[R-sig-ME] spatial auto-correlation or more complicated pseudo-replication?

[Thierry Onkelinx]

Dear Thomas,

I'd say that there is nothing that suggests spatial autocorrelation in the
residuals nor in the random effects. There might be spatial autocorrelation
in the response variable, but that is handled by the covariates in the
model. The pair random effect takes care of the pseudo-replication.

IMHO you can't state that the treatment of the focal pair influences the
surrounding pairs. If that was the case, I'd expect to see spatial
autocorrelation.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx using inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
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Op wo 22 apr. 2020 om 23:24 schreef Thomas Merkling <
thomasmerkling00 using gmail.com>:

> Dear Thierry,
>
> Thanks a lot for your precious help.
>
> I changed the width argument of variogram() and obtained similar patterns
> (for egg
> <https://drive.google.com/open?id=1Ktinx0gm4sRNS6_r5VEAg_pdND51eHQd> and
> for laydate
> <https://drive.google.com/open?id=1YoMIK1jax1dhBe94yswbHvWF_CyKDNL5>).
> Doing the same thing with the random intercepts gave similar patterns too
> (for egg
> <https://drive.google.com/open?id=1fGlXObzhRj2g9J9ZnYIO8V6q6d-PmgS8> and
> for laydate
> <https://drive.google.com/open?id=1U4Q9h7foZM6q54_yteFAFHo6SVHby9mJ>).
>
> Can I then conclude that there is no need to correct for spatial
> auto-correlation?
>
> Given that treatment of a focal pair influences the value of another
> predictor for surrounding pairs, is there any other random effect that I
> should add? Or is this test for spatial auto-correlation enough?
>
> Kind regards,
> Thomas
> On 22/04/2020 19:45, Thierry Onkelinx wrote:
>
> Dear Thomas,
>
> Have a look at the data.frame in the variogram() output. Given your
> variogram I expect a high number of pairs (np variable) at short range and
> a low (< 100) at large ranges. Note the width and cutoff arguments of
> variogram().  The defaults are 1/3 of the diagonal of the bounding box for
> cutoff and cutoff/15 for width. These are likely suboptimal for your data.
> I'd set width to slightly larger than the distance between two adjacent
> nests. Increase the width if the variogram is unstable.
> If you still get a similar picture as the ones you send, then there then
> residuals are iid and thus you don't need to correct for spatial
> autocorrelation.
>
> Given the strong correlation between pair and location, the pair random
> effect will take up some of the spatial autocorrelation. You could make a
> variogram of the random intercepts. There should be a pure nugget effect
> too.
>
> Best regards,
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkelinx using inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
>
> ///////////////////////////////////////////////////////////////////////////////////////////
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> ///////////////////////////////////////////////////////////////////////////////////////////
>
> <https://www.inbo.be>
>
> .....
>>>
>>>

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