Extract the variance-covariance matrix of the residuals, usually noted $$\Sigma$$ in PLN models. This captures the correlation between the species in the latent space.
# S3 method for PLNfit
sigma(object, ...)an R6 object with class PLNfit
additional parameters for S3 compatibility. Not used
A semi definite positive matrix of size p, assuming there are p species in the model.
coef.PLNfit(), standard_error.PLNfit() and vcov.PLNfit() for other ways to access $$\Sigma$$.
data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLN(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
#>
#> Initialization...
#> Adjusting a full covariance PLN model with nlopt optimizer
#> Post-treatments...
#> DONE!
sigma(myPLN) ## Sigma
#> Che Hyc Hym Hys Psy
#> Che 2.527734257 -0.009344912 0.36051824 0.44484795 -0.0177734746
#> Hyc -0.009344912 1.910233618 0.11088664 0.27018082 -0.1462163407
#> Hym 0.360518238 0.110886639 1.24495205 0.86538169 -0.1181925716
#> Hys 0.444847950 0.270180821 0.86538169 2.66399438 -0.1462741758
#> Psy -0.017773475 -0.146216341 -0.11819257 -0.14627418 0.0759307105
#> Aga 0.308896948 -0.131967970 0.51391634 0.42593658 0.0012211584
#> Glo 0.089322923 0.171495067 0.20978700 0.34286134 -0.0496295747
#> Ath 0.352173438 0.110019742 0.38547548 0.60776202 -0.0477698766
#> Cea -0.008878925 0.005234362 -0.02004892 -0.01511599 0.0002358211
#> Ced 0.337660962 0.221739019 0.50810182 0.68112227 -0.0979195090
#> Set -0.059203176 0.477452532 -0.18250369 0.13822860 -0.0912550351
#> All 0.272620279 -0.263659047 0.68131546 0.37023031 -0.0047654768
#> Han -0.182549673 0.624603685 0.20959838 0.13522918 -0.2880156121
#> Hfo -0.362666693 0.560916354 -0.39290753 -0.18177430 -0.1457770643
#> Hsp -0.442015708 0.672963257 -0.33247332 -0.17520759 -0.1912863865
#> Hve 0.312235381 -0.131799658 0.16117708 0.24151549 0.0456368106
#> Sta 0.363864989 0.256329406 0.47804168 0.61396464 -0.1211635529
#> Aga Glo Ath Cea Ced
#> Che 0.308896948 0.089322923 0.35217344 -0.0088789246 0.337660962
#> Hyc -0.131967970 0.171495067 0.11001974 0.0052343620 0.221739019
#> Hym 0.513916344 0.209787004 0.38547548 -0.0200489228 0.508101818
#> Hys 0.425936581 0.342861341 0.60776202 -0.0151159854 0.681122272
#> Psy 0.001221158 -0.049629575 -0.04776988 0.0002358211 -0.097919509
#> Aga 1.101329015 -0.063976931 0.19729936 -0.0208664652 0.219302536
#> Glo -0.063976931 1.120407358 0.22533155 0.0015808456 0.226510499
#> Ath 0.197299360 0.225331547 1.37536750 -0.0063345101 0.442930801
#> Cea -0.020866465 0.001580846 -0.00633451 0.0397071415 -0.007104494
#> Ced 0.219302536 0.226510499 0.44293080 -0.0071044940 0.958290847
#> Set -0.301448464 0.293179694 0.09734287 0.0142972408 0.194585282
#> All 0.593013434 -0.077512635 0.08818927 -0.0232183144 0.080595332
#> Han -0.171202850 -0.189551382 -0.19804638 0.0040281866 0.056140581
#> Hfo -0.812343591 0.301903024 -0.15669801 0.0253502943 -0.130651021
#> Hsp -0.778390992 0.253430490 -0.21589934 0.0235352583 -0.111622405
#> Hve 0.186494772 0.088853993 0.24227274 -0.0065590062 0.204391103
#> Sta 0.440269567 0.016316541 0.30820766 -0.0127951026 0.434550743
#> Set All Han Hfo Hsp Hve
#> Che -0.05920318 0.272620279 -0.182549673 -0.36266669 -0.44201571 0.312235381
#> Hyc 0.47745253 -0.263659047 0.624603685 0.56091635 0.67296326 -0.131799658
#> Hym -0.18250369 0.681315458 0.209598384 -0.39290753 -0.33247332 0.161177077
#> Hys 0.13822860 0.370230310 0.135229185 -0.18177430 -0.17520759 0.241515491
#> Psy -0.09125504 -0.004765477 -0.288015612 -0.14577706 -0.19128639 0.045636811
#> Aga -0.30144846 0.593013434 -0.171202850 -0.81234359 -0.77839099 0.186494772
#> Glo 0.29317969 -0.077512635 -0.189551382 0.30190302 0.25343049 0.088853993
#> Ath 0.09734287 0.088189274 -0.198046381 -0.15669801 -0.21589934 0.242272738
#> Cea 0.01429724 -0.023218314 0.004028187 0.02535029 0.02353526 -0.006559006
#> Ced 0.19458528 0.080595332 0.056140581 -0.13065102 -0.11162240 0.204391103
#> Set 1.58439691 -0.683088983 -0.041273606 0.80829421 0.76580060 -0.040550618
#> All -0.68308898 1.807884367 0.030686503 -0.74037811 -0.65689259 0.146650120
#> Han -0.04127361 0.030686503 3.638537325 0.62029959 0.98330036 -0.599857329
#> Hfo 0.80829421 -0.740378110 0.620299594 2.73416103 1.62460903 -0.342100299
#> Hsp 0.76580060 -0.656892592 0.983300363 1.62460903 2.50055205 -0.479932944
#> Hve -0.04055062 0.146650120 -0.599857329 -0.34210030 -0.47993294 1.349838767
#> Sta 0.05520256 0.200075142 0.463419896 -0.25543593 -0.19278867 0.143566347
#> Sta
#> Che 0.36386499
#> Hyc 0.25632941
#> Hym 0.47804168
#> Hys 0.61396464
#> Psy -0.12116355
#> Aga 0.44026957
#> Glo 0.01631654
#> Ath 0.30820766
#> Cea -0.01279510
#> Ced 0.43455074
#> Set 0.05520256
#> All 0.20007514
#> Han 0.46341990
#> Hfo -0.25543593
#> Hsp -0.19278867
#> Hve 0.14356635
#> Sta 1.02964763