[R-sig-eco] Testing difference between diversity indices with vegan::oecosimu
Chris Howden
chris at trickysolutions.com.au
Thu Apr 26 09:53:51 CEST 2012
Then use a t test, unless the underlying distribution is exceptionally
skewed if they're means and the sample size is large enough u should
be able to assume normality.
If not the try a median test.
However u may find a more accurate result if rather than collapsing
over both communities u incorporate your study design via blocking or
mixed modelling.
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
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chris at trickysolutions.com.au
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On 26/04/2012, at 17:18, Kay Cichini <kay.cichini at gmail.com> wrote:
> @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 at 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 at 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.
>>>
>>>
>>> -----Original Message-----
>>> From: r-sig-ecology-bounces at r-project.org
>>> [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of David Valentim
>>> Dias
>>> Sent: Thursday, 26 April 2012 2:36 PM
>>> To: r-sig-ecology at 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 at 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 at 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 at 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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