Eda,

How many permutations do you use? Have you tried setting the RNG seed via
set.seed() ? Also, if you have borderline p-values that change from run to
run it might indicate not so strong discrimination by the given clustering
of sites.

Cheers,

Peter

--
Péter Sólymos
780-492-8534 | solymos@ualberta.ca | http://psolymos.github.com
Alberta Biodiversity Monitoring Institute http://www.abmi.ca
Boreal Avian Modelling Project http://www.borealbirds.ca


On Wed, Jan 1, 2014 at 7:14 PM, Addicott Eda <
Eda.Addicott@science.dsitia.qld.gov.au> wrote:

> Why do I get inconsistent p-values for indicator values of species when
> I run IndVal (in the labsdv package) on exactly the same dataset? I have
> tested this with a small dataset (40 samples and 55 species) and a
> larger dataset (334 samples and 545 species) and on different numbers of
> clusters ranging from 2 to 8. The 'p' values change enough with
> different test runs to affect the number of significant species in a
> cluster.
>
> thanks
>
> Eda Addicott
> Principal Botanist, Queensland Herbarium,
> Australian Tropical Herbarium
> ph:  07 4232 1807 fax: 07 4232 1842
> Email: Eda.Addicott@qld.gov.au
>
> Australian Tropical Herbarium
> Sir Robert Norman Building (E2) JCU Cairns Campus
> P.O.Box 6811
> Cairns,  QLD 4870
>
>
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