# Class definitions

setClassUnion("character_or_list", c("character", "list"))

setClassUnion("df_or_matrix", c("data.frame", "matrix"))

setClassUnion("list_or_matrix", c("list", "matrix"))

setClassUnion("formulaOrNULL", c("formula", "NULL"))

#' An S4 class to define the glmmSeq output

#'

#' @slot info List including the matched call, dispersions, offset, designMatrix

#' @slot formula The model formula

#' @slot stats Statistics from fitted models

#' @slot predict Predicted values

#' @slot reduced Optional reduced formula for LRT

#' @slot countdata The input expression data with count data in rows

#' @slot metadata The input metadata

#' @slot modelData Model data for predictions

#' @slot optInfo Information on whether the model was singular or converged

#' @slot errors Any errors

#' @slot vars List of variables stored from the original call, including the

#' `id` variable (by default automatically identified from the random effect

#' term in the model) and `removeSingles` argument

setClass("GlmmSeq", slots = list(

info = "list",

formula = "formula",

stats = "list_or_matrix",

predict = "df_or_matrix",

reduced = "formulaOrNULL",

countdata = "df_or_matrix",

metadata = "df_or_matrix",

modelData = "df_or_matrix",

optInfo = "matrix",

errors = "character_or_list",

vars = "list"

))

#' An S4 class to define the lmmSeq output

#'

#' @slot info List including matched call, offset, designMatrix

#' @slot formula The model formula

#' @slot stats Statistics from fitted models

#' @slot predict Predicted values

#' @slot reduced Optional reduced formula for LRT

#' @slot maindata The input expression data with variables in rows

#' @slot metadata The input metadata

#' @slot modelData Model data for predictions

#' @slot optInfo Information on whether the model was singular or converged

#' @slot errors Any errors

#' @slot vars List of variables stored from the original call

setClass("lmmSeq", slots = list(

info = "list",

formula = "formula",

stats = "list_or_matrix",

predict = "df_or_matrix",

reduced = "formulaOrNULL",

maindata = "df_or_matrix",

metadata = "df_or_matrix",

modelData = "df_or_matrix",

optInfo = "matrix",

errors = "character_or_list",

vars = "list"

))