R/cite_easystats.R

In neuropsychology/report: Automated Reporting of Results and Statistical Models

#' Cite the easystats ecosystem
#'
#' A convenient function for those who wish to cite the easystats packages.
#'
#' @param packages A character vector of packages to cite. Can be `"all"` for
#'   all *easystats* pacakges or a vector with specific package names.
#' @param format The format to generate citations. Can be `"text"` for plain text,
#'   `"markdown"` for markdown citations and CSL bibliography (recommended for
#'   writing in RMarkdown), or `"biblatex"` for BibLaTeX citations and bibliography.
#' @param intext_prefix A character vector of length 1 containing text to include
#'   before in-text citations. If `TRUE`, defaults to `"Analyses were conducted
#'   using the easystats collection of packages "`. If `FALSE` or `NA`, no prefix
#'   is included.
#' @param intext_suffix A character vector of length 1 containing text to include
#'   after in-text citations. Defaults to `"."`. If `FALSE` or `NA`, no suffix
#'   is included.
#' @param x,object A `"cite_easystats"` object to print.
#' @param what What elements of the citations to print, can be `"all"`, `"intext"`, or `"refs"`.
#' @param ... Not used. Included for compatibility with the generic function.
#'
#' @return A list of class `"cite_easystats"` with elements:
#'   - `intext`: In-text citations in the requested `format`
#'   - `refs`: References or bibliography in the requested `format`
#'
#' @examples
#' \donttest{
#' # Cite just the 'easystats' umbrella package:
#' cite_easystats()
#' summary(cite_easystats(), what = "all")
#'
#' # Cite every easystats package:
#' cite_easystats(packages = "all")
#' summary(cite_easystats(packages = "all"), what = "all")
#'
#' # Cite specific packages:
#' cite_easystats(packages = c("modelbased", "see"))
#' summary(cite_easystats(packages = c("modelbased", "see")), what = "all")
#'
#' # To cite easystats packages in an RMarkdown document, use:
#'
#' ## In-text citations:
#' print(cite_easystats(format = "markdown"), what = "intext")
#'
#' ## Bibliography (print with the  `output = 'asis'` option on the code chunk)
#' print(cite_easystats(format = "markdown"), what = "refs")
#' }
#'
#' @export
cite_easystats <- function(packages = "easystats",
                           format = c("text", "markdown", "biblatex"),
                           intext_prefix = TRUE,
                           intext_suffix = ".") {
  format <- match.arg(format, choices = c("text", "markdown", "biblatex"))
  installed_packages <- utils::installed.packages()[, "Version"]
  if (length(packages) == 1 && packages == "all") {
    packages <- c(
      "easystats", "insight", "datawizard", "bayestestR",
      "performance", "parameters", "effectsize", "correlation",
      "modelbased", "see", "report"
    )
    packages <- packages[packages %in% names(installed_packages)]
  } else if (length(packages) == 1 && packages == "easystats") {
    if (!packages %in% names(installed_packages)) {
      installed_packages <- c(easystats = "")
    }
  } else {
    missing_packages <- setdiff(packages, names(installed_packages))
    if (length(missing_packages)) {
      message(insight::format_message(
        "Requested package(s) not installed:",
        toString(missing_packages),
        "Citations to these packages omitted."
      ))
      packages <- setdiff(packages, missing_packages)
    }
  }


