best ordination method for binary variables

It is always useful to look at the data in multiple ways. The unique()
function will remove the duplicates in your data so that isoMDS will work:
set.seed(42)
x <- matrix(sample(0:1, 20, replace=TRUE), 10, 2)
x
[,1] [,2]
 [1,]    1    0
 [2,]    1    1
 [3,]    0    1
 [4,]    1    0
 [5,]    1    0
 [6,]    1    1
 [7,]    1    1
 [8,]    0    0
 [9,]    1    0
[10,]    1    1
unique(x)
[,1] [,2]
[1,]    1    0
[2,]    1    1
[3,]    0    1
[4,]    0    0

----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of marco milella
Sent: Wednesday, February 27, 2013 6:09 AM
To: r-help at r-project.org
Subject: [R] best ordination method for binary variables

Dear all,

I'm analyzing a dataset (A) of 400 cases with 11 binary variables.
Unfortunately, several (actually a lot) of cases are identical. NA are
also
present.
I want to to plot distances between cases.
For this, I obtained a distance matrix by dist(A, method="binary"). I
then
analyzed the obtained distance via Principal coordinate analysis with
cmdscale(). Results are fine.
However, do you think this is a wrong approach? After reading the
literature and previous posts, I noticed that non metrical MDS (via
isoMDS
or metaMDS) could be a more correct choice.
The problem is that, when trying this methods, I immediately get
problems
due to the identity between several of mycases or the presence of NA.

Typical error messages are

*"Error in isoMDS(DistB, k = 3) : zero or negative distance between
objects
1 and 2"*

or

*"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 factor"*

Do you think Principal coordinate analysis on a binary distance matrix
is a
decent strategy?
Thanks for any suggestion
marco

	[[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.

best ordination method for binary variables

Thread (2 messages)