PLN() model objectR/PLNfit-S3methods.R
vcov.PLNfit.RdReturns the variance-covariance matrix of the main parameters of a fitted PLN() model object. The main parameters of the model correspond to $$B$$, as returned by coef.PLNfit(). The function can also be used to return the variance-covariance matrix of the residuals. The latter matrix can also be accessed via sigma.PLNfit()
an R6 object with class PLNfit
type of parameter that should be extracted. Either "main" (default) for $$B$$ or "covariance" for $$\Sigma$$
additional parameters for S3 compatibility. Not used
A matrix of variance/covariance extracted from the PLNfit model. If type="main" and \(B\) is a matrix of size d * p, the result is a block-diagonal matrix with p (number of species) blocks of size d (number of covariates). if type="main", it is a symmetric matrix of size p. .
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!
vcov(myPLN, type = "covariance") ## 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