# vcov.PLNfit: Calculate Variance-Covariance Matrix for a fitted 'PLN()'... In PLN-team/PLNmodels: Poisson Lognormal Models

 vcov.PLNfit R Documentation

## Calculate Variance-Covariance Matrix for a fitted `PLN()` model object

### Description

Returns the variance-covariance matrix of the main parameters of a fitted `PLN()` model object. The main parameters of the model correspond to

`B`

, as returned by `coef.PLNfit()`. The function can also be used to return the variance-covariance matrix of the residuals. The latter matrix can also be accessed via `sigma.PLNfit()`

### Usage

``````## S3 method for class 'PLNfit'
vcov(object, type = c("main", "covariance"), ...)
``````

### Arguments

 `object` an R6 object with class `PLNfit` `type` type of parameter that should be extracted. Either "main" (default) for `B` or "covariance" for `\Sigma` `...` additional parameters for S3 compatibility. Not used

### Value

A matrix of variance/covariance extracted from the PLNfit model. If type="main" and `B` is a matrix of size d * p, the result is a block-diagonal matrix with p (number of species) blocks of size d (number of covariates). if type="main", it is a symmetric matrix of size p. .

`sigma.PLNfit()`, `coef.PLNfit()`, `standard_error.PLNfit()`

### Examples

``````data(trichoptera)
trichoptera <- prepare_data(trichoptera\$Abundance, trichoptera\$Covariate)
myPLN <- PLN(Abundance ~ 1 + offset(log(Offset)), data = trichoptera)
vcov(myPLN, type = "covariance") ## Sigma
``````

PLN-team/PLNmodels documentation built on Sept. 11, 2024, 4:08 p.m.