Perform sparse inverse covariance estimation for the Zero Inflated Poisson lognormal model using a variational algorithm. Iterate over a range of logarithmically spaced sparsity parameter values. Use the (g)lm syntax to specify the model (including covariates and offsets).
PLNnetwork(
formula,
data,
subset,
weights,
penalties = NULL,
control = PLNnetwork_param()
)an object of class "formula": a symbolic description of the model to be fitted.
an optional data frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which lm is called.
an optional vector specifying a subset of observations to be used in the fitting process.
an optional vector of observation weights to be used in the fitting process.
an optional vector of positive real number controlling the level of sparsity of the underlying network. if NULL (the default), will be set internally. See PLNnetwork_param() for additional tuning of the penalty.
a list-like structure for controlling the optimization, with default generated by PLNnetwork_param(). See the corresponding documentation for details;
an R6 object with class PLNnetworkfamily, which contains
a collection of models with class PLNnetworkfit
The classes PLNnetworkfamily and PLNnetworkfit, and the and the configuration function PLNnetwork_param().
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!