Hello Rich, I may be able to provide some insight into this... Apologies in advance if my response is too big. (First time user)

1:
 I would think they are included because of familiarity and different 
usage scenario's. (see 2). ANOSIM has some advantages under very 
specific usage scenario's, which would make it hang around, and also, 
when it comes to things like this, where there are multiple options for 
multiple different usage scenarios, it makes sense to keep as many 
packages "online": This would provide alternative choices in the event 
of a package failing to operate, or user preference.

2: The main thing that ADONIS has over ANOSIM/MRPP is partitioning of variance, allowing for interaction terms. 

ANOSIM
 isn't as nice in it's approach, simply clumping together "replicates" 
and doing seperate permutations (As you know already). mrpp also does 
this (Does not allow for interpretation of complex experimental design).


ANOSIM/MRPP
 would be used for simple experiments, where you would believe there to 
be no interactions, typically 1 factor designs (eg; Is there a 
difference in species composition at two sites on an urban road). Also, 
the similarity co-efficients used are different; As far as I am aware, 
ANOSIM uses Bray-Curtis measures, whereas MRPP has got options.

This
 further differentiates ANOSIM from MRPP: Essentially, MRPP can be used 
for different data types (in combination with experimental designs) 
wheras in my experience, ANOSIM is restricted to Bray-Curtis, eg: I'd 
use MRPP for 1 factor presence/absence, and ANOSIM for 1 factor 
abundance indices. 

Having said all of that; from my personal 
experience I'd recommend to just default to ADONIS: It allows for 
multi-factorial designs with interactions, multivariate designs with 
interactions, the amount of information it retains is better than ANOSIM
 and MRPP (ANOSIM/MRPP are rank based, whereas ADONIS uses the actual 
indice), and generally speaking, the results are easier to interpret.

Cheers

Date: Mon, 4 Nov 2013 08:17:13 -0800
From: ml-node+s471788n7578489h2@n2.nabble.com
To: alexander.angeloski@hotmail.com
Subject: Multivariate Analyses of Ecological Communities



	   I've read the docs for anosim, adonis, and mrpp and am currently reading

the vegan tutorial. Toward the end of the anosim and mprr docs the author

writes that each has potential shortcomings and recommends the adonis

package be used instead. This leads to my two questions:


   1) Why are anosin and mrpp packages still maintained and included? That

they are suggests question


   2) Under what circumstances are these two packages appropriately used?


TIA,


Rich


-- 

Richard B. Shepard, Ph.D.          |      Have knowledge, will travel.

Applied Ecosystem Services, Inc.   |

<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863


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