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 = 7.264447 
	sparsifying penalty = 6.709958 
	sparsifying penalty = 6.197792 
	sparsifying penalty = 5.72472 
	sparsifying penalty = 5.287757 
	sparsifying penalty = 4.884147 
	sparsifying penalty = 4.511344 
	sparsifying penalty = 4.166997 
	sparsifying penalty = 3.848934 
	sparsifying penalty = 3.555148 
	sparsifying penalty = 3.283787 
	sparsifying penalty = 3.033138 
	sparsifying penalty = 2.801621 
	sparsifying penalty = 2.587776 
	sparsifying penalty = 2.390253 
	sparsifying penalty = 2.207807 
	sparsifying penalty = 2.039287 
	sparsifying penalty = 1.88363 
	sparsifying penalty = 1.739854 
	sparsifying penalty = 1.607053 
	sparsifying penalty = 1.484388 
	sparsifying penalty = 1.371086 
	sparsifying penalty = 1.266432 
	sparsifying penalty = 1.169766 
	sparsifying penalty = 1.080479 
	sparsifying penalty = 0.998007 
	sparsifying penalty = 0.9218299 
	sparsifying penalty = 0.8514675 
	sparsifying penalty = 0.7864757 
	sparsifying penalty = 0.7264447 

#>  Post-treatments
#>  DONE!
head(coefficient_path(fits))
#>   Node1 Node2 Coeff  Penalty    Edge
#> 1   Aga   Che     0 7.264447 Aga|Che
#> 2   Ath   Che     0 7.264447 Ath|Che
#> 3   Cea   Che     0 7.264447 Cea|Che
#> 4   Ced   Che     0 7.264447 Ced|Che
#> 5   All   Che     0 7.264447 All|Che
#> 6   Che   Hyc     0 7.264447 Che|Hyc