Extracts model coefficients from objects returned by PLN() and its variants
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 coefficients extracted from the PLNfit model.
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!
coef(myPLN) ## B
#> Che Hyc Hym Hys Psy Aga
#> (Intercept) -8.175518 -8.27716 -2.978746 -7.08388 -0.5450817 -4.085848
#> Glo Ath Cea Ced Set All
#> (Intercept) -6.337664 -6.042759 -7.087829 -3.637312 -4.404593 -4.920383
#> Han Hfo Hsp Hve Sta
#> (Intercept) -4.816382 -6.117446 -4.222235 -6.846656 -2.884514
coef(myPLN, type = "covariance") ## Sigma
#> Che Hyc Hym Hys Psy
#> Che 2.525696262 -0.008889967 0.36027330 0.44486018 -0.0178286663
#> Hyc -0.008889967 1.902834377 0.11148304 0.27076270 -0.1460638197
#> Hym 0.360273301 0.111483044 1.24452604 0.86586029 -0.1185245031
#> Hys 0.444860180 0.270762697 0.86586029 2.66473064 -0.1467390342
#> Psy -0.017828666 -0.146063820 -0.11852450 -0.14673903 0.0760951060
#> Aga 0.308718806 -0.132013432 0.51328365 0.42537030 0.0014322554
#> Glo 0.089491453 0.171747059 0.21033964 0.34353031 -0.0498965778
#> Ath 0.351997701 0.110806937 0.38595496 0.60848949 -0.0481522022
#> Cea -0.009267821 0.005493519 -0.02087036 -0.01572361 0.0002240197
#> Ced 0.337607492 0.222051227 0.50814378 0.68169904 -0.0982107956
#> Set -0.058763359 0.476607081 -0.18154484 0.13917373 -0.0913642510
#> All 0.272171175 -0.263256988 0.68023706 0.36946459 -0.0046224011
#> Han -0.183749462 0.623581723 0.20911232 0.13492705 -0.2887434511
#> Hfo -0.360194140 0.557687955 -0.38889288 -0.17842050 -0.1455521608
#> Hsp -0.441378467 0.671299294 -0.33075908 -0.17368654 -0.1916044191
#> Hve 0.311973113 -0.130460973 0.16145128 0.24183231 0.0453625525
#> Sta 0.363707224 0.255974709 0.47815928 0.61431349 -0.1213001472
#> Aga Glo Ath Cea Ced
#> Che 0.308718806 0.089491453 0.351997701 -0.0092678210 0.33760749
#> Hyc -0.132013432 0.171747059 0.110806937 0.0054935194 0.22205123
#> Hym 0.513283648 0.210339636 0.385954958 -0.0208703617 0.50814378
#> Hys 0.425370300 0.343530307 0.608489489 -0.0157236060 0.68169904
#> Psy 0.001432255 -0.049896578 -0.048152202 0.0002240197 -0.09821080
#> Aga 1.101578757 -0.064094359 0.197020809 -0.0218363758 0.21879584
#> Glo -0.064094359 1.118559091 0.225551635 0.0016621253 0.22693613
#> Ath 0.197020809 0.225551635 1.374600282 -0.0065870434 0.44325799
#> Cea -0.021836376 0.001662125 -0.006587043 0.0420661716 -0.00737414
#> Ced 0.218795840 0.226936125 0.443257994 -0.0073741396 0.95835860
#> Set -0.301737821 0.293415478 0.097936608 0.0149285852 0.19523267
#> All 0.592832929 -0.077292625 0.088158499 -0.0242050007 0.08003542
#> Han -0.173249089 -0.189928168 -0.197882342 0.0044098369 0.05610323
#> Hfo -0.809757806 0.301569164 -0.154089568 0.0264132114 -0.12772661
#> Hsp -0.778892849 0.253818503 -0.214399448 0.0246539660 -0.11030576
#> Hve 0.186616730 0.088845278 0.241904609 -0.0068928218 0.20452202
#> Sta 0.440007243 0.016756529 0.308476215 -0.0133814740 0.43463890
#> Set All Han Hfo Hsp Hve
#> Che -0.05876336 0.272171175 -0.183749462 -0.36019414 -0.44137847 0.311973113
#> Hyc 0.47660708 -0.263256988 0.623581723 0.55768796 0.67129929 -0.130460973
#> Hym -0.18154484 0.680237057 0.209112319 -0.38889288 -0.33075908 0.161451277
#> Hys 0.13917373 0.369464586 0.134927055 -0.17842050 -0.17368654 0.241832309
#> Psy -0.09136425 -0.004622401 -0.288743451 -0.14555216 -0.19160442 0.045362552
#> Aga -0.30173782 0.592832929 -0.173249089 -0.80975781 -0.77889285 0.186616730
#> Glo 0.29341548 -0.077292625 -0.189928168 0.30156916 0.25381850 0.088845278
#> Ath 0.09793661 0.088158499 -0.197882342 -0.15408957 -0.21439945 0.241904609
#> Cea 0.01492859 -0.024205001 0.004409837 0.02641321 0.02465397 -0.006892822
#> Ced 0.19523267 0.080035419 0.056103234 -0.12772661 -0.11030576 0.204522016
#> Set 1.58461789 -0.682673708 -0.041649354 0.80528196 0.76519763 -0.040055945
#> All -0.68267371 1.806384100 0.028266637 -0.73716820 -0.65633758 0.146813706
#> Han -0.04164935 0.028266637 3.659210234 0.61884176 0.98573915 -0.600081826
#> Hfo 0.80528196 -0.737168205 0.618841759 2.71280679 1.61721155 -0.339587343
#> Hsp 0.76519763 -0.656337582 0.985739154 1.61721155 2.49943271 -0.478673075
#> Hve -0.04005595 0.146813706 -0.600081826 -0.33958734 -0.47867308 1.347221211
#> Sta 0.05519276 0.199649842 0.464261169 -0.25379463 -0.19247242 0.143839484
#> Sta
#> Che 0.36370722
#> Hyc 0.25597471
#> Hym 0.47815928
#> Hys 0.61431349
#> Psy -0.12130015
#> Aga 0.44000724
#> Glo 0.01675653
#> Ath 0.30847621
#> Cea -0.01338147
#> Ced 0.43463890
#> Set 0.05519276
#> All 0.19964984
#> Han 0.46426117
#> Hfo -0.25379463
#> Hsp -0.19247242
#> Hve 0.14383948
#> Sta 1.02926865