Mean distance values (and errors) between groups of samples using vegan

Andr?s,

To get statistics other than the mean (SD ~ error as you wrote) you can
stack the dist object (e.g. stack.dist in mefa pkg with dim.names = TRUE)
and then calculate statistics for subsets based on your grouping variable.

Cheers,

Peter

--
P?ter S?lymos, Dept Biol Sci, Univ Alberta, T6G 2E9, Canada AB
solymos at ualberta.ca, Ph 780.492.8534, http://psolymos.github.com
Alberta Biodiversity Monitoring Institute, http://www.abmi.ca
Boreal Avian Modelling Project, http://www.borealbirds.ca


On Mon, Dec 16, 2013 at 12:23 PM, Jari Oksanen <jari.oksanen at oulu.fi> wrote:

Function meandist() should do this. Its name is kind of hint.

Cheers, Jari Oksanen
On 16/12/2013, at 21:16 PM, Andres Mellado Diaz wrote:

Dear list memnbers,

I would greatly appreciate any suggestion on how to get averaged

distance values (and errors) between groups of samples using vegan
(vegdist, dist,...).

As an example, I have a faunal table (samples by taxa, "mMCINVmmh") and

some grouping factors (for example: "gradreg_mmh") that I want to test,
like this:

vegdist(mMCINVmmh, method="bray", binary=FALSE, diag=F,

upper=F)->vegdist1

vegdist1

         TR_1_2    TR_1_3    TR_2_2    TR_2_3    TR_3_1    TR_3_2
TR_1_3 0.7361704
TR_2_2 0.1509007 0.7785157
TR_2_3 0.6465259 0.4095644 0.6832353
TR_3_1 0.8717468 0.9572968 0.8551546 0.9373980
TR_3_2 0.6925163 0.7197110 0.7428020 0.4742819 0.7800620
TR_3_3 0.8166542 0.7199418 0.8365397 0.6215122 0.8582932 0.5364242

gradreg_mmh

[1] 0 0 3 3 5 5 5

Levels: 0 3 5

So I want to get the pairwise mean distances and errors between groups

0, 3 and 5...

many thanks in advance,

Andr?s

--
Andr?s Mellado D?az

Centre for Hydrological Studies CEH-CEDEX
Water Quality Department
P? bajo de la Virgen del Puerto, 3
28005, Madrid
SPAIN


--
Andr?s Mellado D?az

Centre for Hydrological Studies CEH-CEDEX
Water Quality Department
P? bajo de la Virgen del Puerto, 3
28005, Madrid
SPAIN