[R-sig-eco] Mean distance values (and errors) between groups of samples using vegan

[Andres Mellado Diaz]

Dear Peter & Jari,

Thank you very much indeed for your quick and useful responses, I'm  
using both functions (meandist and stack.dist) for my analyses,

cheers,

Andres


Peter Solymos <solymos at ualberta.ca> escribió:

> Andrés,
>
> 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
>
> --
> Péter Sólymos, 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,
>> >
>> > Andrés
>> >
>> > --
>> > Andrés Mellado Díaz
>> >
>> > Centre for Hydrological Studies CEH-CEDEX
>> > Water Quality Department
>> > Pº bajo de la Virgen del Puerto, 3
>> > 28005, Madrid
>> > SPAIN
>> >
>> >
>> > --
>> > Andrés Mellado Díaz
>> >
>> > Centre for Hydrological Studies CEH-CEDEX
>> > Water Quality Department
>> > Pº bajo de la Virgen del Puerto, 3
>> > 28005, Madrid
>> > SPAIN
>> >
>> > _______________________________________________
>> > R-sig-ecology mailing list
>> > R-sig-ecology at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
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>>
>>
>



-- 
Andrés Mellado Díaz

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