@David,
to ask for statistical *and* biological significance (effect size) is
indeed essential and
this statement does apply in general - but it does not contribute to a
solution of my problem at all..

@Chris,
as I want to test total diversity of each community (diversity calculated
from samples collapsed over groups) I have only two values and thus
ANOVA-like tests are not an option.

Kind regards,
Kay

ps: Sorry Chris for double posting.


>
> 2012/4/26 Chris Howden <chris@trickysolutions.com.au>
>
>> Standard Hypothesis statistical testing often starts with the null
>> hypothesis that 2 things are identical, or that 2 population means are
>> identical. The p value is then used to reject this null and accept the
>> alternative, that they are indeed different.
>>
>> Practically we're actually asking if we have enough information to indeed
>> say they are different.
>>
>> I do agree though that stopping there is a bit silly. If there is a
>> statistical difference then we next need to look at the effect size or in
>> other words the magnitude of the difference and decide if this is
>> ecologically meaningful.
>>
>>
>> Chris Howden B.Sc. (Hons) GStat.
>> Founding Partner
>> Evidence Based Strategic Development, IP Commercialisation and Innovation,
>> Data Analysis, Modelling and Training
>> (mobile) 0410 689 945
>> (fax) +612 4782 9023
>> chris@trickysolutions.com.au
>>
>>
>>
>>
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>> expressly stated, the views of the writer are not those of the company.
>> Tricky Solutions always does our best to provide accurate forecasts and
>> analyses based on the data supplied, however it is possible that some
>> important predictors were not included in the data sent to us. Information
>> provided by us should not be solely relied upon when making decisions and
>> clients should use their own judgement.
>>
>>
>> -----Original Message-----
>> From: r-sig-ecology-bounces@r-project.org
>> [mailto:r-sig-ecology-bounces@r-project.org] On Behalf Of David Valentim
>> Dias
>> Sent: Thursday, 26 April 2012 2:36 PM
>> To: r-sig-ecology@r-project.org
>> Subject: Re: [R-sig-eco] Testing difference between diversity indices with
>> vegan::oecosimu
>>
>> Hello Cichini,
>>
>> I cannot help with your code but seems like you have a silly hypothesis.
>> Think about it: Probability of two communities to be identical?
>> You need to restate it in some more useful way. We already know most
>> things are different but with what magnitude? Which factors are causing
>> these changes? How these changes matter from the environment and us?
>>
>> 2012/4/25 Chris Howden <chris@trickysolutions.com.au>
>>
>> > Why not try some type of ANOVA style glm?
>> >
>> > Chris Howden
>> > Founding Partner
>> > Tricky Solutions
>> > Tricky Solutions 4 Tricky Problems
>> > Evidence Based Strategic Development, IP Commercialisation and
>> > Innovation, Data Analysis, Modelling and Training
>> >
>> > (mobile) 0410 689 945
>> > (fax / office)
>> > chris@trickysolutions.com.au
>> >
>> > Disclaimer: The information in this email and any attachments to it
>> > are confidential and may contain legally privileged information. If
>> > you are not the named or intended recipient, please delete this
>> > communication and contact us immediately. Please note you are not
>> > authorised to copy, use or disclose this communication or any
>> > attachments without our consent. Although this email has been checked
>> > by anti-virus software, there is a risk that email messages may be
>> > corrupted or infected by viruses or other interferences. No
>> > responsibility is accepted for such interference. Unless expressly
>> > stated, the views of the writer are not those of the company. Tricky
>> > Solutions always does our best to provide accurate forecasts and
>> > analyses based on the data supplied, however it is possible that some
>> > important predictors were not included in the data sent to us.
>> > Information provided by us should not be solely relied upon when
>> > making decisions and clients should use their own judgement.
>> >
>> > On 26/04/2012, at 7:19, Kay Cichini <kay.cichini@gmail.com> wrote:
>> >
>> > > Hello all,
>> > >
>> > > I'd like to test if total diversity differs between two communities.
>> > > For each community several samples were taken and abundances
>> > > collapsed over groups to compute total diversity for each group. I
>> > > tried to use vegan::oecosimu to test non-randomness of my statisitc
>> > > (difference in Simpson-Diversity indices of collapsed abundances) -
>> > > however, I am not quite sure if I oversee posssible pitfalls:
>> > >
>> > > library(vegan)
>> > > data(dune)
>> > >
>> > > # a grouping variable:
>> > > gr <- gl(2, nrow(dune)/2)
>> > >
>> > > divdiff <- function(x) abs(diversity(colSums(x[gr == "1", ]), "simp")
>> -
>> > >                           diversity(colSums(x[gr == "2", ]),
>> > > "simp")) # testing function:
>> > > divdiff(dune)
>> > >
>> > > oecosimu(dune, divdiff, "r2dtable", nsimul = 1999) # oecosimu with
>> > > 1999 simulations # simulation method r2dtable # alternative
>> > > hypothesis: true mean is not equal to the statistic
>> > > #           statistic        z     2.5%      50% 97.5% Pr(sim.)
>> > > # statistic   0.00275 -0.20996  0.00013  0.00280  0.01     0.98
>> > >
>> > >    [[alternative HTML version deleted]]
>> > >
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>>
>>
>> --
>> Currmculo: http://lattes.cnpq.br/7541377569511492
>>
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