ZIPLN: Zero Inflated Poisson lognormal model
In PLN-team/PLNmodels: Poisson Lognormal Models

ZIPLN

R Documentation

Zero Inflated Poisson lognormal model

Description

Fit the multivariate Zero Inflated Poisson lognormal model with a variational algorithm. Use the (g)lm syntax for model specification (covariates, offsets, subset).

Usage

ZIPLN(
  formula,
  data,
  subset,
  zi = c("single", "row", "col"),
  control = ZIPLN_param()
)

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 PLN is called.
`subset`	an optional vector specifying a subset of observations to be used in the fitting process.
`zi`	a character describing the model used for zero inflation, either of "single" (default, one parameter shared by all counts) "col" (one parameter per variable / feature) "row" (one parameter per sample / individual). If covariates are specified in the formula RHS (see details) this parameter is ignored.
`control`	a list-like structure for controlling the optimization, with default generated by `ZIPLN_param()`. See the associated documentation for details.

Details

Covariates for the Zero-Inflation parameter (using a logistic regression model) can be specified in the formula RHS using the pipe (⁠~ PLN effect | ZI effect⁠) to separate covariates for the PLN part of the model from those for the Zero-Inflation part. Note that different covariates can be used for each part.

Value

an R6 object with class ZIPLNfit

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
## Use different models for zero-inflation...
myZIPLN_single <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "single")
## Not run: 
myZIPLN_row    <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "row")
myZIPLN_col    <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "col")
## ...including logistic regression on covariates
myZIPLN_covar  <- ZIPLN(Abundance ~ 1 | 1 + Wind, data = trichoptera)

## End(Not run)

PLN-team/PLNmodels documentation built on April 15, 2024, 9:01 a.m.