[R-sig-eco] What package and steps needed to emulate legacy NTSYS ?

[Bruce Miller]

Hi all,

Especially Jari....

There are now  a lot of clustering algorithm packages in R. What would 
be the most usable package to run similar analyses as the older NTSYSpc?

I was able to dig through an older backup image of one of my hard drives 
and resurrected NTSYSpc v. 2.11 but would prefer to set up similar 
analyses in R.

To have similar results the starting matrix data frame would be OTUs 
(critters) as rows and the columns are values of things needing to be 
compared.  These are comprised of both 1/0 data for locations and 
continuous variables for measurement data (critter sizes and in this 
case echolocation call parameters).

Running NTSYSpc the initial data matrix may or may not first be 
standardized.
Then a similarity coefficients are computed to generate a new matrix 
which is used as input for a clustering SAHN (UPGMA using Euclidean 
distance) then graphically the tree is displayed (GGPLOT2?)

I am sure there is a way to do this, but have not found vignettes for 
the various R packages to explain code to set this up.

Thanks for any suggestions.

Bruce