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 Networkfamily, 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 = 7.353689 
	sparsifying penalty = 6.792388 
	sparsifying penalty = 6.273931 
	sparsifying penalty = 5.795047 
	sparsifying penalty = 5.352716 
	sparsifying penalty = 4.944148 
	sparsifying penalty = 4.566765 
	sparsifying penalty = 4.218188 
	sparsifying penalty = 3.896217 
	sparsifying penalty = 3.598823 
	sparsifying penalty = 3.324127 
	sparsifying penalty = 3.0704 
	sparsifying penalty = 2.836039 
	sparsifying penalty = 2.619566 
	sparsifying penalty = 2.419617 
	sparsifying penalty = 2.23493 
	sparsifying penalty = 2.064339 
	sparsifying penalty = 1.90677 
	sparsifying penalty = 1.761228 
	sparsifying penalty = 1.626795 
	sparsifying penalty = 1.502623 
	sparsifying penalty = 1.387929 
	sparsifying penalty = 1.28199 
	sparsifying penalty = 1.184137 
	sparsifying penalty = 1.093752 
	sparsifying penalty = 1.010267 
	sparsifying penalty = 0.9331545 
	sparsifying penalty = 0.8619276 
	sparsifying penalty = 0.7961374 
	sparsifying penalty = 0.7353689 

#>  Post-treatments
#>  DONE!
head(coefficient_path(fits))
#>   Node1 Node2 Coeff  Penalty    Edge
#> 1   Aga   Che     0 7.353689 Aga|Che
#> 2   Ath   Che     0 7.353689 Ath|Che
#> 3   Cea   Che     0 7.353689 Cea|Che
#> 4   Ced   Che     0 7.353689 Ced|Che
#> 5   All   Che     0 7.353689 All|Che
#> 6   Che   Hyc     0 7.353689 Che|Hyc