PLNmodels (version 1.3.1)

PLNmixture: Poisson lognormal mixture model

Description

Fit the mixture variants of the Poisson lognormal with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets).

Usage

PLNmixture(formula, data, subset, clusters = 1:5, control = PLNmixture_param())

Value

an R6 object with class PLNmixturefamily, which contains a collection of models with class PLNmixturefit

Arguments

formula

an object of class "formula": a symbolic description of the model to be fitted.

data

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 the model is called.

subset

an optional vector specifying a subset of observations to be used in the fitting process.

clusters

a vector of integer containing the successive number of clusters (or components) to be considered

control

a list-like structure for controlling the optimization, with default generated by PLNmixture_param(). See the associated documentation for details.

See Also

The classes PLNmixturefamily, PLNmixturefit and PLNmixture_param()

Examples

## Use parallel to dispatch the computations on 2 workers
if (FALSE) {
options(mc.cores = 2)
}

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myMixtures <- PLNmixture(Abundance ~ 1 + offset(log(Offset)), clusters = 1:4, data = trichoptera,
                         control = PLNmixture_param(smoothing = 'none'))

if (FALSE) {
options(mc.cores = 1)
}