spatial auto-correlation or more complicated pseudo-replication?

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 at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be


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