R/find_algorithm.R

In easystats/insight: Easy Access to Model Information for Various Model Objects

#' @title Find sampling algorithm and optimizers
#' @name find_algorithm
#'
#' @description Returns information on the sampling or estimation algorithm
#'   as well as optimization functions, or for Bayesian model information on
#'   chains, iterations and warmup-samples.
#'
#' @inheritParams find_parameters
#'
#' @return A list with elements depending on the model.
#'
#'   For frequentist models:
#'   - `algorithm`, for instance `"OLS"` or `"ML"`
#'   - `optimizer`, name of optimizing function, only applies to
#'      specific models (like `gam`)
#'
#'   For frequentist mixed models:
#'   - `algorithm`, for instance `"REML"` or `"ML"`
#'   - `optimizer`, name of optimizing function
#'
#'   For Bayesian models:
#'   - `algorithm`, the algorithm
#'   - `chains`, number of chains
#'   - `iterations`, number of iterations per chain
#'   - `warmup`, number of warmups per chain
#'
#' @examplesIf require("lme4", quietly = TRUE)
#' data(sleepstudy, package = "lme4")
#' m <- lme4::lmer(Reaction ~ Days + (1 | Subject), data = sleepstudy)
#' find_algorithm(m)
#'
#' @examplesIf require("rstanarm") && require("lme4")
#' \donttest{
#' data(sleepstudy, package = "lme4")
#' m <- suppressWarnings(rstanarm::stan_lmer(
#'   Reaction ~ Days + (1 | Subject),
#'   data = sleepstudy,
#'   refresh = 0
#' ))
#' find_algorithm(m)
#' }
#' @export
find_algorithm <- function(x, ...) {
  UseMethod("find_algorithm")
}


#' @export
find_algorithm.default <- function(x, ...) {
  format_warning(sprintf("Objects of class `%s` are not supported.", class(x)[1]))
  NULL
}


#' @export
find_algorithm.Gam <- function(x, ...) {
  list(algorithm = "IWLS")
}


#' @export
find_algorithm.lmRob <- function(x, ...) {
  list(algorithm = x$robust.control$final.alg)
}


#' @export
find_algorithm.lmrob <- function(x, ...) {
  list(algorithm = x$control$method)
}


#' @export
find_algorithm.glmrob <- function(x, ...) {
  list(algorithm = x$method)
}


#' @export
find_algorithm.logistf <- function(x, ...) {
  list(algorithm = x$method)
}

#' @export
find_algorithm.flac <- find_algorithm.logistf

#' @export
find_algorithm.flic <- find_algorithm.logistf


#' @export
find_algorithm.bigglm <- function(x, ...) {
  list(algorithm = "ML")
}


#' @export
find_algorithm.BBreg <- function(x, ...) {
  list(algorithm = "ML")
}


#' @export
find_algorithm.Arima <- function(x, ...) {
  list(algorithm = "ML")
}


#' @export
find_algorithm.glimML <- function(x, ...) {
  list(algorithm = "ML")
}


#' @export
find_algorithm.BBmm <- function(x, ...) {
  method <- parse(text = safe_deparse(x$call))[[1]]$method
  if (is.null(method)) method <- "BB-NR"
  list(algorithm = "extended likelihood", optimizer = method)
}


#' @export
find_algorithm.biglm <- function(x, ...) {
  list(algorithm = "OLS")
}


#' @export
find_algorithm.gamlss <- function(x, ...) {
  list(algorithm = as.character(x$method)[1])
}


#' @export
find_algorithm.gam <- function(x, ...) {
  list(
    algorithm = x$method,
    optimizer = x$optimizer
  )
}

#' @export
find_algorithm.scam <- find_algorithm.gam


#' @export
find_algorithm.lm <- function(x, ...) {
  list(algorithm = "OLS")
}


#' @export
find_algorithm.systemfit <- function(x, ...) {
  list(algorithm = x$method)
}


