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

[Thomas Merkling]

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
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