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 2.533889720 -0.009175274 0.35957652 0.44466341 -0.0177497070
#> Hyc -0.009175274 1.905879266 0.11079420 0.27009605 -0.1465535916
#> Hym 0.359576519 0.110794195 1.24533901 0.86551787 -0.1186220053
#> Hys 0.444663406 0.270096053 0.86551787 2.66556486 -0.1467153805
#> Psy -0.017749707 -0.146553592 -0.11862201 -0.14671538 0.0762253676
#> Aga 0.308321103 -0.132763441 0.51430623 0.42597249 0.0014030755
#> Glo 0.089673185 0.171534660 0.20986385 0.34296412 -0.0498898408
#> Ath 0.352594596 0.110096779 0.38518930 0.60794017 -0.0479791664
#> Cea -0.012865858 0.008339850 -0.02989049 -0.02216642 0.0001971436
#> Ced 0.337752005 0.222223228 0.50794425 0.68137474 -0.0983619419
#> Set -0.057984731 0.477377565 -0.18190346 0.13879491 -0.0915290277
#> All 0.271550918 -0.264260088 0.68178886 0.37027126 -0.0046779521
#> Han -0.183825874 0.625434397 0.20947619 0.13505358 -0.2887008025
#> Hfo -0.362486242 0.562768586 -0.39308133 -0.18182254 -0.1466276209
#> Hsp -0.440850931 0.672803405 -0.33156766 -0.17514684 -0.1917594046
#> Hve 0.312710542 -0.132538210 0.16092145 0.24110818 0.0459239339
#> Sta 0.363674354 0.256553019 0.47822213 0.61413322 -0.1214490338
#> Aga Glo Ath Cea Ced
#> Che 0.308321103 0.089673185 0.352594596 -0.0128658585 0.33775200
#> Hyc -0.132763441 0.171534660 0.110096779 0.0083398498 0.22222323
#> Hym 0.514306230 0.209863852 0.385189302 -0.0298904888 0.50794425
#> Hys 0.425972486 0.342964118 0.607940170 -0.0221664157 0.68137474
#> Psy 0.001403075 -0.049889841 -0.047979166 0.0001971436 -0.09836194
#> Aga 1.101569698 -0.063875964 0.197235416 -0.0314309541 0.21881525
#> Glo -0.063875964 1.118991217 0.225184485 0.0025360967 0.22678393
#> Ath 0.197235416 0.225184485 1.376146797 -0.0091019457 0.44314315
#> Cea -0.031430954 0.002536097 -0.009101946 0.0654281204 -0.01006807
#> Ced 0.218815247 0.226783927 0.443143154 -0.0100680670 0.95893264
#> Set -0.301831869 0.293079136 0.097799325 0.0219083881 0.19555373
#> All 0.593993436 -0.077455058 0.087851750 -0.0351846095 0.07998615
#> Han -0.172684447 -0.188895362 -0.197875167 0.0068488109 0.05656817
#> Hfo -0.814522552 0.301939203 -0.157041946 0.0384375867 -0.12949792
#> Hsp -0.778037422 0.252204569 -0.216016044 0.0356050763 -0.11037546
#> Hve 0.187362344 0.088242670 0.242045904 -0.0098605695 0.20386452
#> Sta 0.439979141 0.016824335 0.308424290 -0.0187003167 0.43470270
#> Set All Han Hfo Hsp Hve
#> Che -0.05798473 0.271550918 -0.183825874 -0.36248624 -0.44085093 0.31271054
#> Hyc 0.47737756 -0.264260088 0.625434397 0.56276859 0.67280340 -0.13253821
#> Hym -0.18190346 0.681788864 0.209476188 -0.39308133 -0.33156766 0.16092145
#> Hys 0.13879491 0.370271261 0.135053582 -0.18182254 -0.17514684 0.24110818
#> Psy -0.09152903 -0.004677952 -0.288700802 -0.14662762 -0.19175940 0.04592393
#> Aga -0.30183187 0.593993436 -0.172684447 -0.81452255 -0.77803742 0.18736234
#> Glo 0.29307914 -0.077455058 -0.188895362 0.30193920 0.25220457 0.08824267
#> Ath 0.09779933 0.087851750 -0.197875167 -0.15704195 -0.21601604 0.24204590
#> Cea 0.02190839 -0.035184609 0.006848811 0.03843759 0.03560508 -0.00986057
#> Ced 0.19555373 0.079986150 0.056568170 -0.12949792 -0.11037546 0.20386452
#> Set 1.58232207 -0.682943148 -0.040351378 0.80960874 0.76426656 -0.04129266
#> All -0.68294315 1.808582280 0.028944720 -0.74247834 -0.65677918 0.14736677
#> Han -0.04035138 0.028944720 3.643028041 0.62396079 0.98584688 -0.60099103
#> Hfo 0.80960874 -0.742478342 0.623960795 2.74198623 1.62545708 -0.34459986
#> Hsp 0.76426656 -0.656779179 0.985846881 1.62545708 2.49072135 -0.48151031
#> Hve -0.04129266 0.147366767 -0.600991032 -0.34459986 -0.48151031 1.34986122
#> Sta 0.05561555 0.199889141 0.463860791 -0.25480433 -0.19111380 0.14335148
#> Sta
#> Che 0.36367435
#> Hyc 0.25655302
#> Hym 0.47822213
#> Hys 0.61413322
#> Psy -0.12144903
#> Aga 0.43997914
#> Glo 0.01682434
#> Ath 0.30842429
#> Cea -0.01870032
#> Ced 0.43470270
#> Set 0.05561555
#> All 0.19988914
#> Han 0.46386079
#> Hfo -0.25480433
#> Hsp -0.19111380
#> Hve 0.14335148
#> Sta 1.02963242