R/onload.R

In papaja: Prepare American Psychological Association Journal Articles with R Markdown

.onLoad <- function(libname, pkgname) { # nocov start
  if(length(knitr::opts_knit$get("rmarkdown.pandoc.to")) > 0 && !is.null(rmarkdown::metadata$lang)) {
    lang <- parse_bcp47(rmarkdown::metadata$lang)
  } else {
    lang <- "english"
  }

  op <- options()
  op_papaja <- list(
    # papaja.language = lang
    papaja.terms = localize(lang)
    , papaja.na_string = "NA"
    , papaja.plot_colors = "greyscale"
    , papaja.mse = !package_available("effectsize")
    , papaja.sphericity_correction = "GG"
  )

  if(package_available("effectsize")) {
    effectsize_eta_squared <- function(x, observed = NULL, include_intercept = FALSE, ...) {

      if(is.null(observed)) {
        generalized <- character(0L)
      } else {
        generalized <- observed
      }

      effectsize::eta_squared(
        x
        , generalized = generalized
        , include_intercept = include_intercept
        , ...
      )
    }

    op_papaja$papaja.estimate_anova <- effectsize_eta_squared

    # Revert to using a two-sided 90% CI to provide additional information for
    # testing minimal effects (Steiger, 2004).
    if(utils::packageVersion("effectsize") >= "0.5") {
      op_papaja$papaja.estimate_anova <- function(
        ...
        , observed = NULL
        , include_intercept = FALSE
        , alternative = "two.sided"
        , ci = 0.9
      ) {
        effectsize_eta_squared(
          ...
          , observed = observed
          , alternative = alternative
          , ci = ci
          , include_intercept = include_intercept
        )
      }
    }

    # A fallback option should be specified in the function definition via
    # getOption("papaja.estimate_anova", default = "ges"), which ensures that
    # the default is available even if papaja is not loaded.
  }


  toset <- !(names(op_papaja) %in% names(op))
  if(any(toset)) options(op_papaja[toset])


  # Fix dplyr R CMD Check note
  if(getRversion() >= "2.15.1")  utils::globalVariables(c("."))

  invisible()
} # nocov end