R/glm.r

In xiaodaigh/disk.frame: Larger-than-RAM Disk-Based Data Manipulation Framework

#' Fit generalized linear models (glm) with disk.frame
#'
#' @inherit biglm::bigglm
#' 
#' @description  
#' Fits GLMs using `{speedglm}` or `{biglm}`. The return object will be exactly as
#' those return by those functions. This is a convenience wrapper
#'
#' @param glm_backend Which package to use for fitting GLMs. The default is
#'   "biglm", which has known issues with factor level if different levels are
#'   present in different chunks. The "speedglm" option is more robust, but does not
#'   implement `predict` which makes prediction and implementation impossible.
#'
#' @family Machine Learning (ML)
#' @export
#'
#' @examples
#' cars.df = as.disk.frame(cars)
#' m = dfglm(dist ~ speed, data = cars.df)
#'
#' # can use normal R functions
#' # Only works in version > R 3.6
#' majorv = as.integer(version$major)
#' minorv = as.integer(strsplit(version$minor, ".", fixed=TRUE)[[1]][1])
#' if(((majorv == 3) & (minorv >= 6)) | (majorv > 3)) {
#'   summary(m)
#'   predict(m, get_chunk(cars.df, 1))
#'   predict(m, collect(cars.df))
#'   # can use broom to tidy up the returned info
#'   broom::tidy(m)
#' }
#'
#' # clean up
#' delete(cars.df)
dfglm <- function(formula, data, ..., glm_backend = c("biglm", "speedglm", "biglmm")) {
  glm_backend = match.arg(glm_backend)
  
  # compute the major version
  majorv = as.integer(version$major)
  minorv = as.integer(strsplit(version$minor, ".", fixed=TRUE)[[1]][1])
  
  if((majorv == 3) & (minorv < 6) & (glm_backend == "biglm")) {
    warning("{bigglm} is not supported for R version below 3.6; auto switched to {speedglm}")
    glm_backend = "speedglm"
  }
  
  stopifnot(is_disk.frame(data))
  streaming_fn <- make_glm_streaming_fn(data)
  
  if(glm_backend == "speedglm") {
    if(!requireNamespace("speedglm")) {
      stop("speedglm package not installed. To install run `install.packages('speedglm')`")
    }
    speedglm::shglm(formula, streaming_fn, ...)
  } else if (glm_backend == "biglm"){
    if(!requireNamespace("biglm")) {
      stop("biglm package not installed. To install run `install.packages('biglm')`")
    }
    biglm::bigglm(formula, data = streaming_fn, ...)
  } else if (glm_backend == "biglmm"){
    if(!requireNamespace("biglmm")) {
      stop("biglmm package not installed. To install run `install.packages('biglmm')`")
    }
    biglmm::bigglm(formula, data = streaming_fn, ...)
  } else {
    stop("glm_backend must be one of 'speedglm' or 'biglm' or 'biglmm'")
  }
}