Re: [R-sig-eco] metaMDS - avoid species overlap in plots
Hello,
This so frequently asked that it is a FAQ. Try
vegandocs("FAQ")
in R and see question 2.18.
It is also such a typical problem that it is in vegan intro: try
vegandocs("intro")
in R after loading vegan and see chapter 2.1.
Gavin Simpson has a blog article on plots, but I'm now on my phone and can't
check the web easily.
HTH, Jari Oksanen
alkuperäinen viesti
Lähettäjä: Gian Maria Niccolò Benucci
Lähetetty: 25.06.2012, 12:40
Vastaanottaja: r-sig-ecology@r-project.org
Aihe: [R-sig-eco] metaMDS - avoid species overlap in plots
Hi community,
Very simple question. How to avoid overlap plot of species in a metaMDS()
diagram?
I used this command...
> text(metaMDS_new2, display=c("species"), cex=0.6)
but some species are plotted one over the other and is not simple to read
the diagram.
Thanks for helping,
--
Gian
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[R-sig-eco] Fwd: metaMDS - avoid species overlap in plots
Hi!
library(vegan)
data(dune)
sol <- metaMDS(dune)
# use argument air! see ?orditorp:
plot(sol, type = "n")
orditorp(sol, displ = "sp", air = 1)
# or use pointLabel() from maptools package. this should avoid overplotting
of text -
# here is an example where I added cex according to species frequencies.
library(maptools)
x = as.vector(sol$species[,1])
y = as.vector(sol$species[,2])
w = row.names(sol$species)
cex.lab = colSums(dune > 0) / nrow(dune) + 1
col.lab = rgb(0.2, 0.5, 0.4, alpha = 0.6)
plot(sol, type = "n")
points(sol, displ = "species", cex = 1, pch = 4, col = 3)
pointLabel(x, y, w, col = col.lab, cex = cex.lab)
HTH,
Kay
2012/6/25 Gian Maria Niccolò Benucci
> Hi community,
>
> Very simple question. How to avoid overlap plot of species in a metaMDS()
> diagram?
>
> I used this command...
>
> > text(metaMDS_new2, display=c("species"), cex=0.6)
>
> but some species are plotted one over the other and is not simple to read
> the diagram.
>
> Thanks for helping,
>
> --
> Gian
>
>[[alternative HTML version deleted]]
>
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> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
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[R-sig-eco] Does anybody know how many records adehabitat can manage to perform kernelUD on as R keeps crashing
Hello
I am trying hard to use adehabitat for estimating kernel home range using the
LSCV method of smoothing but R crashes every time I try to perform this
analysis on data sets that have over 15,000 rows in a .csv file - whereas if I
am using the adhoc method of smoothing it works fine.
Any suggestions?
Many thanks
Louise
R code below:
data<-read.csv("BoobyFutm.csv")
xy = data[c("X", "Y")]
id<-data[,c("ID")]
coordinates(data) = c("X", "Y")
class(data)
kud<-kernelUD(data, h="LSCV", hlim=c(0.01,10)
School of Environmental Sciences
University of Liverpool
Brownlow Hill
L69 3GP
www.puffinisland.org.uk
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[R-sig-eco] metaMDS - avoid species overlap in plots
Hi community,
Very simple question. How to avoid overlap plot of species in a metaMDS()
diagram?
I used this command...
> text(metaMDS_new2, display=c("species"), cex=0.6)
but some species are plotted one over the other and is not simple to read
the diagram.
Thanks for helping,
--
Gian
[[alternative HTML version deleted]]
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