Dear List,
I have an environmental data set with several missing values that I
am trying to relate to a community structure data set using a mantel
test. One solution to the missing data problem seems to be multiple
imputation; I am using the Amelia package. This generates several (five in
Hi Jacob, comments below.
On Aug 18, 2013 2:31 PM, "Jacob Cram" wrote:
>
> Dear List,
> I have an environmental data set with several missing values that I
> am trying to relate to a community structure data set using a mantel
> test. One solution to the missing data problem seems to be m
Krzystof,
Thank you for your reply. It is promising that you think that Li's
method should work for imputed mantel results. That said, I am a bit over
my head with the math in the Li et al reference. Could you (or anyone on
this list) provide an R-code example of how D would be calculated
Dear List,
This is Elaine.
I am using metaMDS in package vegan to plot NMDS.
However, I want to draw the points using different colors according to
island sites.
For example:
island site 1: island B, C, D => blue
island site 2: island A, E, F => green
island site 3: island G, H, J => red
I think D is the easy part, it should be the mean Mantel test statistic
from all the imputed data sets. The rest I'm not sure yet, but if you get
a good answer from someone else, I'd appreciate it if you shared it.
Krzysztof
On Aug 18, 2013 4:44 PM, "Jacob Cram" wrote:
> Krzystof,
>Thank
I assume that the dataset "island" is yours so I've made that equivalent to an
example dataset in vegan named "dune". Below is a rather brute force way to
assign colors.
library(MASS)
library(vegan)
data(dune)
island = dune
island.NMDS <- metaMDS(island,k=2, distfun = betadiver,
distance
