R/effects.R

In gavinsimpson/gratia: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

#' Extract fixed effects estimates
#'
#' @param object a fitted GAM
#' @param ... arguments passed to other methods
#'
#' @importFrom nlme fixef
#' @name fixef
#' @export
NULL

#' Extract fixed effects estimates from a fitted GAM
#'
#' @param object a fitted GAM
#' @param ... arguments passed to other methods
#'
#' @export
#'
#' @examples
#' load_mgcv()
#'
#' # run example if lme4 is available
#' if (require("lme4")) {
#'   data(sleepstudy, package = "lme4")
#'   m <- gam(
#'     Reaction ~ Days + s(Subject, bs = "re") +
#'       s(Days, Subject, bs = "re"),
#'     data = sleepstudy, method = "REML"
#'   )
#'   fixef(m)
#' }
`fixef.gam` <- function(object, ...) {
  coefs <- coef(object)
  nms <- names(coefs)
  # drop everything that starts with s, te, ti, or t2 and is followed by a (
  sm_terms <- grepl("^[s te ti t2](?=\\()", names(coef(object)), perl = TRUE)
  nms <- nms[!sm_terms]
  # return
  coefs[nms]
}

#' @rdname fixef.gam
#' @export
`fixef.gamm` <- function(object, ...) {
  object <- object$gam
  fixef(object)
}

#' @rdname fixef.gam
#' @export
`fixef.lm` <- function(object, ...) {
  coef(object)
}

#' @rdname fixef.gam
#' @export
`fixef.glm` <- function(object, ...) {
  coef(object)
}

#' @rdname fixef.gam
#' @export
`fixed_effects` <- function(object, ...) {
  UseMethod("fixed_effects")
}

#' @rdname fixef.gam
#' @export
`fixed_effects.default` <- function(object, ...) {
  fixef(object, ...)
}