sigma.PLNmixturefit: Extract variance-covariance of residuals 'Sigma'

In PLNmodels: Poisson Lognormal Models

Extract variance-covariance of residuals 'Sigma'

Description

Extract the variance-covariance matrix of the residuals, usually noted

\Sigma

in PLN models. This captures the correlation between the species in the latent space. or PLNmixture, it is a weighted mean of the variance-covariance matrices of each component.

Usage

## S3 method for class 'PLNmixturefit'
sigma(object, ...)

Arguments

object	an R6 object with class PLNmixturefit
...	additional parameters for S3 compatibility. Not used

Value

A semi definite positive matrix of size p, assuming there are p species in the model.

See Also

coef.PLNmixturefit() for other ways to access

\Sigma

.

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
           data = trichoptera, control = PLNmixture_param(smoothing = "none"))  %>% getBestModel()
sigma(myPLN) ## Sigma

PLNmodels documentation built on Aug. 24, 2023, 5:11 p.m.