[R-sig-eco] Thresholds of Synchrony in R

[Zoltan Botta-Dukat]

Dear Tania,

I suspect that there is no general threshold.
You can check significance of departure from 0.5 by randomization test:
1)  randomize your data,
2) calculate synchrony for the randomized data
3) repeat step 1 and 2 many times (at least 999)
4) p-value = min(# cases where observed S is higher than random; # cases 
where observed S is lower than random)/(number of randoms +1)

There are (at least) two ways of randomization:
- simply shuffling values within one species' time series - it is 
simple, but destroys the temporal autocorrelation within time series
- shifting values within one one species' time series (as it would be 
circular data) - it preserves the autocorrelation, so I would use it.

Best wishes,

Zoltan

2017.08.02. 18:58 keltezéssel, Tania Bird írta:
> Hi all,
> Apologies if this is more a stats question than an R question but I do need
> help with R for the solution.
>
> I'm calculating the degree of synchrony of population fluctuations through
> time in a community, based on Loreau & Mazencourt 2008 paper.
> Loreau, Michel, and Claire de Mazancourt. (2008) "Species synchrony and its
> drivers: Neutral and nonneutral community dynamics in fluctuating
> environments." The American Naturalist 172, no. 2: E48-66.
> doi:10.1086/589746.
>
> I am using this code:
>
> dat = cbind(sp1 = rnorm(100, 10, 2), sp2 = rnorm(100, 10, 2))
>      #Two species with random independent abundance sampled 100 times.
> V = var(dat)   # variance-covariance matrix for all species
>      # calculate synchrony index from covariance matrix
> synchrony = function(V) {
> d = sqrt(diag(V))
> sum(V) /sum(d%*%t(d))
> }
>
> S = synchrony(V)
>
> S runs from 0 (total Asynchrony) to 1 (total Synchrony) with 0.5 = random
> or no synchrony as described by the authors.
>
> I am wondering if there is a to calculate a threshold or value of S at
> which I can say that there is "significant Asynchrony in this community" or
>   significant Synchrony in this community". For example is 0.3 asynchronous
> or not really ?
>
> Should this threshold based on the data range or the variation itself?
> In which case how would I code this calculation?
>
> Or should I just say that anything <0.25 is significantly/very
> Asynchronous?
> In which case how can I generate a column to say
>   if S <0.25 its asynchronous or if its >0.75 its synchronous?
>
> Thanks for your feedback
> Tania
>
>
> Tania Bird MSc
> PhD Student,
> Geo Ecology Lab
> Ben Gurion University
>
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>
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-- 

Botta-Dukát Zoltán                                Zoltán BOTTA-Dukát
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Ökológiai és Botanikai Intézet                    Institute of Ecology and Botany
Magyar Tudományos Akadémia                        Hungarian Academy of Sciences
Ökológiai Kutatóközpont                           Centre for Ecological Research
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