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 = 7.54443 
	sparsifying penalty = 6.96857 
	sparsifying penalty = 6.436665 
	sparsifying penalty = 5.94536 
	sparsifying penalty = 5.491556 
	sparsifying penalty = 5.07239 
	sparsifying penalty = 4.685219 
	sparsifying penalty = 4.3276 
	sparsifying penalty = 3.997278 
	sparsifying penalty = 3.692169 
	sparsifying penalty = 3.410349 
	sparsifying penalty = 3.15004 
	sparsifying penalty = 2.9096 
	sparsifying penalty = 2.687513 
	sparsifying penalty = 2.482377 
	sparsifying penalty = 2.2929 
	sparsifying penalty = 2.117885 
	sparsifying penalty = 1.956228 
	sparsifying penalty = 1.806911 
	sparsifying penalty = 1.668991 
	sparsifying penalty = 1.541598 
	sparsifying penalty = 1.42393 
	sparsifying penalty = 1.315242 
	sparsifying penalty = 1.214851 
	sparsifying penalty = 1.122122 
	sparsifying penalty = 1.036472 
	sparsifying penalty = 0.9573588 
	sparsifying penalty = 0.8842844 
	sparsifying penalty = 0.8167877 
	sparsifying penalty = 0.754443 

#>  Post-treatments
#>  DONE!
head(coefficient_path(fits))
#>   Node1 Node2 Coeff Penalty    Edge
#> 1   Aga   Che     0 7.54443 Aga|Che
#> 2   Ath   Che     0 7.54443 Ath|Che
#> 3   Cea   Che     0 7.54443 Cea|Che
#> 4   Ced   Che     0 7.54443 Ced|Che
#> 5   All   Che     0 7.54443 All|Che
#> 6   Che   Hyc     0 7.54443 Che|Hyc