different symbols to NMDS graph: it works PARTIALLY!??!?

Cristabel:

check that the number of scores equals the length of your
naming vector, i.e.,

dim(ScoresNMDS) [1]

shoud be equal to

length(pos$for_pos_anl)

And check also  that the mentioned categories are realy
present in the vector, e.g.:

table(pos$for_pos_anl)

HTH,

Marcelino


At 08:50 13/01/2011,
cristabel.duran at waldbau.uni-freiburg.de wrote:

Dear list, I have a problem adding points with different

symbols to my NMDS ordination graph. I performed a NMDS
ordination with this vegan function (metaMSD) as follow:
      metaf <- metaMDS(spp, distance = "bray", k = 3,
trymax = 1000, wascores = T, autotrasform = F, shrink=T,
noshare = 1) spp is my species matrix. Then, I want to
assign different colors and symbols to my plots ("sites")
according to three categories. These categories are in
the vector called pos with the categories "gap", "border"
and "forest". For that I am using the following functions
and commands:      ScoresNMDS<-scores(metaf)
plot(metaf,type="none",choices = c(1,3))
points.metaMDS(ScoresNMDS[pos$for_pos_anl=="border",],
display="sites",choices = c(1,3), pch=16, cex=0.8,
col="green")

= c(1,3),pch=17, cex=0.8, col="black")

= c(1,3), pch=4,col="red",cex=0.8, bg="red") The problem:
I get a empty ordination graph, were I am able to add the
points corresponding to the first two categories
("border" and "gap"). The strange thing, is that it is
impossible to add the third category, I get this error
message:       Error in dimnames(x) <- dn :    length of
'dimnames' [1] not equal to array extent Already tried: -
The length of my explanatory variable (pos) have the same
length that the species matrix. - Changing the name from
my open office spreadsheet, in the case there is a
strange character. - Change colors and symbols. -
etc...etc. What I also do not understand, is why it works
for some categories of the same vector and why not for
the last category. The same happens with ordiellipse and
ordihull. I would appreciate your help! Thanks in advance
and have a nice day! Cristabel. Cristabel Dur??n Rangel.
PhD Student. Institute of Silviculture. Faculty of Forest
and Environmental Sciences. University of Freiburg.
Germany Telf: +49 (761) 203 8604 (ofc) ?Man lernt die
Physiognomie einer Landschaaft desto besser kennen, je
genauer man die einzelnen Z??ge auffa??t, sie
untereinander vergleicht und so auf dem Wege der Analysis
den Quellen der Gen??sse nachgeht, die uns das gro??e
Naturgem??lde bietet.??? Alexander von Humboldt, 1799

Hola Marcelino,

I did now what you suggested,
the lengths of dim(ScoresNMDS) [1] and
length(pos$for_pos_anl) are the same.
and all the three categories exits in the vector...
I still do not find the solution for the problem.

On 13/01/11 11:03 AM,
"cristabel.duran at waldbau.uni-freiburg.de"
<cristabel.duran at waldbau.uni-freiburg.de> wrote:

Hola Marcelino,

I did now what you suggested,
the lengths of dim(ScoresNMDS) [1] and
length(pos$for_pos_anl) are the same.
and all the three categories exits in the vector...
I still do not find the solution for the problem.

Cristabel,

Do not argue with computers: you'll lose. If the computer
doesn't find an
item, it doesn't exist. Computers are more pedantic than
we humans, and they
are correct. It may happen, for instance, that the name
of your item is
"forest " (note the blank), and then there is no "forest"
(note the missing
blank). It is rather easy to see what you get with

ScoresNMDS[pos$for_pos_anl=="forest",]

If those three cases you listed in your message are the
only things that you
should display, the following (or a variant of this)
should work if 'metaf'
is a metaMDS() result, and pos$for_pos_anl is a factor
where levels are
ordered as c("border", "gap", "forest"):
 
plot(metaf,type="none",choices = c(1,3))
## must be a factor
indx <- as.numeric(pos$for_pos_anl)
points(metaf,
display="sites",choices = c(1,3),
  pch=c(16,17,4)[indx], cex=0.8,

  col=c("green", "black", "red")[indx] )
## these use internal ordering of levels: check
legend("topleft", levels(pos$for_pos_ani),
pch=c(16,17,4), col =
c("green","black", "red"))

All this is completely unchecked, and probably your
factor levels are in
different order and you must change the arguments
correspondingly.

Cheers, Jari Oksanen

Cheers, jari Oksanen