Extract the regularization path of a PLNnetwork fit

Usage

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 = 4.479926 
	sparsifying penalty = 4.137977 
	sparsifying penalty = 3.822129 
	sparsifying penalty = 3.530389 
	sparsifying penalty = 3.260917 
	sparsifying penalty = 3.012014 
	sparsifying penalty = 2.78211 
	sparsifying penalty = 2.569754 
	sparsifying penalty = 2.373607 
	sparsifying penalty = 2.192431 
	sparsifying penalty = 2.025085 
	sparsifying penalty = 1.870512 
	sparsifying penalty = 1.727737 
	sparsifying penalty = 1.595861 
	sparsifying penalty = 1.47405 
	sparsifying penalty = 1.361537 
	sparsifying penalty = 1.257612 
	sparsifying penalty = 1.16162 
	sparsifying penalty = 1.072954 
	sparsifying penalty = 0.9910565 
	sparsifying penalty = 0.91541 
	sparsifying penalty = 0.8455375 
	sparsifying penalty = 0.7809984 
	sparsifying penalty = 0.7213854 
	sparsifying penalty = 0.6663227 
	sparsifying penalty = 0.6154629 
	sparsifying penalty = 0.5684851 
	sparsifying penalty = 0.5250931 
	sparsifying penalty = 0.4850132 
	sparsifying penalty = 0.4479926 

#>  Post-treatments
#>  DONE!
head(coefficient_path(fits))
#>   Node1 Node2 Coeff  Penalty    Edge
#> 1   Aga   Che     0 4.479926 Aga|Che
#> 2   Ath   Che     0 4.479926 Ath|Che
#> 3   Cea   Che     0 4.479926 Cea|Che
#> 4   Ced   Che     0 4.479926 Ced|Che
#> 5   All   Che     0 4.479926 All|Che
#> 6   Che   Hyc     0 4.479926 Che|Hyc