R: Poisson lognormal model towards Linear Discriminant Analysis

PLNLDA {PLNmodels} | R Documentation

## Poisson lognormal model towards Linear Discriminant Analysis

### Description

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

### Usage

    PLNLDA(formula, data, subset, weights, grouping, control = list())

### 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 lm is called.
`subset` | an optional vector specifying a subset of observations to be used in the fitting process.
`weights` | an optional vector of observation weights to be used in the fitting process.
`grouping` | a factor specifying the class of each observation used for discriminant analysis.
`control` | a list for controlling the optimization process. See details.

### Details

The parameter `control` is a list controlling the optimization with the following entries:

- "covariance" character setting the model for the covariance matrix. Either "full" or "spherical". Default is "full".

- "trace" integer for verbosity.

- "inception" Set up the initialization. By default, the model is initialized with a multivariate linear model applied on log-transformed data. However, the user can provide a PLNfit (typically obtained from a previous fit), which often speed up the inference.

- "ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

- "ftol_abs" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 0

- "xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-4

- "xtol_abs" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 0

- "maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

- "maxtime" stop when the optimization time (in seconds) exceeds maxtime. Default is -1 (no restriction)

- "algorithm" the optimization method used by NLOPT among LD type, i.e. "CCSAQ", "MMA", "LBFGS", "VAR1", "VAR2". See NLOPT documentation for further details. Default is "CCSAQ".

### Value

an R6 object with class `PLNLDAfit()`

### See Also

The class `PLNLDAfit`

### Examples

    data(trichoptera)
    trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
    myPLNLDA <- PLNLDA(Abundance ~ 1, grouping = Group, data = trichoptera)

[Package PLNmodels version 0.10.6 Index]