#' Refit mixed effects model

#'

#' Based on a 'GlmmSeq' or 'lmmSeq' class result object, this function attempts

#' to refit an identical model for a specific gene based on the data and fitting

#' parameters stored in the results object and refitting using either

#' [lme4::glmer()] for `GlmmSeq` objects or `lmer()` for `lmmSeq` objects. The

#' fitted model can then be passed on to other packages such as `emmeans` to

#' look at estimated marginal means for the model.

#'

#' @param object A fitted results object of class `GlmmSeq` or `lmmSeq`

#' @param gene A character value specifying a single gene to extract a fitted

#' model for

#' @param formula Optional formula to use when refitting model

#' @param control Optional control parameters, see [lme4::lmerControl()] or

#' [lme4::glmerControl()]

#' @param family Optional GLM family when refitting GLMM using [lme4::glmer()]

#' or [glmmTMB()]

#' @param ... Optional arguments passed to either [lme4::glmer()] or

#' [lme4::lmer()]

#' @return Fitted model of class `lmerMod` in the case of LMM, or `glmerMod` or

#' `glmmTMB` for a GLMM dependent on the original method.

#'

#' @examples

#' data(PEAC_minimal_load)

#' disp <- apply(tpm, 1, function(x) {

#' (var(x, na.rm = TRUE)-mean(x, na.rm = TRUE))/(mean(x, na.rm = TRUE)**2)

#' })

#' glmmtest <- glmmSeq(~ Timepoint * EULAR_6m (1 | PATID),

#' countdata = tpm[1:2, ],

#' metadata = metadata,

#' dispersion = disp,

#' verbose = FALSE)

#'

#' # show summary for single gene

#' summary(glmmtest, "MS4A1")

#'

#' # refit a single model using lme4::glmer()

#' fit <- glmmRefit(glmmtest, "MS4A1")

#'

#' # refit model with reduced formula

#' fit2 <- glmmRefit(glmmtest, "MS4A1",

#' formula = count ~ Timepoint EULAR_6m (1 | PATID))

#'

#' # LRT

#' anova(fit, fit2)

#'

#' @export

glmmRefit <- function(object, gene, ...) {

UseMethod("glmmRefit")

}

#' @rdname glmmRefit

#' @export

glmmRefit.lmmSeq <- function(object, gene,

}

#' @rdname glmmRefit

#' @export

glmmRefit.GlmmSeq <- function(object, gene,

}