#' @export
find_algorithm.afex_aov <- function(x, ...) {
  list(algorithm = "OLS")
}


#' @export
find_algorithm.speedlm <- function(x, ...) {
  list(algorithm = x$method)
}


#' @export
find_algorithm.blavaan <- function(x, ...) {
  check_if_installed("blavaan")

  list(
    chains = blavaan::blavInspect(x, "n.chains"),
    sample = x@external$sample,
    warmup = x@external$burnin
  )
}


#' @export
find_algorithm.speedglm <- function(x, ...) {
  list(algorithm = x$method)
}


#' @export
find_algorithm.rq <- function(x, ...) {
  list(algorithm = x$method)
}

#' @export
find_algorithm.rqs <- find_algorithm.rq

#' @export
find_algorithm.rqss <- find_algorithm.rq


#' @export
find_algorithm.bayesx <- function(x, ...) {
  list(
    algorithm = x$method,
    iterations = x$iterations,
    warmup = x$burnin
  )
}


#' @export
find_algorithm.crq <- function(x, ...) {
  list(algorithm = x$method)
}


#' @export
find_algorithm.glm <- function(x, ...) {
  list(algorithm = "ML")
}


#' @export
find_algorithm.nestedLogit <- function(x, ...) {
  list(algorithm = "ML")
}


#' @export
find_algorithm.LORgee <- function(x, ...) {
  list(algorithm = "Fisher's scoring ML")
}


#' @export
find_algorithm.merMod <- function(x, ...) {
  algorithm <- ifelse(as.logical(x@devcomp$dims[["REML"]]), "REML", "ML")

  list(
    algorithm = algorithm,
    optimizer = as.character(x@optinfo$optimizer)
  )
}

#' @export
find_algorithm.rlmerMod <- find_algorithm.merMod

#' @export
find_algorithm.merModList <- function(x, ...) {
  find_algorithm(x[[1]], ...)
}


#' @export
find_algorithm.mixed <- function(x, ...) {
  x <- x$full_model
  algorithm <- ifelse(as.logical(x@devcomp$dims[["REML"]]), "REML", "ML")

  list(
    algorithm = algorithm,
    optimizer = as.character(x@optinfo$optimizer)
  )
}


#' @export
find_algorithm.lme <- function(x, ...) {
  optimizer <- "nlminb"
  if (!is.null(x$call$control) && "optim" %in% as.character(x$call$control)) {
    optimizer <- "optim"
  }

  list(
    algorithm = x$method,
    optimizer = optimizer
  )
}


#' @export
find_algorithm.MixMod <- function(x, ...) {
  list(
    ## FIXME
    algorithm = "quasi-Newton",
    optimizer = x$control$optimizer
  )
}


#' @export
find_algorithm.glmmTMB <- function(x, ...) {
  algorithm <- ifelse(x$modelInfo$REML, "REML", "ML")

  list(
    algorithm = algorithm,
    optimizer = "nlminb"
  )
}


#' @export
find_algorithm.stanreg <- function(x, ...) {
  info <- x$stanfit@sim

  list(
    algorithm = x$algorithm,
    chains = info$chains,
    iterations = info$iter,
    warmup = info$warmup
  )
}


#' @export
find_algorithm.stanfit <- function(x, ...) {
  info <- x@sim
  algorithm <- unlist(x@stan_args)

  list(
    algorithm = as.vector(algorithm["algorithm"]),
    chains = info$chains,
    iterations = info$iter,
    warmup = info$warmup
  )
}


#' @export
find_algorithm.bayesQR <- function(x, ...) {
  list(
    algorithm = x[[1]]$method,
    iterations = nrow(x[[1]]$betadraw)
  )
}


#' @export
find_algorithm.brmsfit <- function(x, ...) {
  info <- x$fit@sim

  list(
    algorithm = x$algorithm,
    chains = info$chains,
    iterations = info$iter,
    warmup = info$warmup
  )
}