Extract the regularization path of a PLNnetwork fit

Extract the regularization path of a PLNnetwork fit

coefficient_path(Robject, precision = TRUE, corr = TRUE)

Arguments

Robject

an object with class PLNnetworkfamily, i.e. an output from PLNnetwork()

precision

a logical, should the coefficients of the precision matrix Omega or the covariance matrix Sigma be sent back. Default is TRUE.

corr

a logical, should the correlation (partial in case precision = TRUE) be sent back. Default is TRUE.

Value

Sends back a tibble/data.frame.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
fits <- PLNnetwork(Abundance ~ 1, data = trichoptera)
#> 
#>  Initialization...
#>  Adjusting 30 PLN with sparse inverse covariance estimation
#> 	Joint optimization alternating gradient descent and graphical-lasso
#> 	sparsifying penalty = 7.541317 
	sparsifying penalty = 6.965695 
	sparsifying penalty = 6.43401 
	sparsifying penalty = 5.942907 
	sparsifying penalty = 5.48929 
	sparsifying penalty = 5.070297 
	sparsifying penalty = 4.683286 
	sparsifying penalty = 4.325815 
	sparsifying penalty = 3.995629 
	sparsifying penalty = 3.690646 
	sparsifying penalty = 3.408942 
	sparsifying penalty = 3.148741 
	sparsifying penalty = 2.9084 
	sparsifying penalty = 2.686404 
	sparsifying penalty = 2.481353 
	sparsifying penalty = 2.291954 
	sparsifying penalty = 2.117011 
	sparsifying penalty = 1.955421 
	sparsifying penalty = 1.806166 
	sparsifying penalty = 1.668303 
	sparsifying penalty = 1.540962 
	sparsifying penalty = 1.423342 
	sparsifying penalty = 1.3147 
	sparsifying penalty = 1.21435 
	sparsifying penalty = 1.121659 
	sparsifying penalty = 1.036044 
	sparsifying penalty = 0.9569638 
	sparsifying penalty = 0.8839195 
	sparsifying penalty = 0.8164507 
	sparsifying penalty = 0.7541317 

#>  Post-treatments
#>  DONE!
head(coefficient_path(fits))
#>   Node1 Node2 Coeff  Penalty    Edge
#> 1   Aga   Che     0 7.541317 Aga|Che
#> 2   Ath   Che     0 7.541317 Ath|Che
#> 3   Cea   Che     0 7.541317 Cea|Che
#> 4   Ced   Che     0 7.541317 Ced|Che
#> 5   All   Che     0 7.541317 All|Che
#> 6   Che   Hyc     0 7.541317 Che|Hyc