but that doesn't seem
to be the problem here.

Any idea?
Thank's!
Hila



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