  # in-text
  if (format == "text") {
    letters_ludeckePackages <- .disamguation_letters(c(
      "easystats", "insight",
      "performance", "parameters",
      "see"
    ) %in% packages)
    if (sum(letters_ludeckePackages != "") == 1) {
      letters_ludeckePackages <- rep("", length(letters_ludeckePackages))
    }
    letters_ludeckeArticles <- .disamguation_letters(c("performance", "see") %in% packages)
    if (sum(letters_ludeckeArticles != "") == 1) {
      letters_ludeckeArticles <- rep("", length(letters_ludeckeArticles))
    }
    letters_makowskiPackages <- .disamguation_letters(c(
      "datawizard", "bayestestR",
      "correlation", "modelbased",
      "report"
    ) %in% packages)
    if (sum(letters_makowskiPackages != "") == 1) {
      letters_makowskiPackages <- rep("", length(letters_makowskiPackages))
    }
    easystats <- "_easystats_"
    cit_packages <- sprintf(
      "(%s)",
      toString(c(
        easystats = sprintf("L\u00fcdecke et al., 2019/2023%s", letters_ludeckePackages[1]),
        insight = sprintf("L\u00fcdecke et al., 2019, 2019/2022%s", letters_ludeckePackages[2]),
        datawizard = sprintf("Makowski et al., 2021/2022%s", letters_makowskiPackages[1]),
        bayestestR = sprintf("Makowski et al., 2019, 2019/2022%s", letters_makowskiPackages[2]),
        performance = sprintf(
          "L\u00fcdecke et al., 2021%s, 2019/2022%s",
          letters_ludeckeArticles[1], letters_ludeckePackages[3]
        ),
        parameters = sprintf("L\u00fcdecke et al., 2020, 2019/2022%s", letters_ludeckePackages[4]),
        effectsize = "Ben-Shachar et al., 2020, 2019/2022",
        correlation = sprintf("Makowski et al., 2020, 2020/2022%s", letters_makowskiPackages[3]),
        modelbased = sprintf("Makowski et al., 2020/2022%s", letters_makowskiPackages[4]),
        see = sprintf(
          "L\u00fcdecke et al., 2021%s, 2019/2022%s",
          letters_ludeckeArticles[2], letters_ludeckePackages[5]
        ),
        report = sprintf("Makowski et al., 2021/2023%s", letters_makowskiPackages[5])
      )[packages])
    )
  } else if (format == "markdown") {
    easystats <- "_easystats_"
    cit_packages <- sprintf(
      "[%s]",
      toString(c(
        easystats = "@easystatsPackage",
        insight = "@insightArticle, @insightPackage",
        datawizard = "@datawizardPackage",
        bayestestR = "@bayestestRArticle, @bayestestRPackage",
        performance = "@performanceArticle, @performancePackage",
        parameters = "@parametersArticle, @parametersPackage",
        effectsize = "@effectsizeArticle, @effectsizePackage",
        correlation = "@correlationArticle, @correlationPackage",
        modelbased = "@modelbasedPackage",
        see = "@seeArticle, @seePackage",
        report = "@reportPackage"
      )[packages])
    )
  } else {
    easystats <- "\\emph{easystats}"
    cit_packages <- sprintf(
      "\\cite{%s}",
      toString(c(
        easystats = "easystatsPackage",
        insight = "insightArticle, insightPackage",
        datawizard = "datawizardPackage",
        bayestestR = "bayestestRArticle, bayestestRPackage",
        performance = "performanceArticle, performancePackage",
        parameters = "parametersArticle, parametersPackage",
        effectsize = "effectsizeArticle, effectsizePackage",
        correlation = "correlationArticle, correlationPackage",
        modelbased = "modelbasedPackage",
        see = "seeArticle, seePackage",
        report = "reportPackage"
      )[packages])
    )
  }

  if (isTRUE(intext_prefix)) {
    intext_prefix <- sprintf("Analyses were conducted using the %s collection of packages ", easystats)
  } else if (isFALSE(intext_prefix)) {
    intext_prefix <- ""
  }
  if (isTRUE(intext_suffix)) {
    intext_suffix <- "."
  }
  if (isFALSE(intext_suffix) || is.na(intext_suffix)) {
    intext_suffix <- ""
  }
  intext <- sprintf("%s%s%s", intext_prefix, cit_packages, intext_suffix)


  # references
  if (format == "text") {
    ref_packages <- paste0(
      "- ",
      sort(unlist(list(
        easystats = sprintf(
          paste(
            "L\u00fcdecke, D., Makowski, D., Ben-Shachar, M. S., Patil, I., Wiernik, B. M.,",
            "Bacher, Etienne, & Th\U00E9riault, R. (2023).",
            "easystats: Streamline model interpretation, visualization, and reporting%s [R package].",
            "https://easystats.github.io/easystats/ (Original work published 2019)"
          ),
          ifelse(installed_packages["easystats"] == "", "", paste0(" (", installed_packages["easystats"], ")"))
        ),
        insight = c(
          article = paste(
            "L\u00fcdecke, D., Waggoner, P., & Makowski, D. (2019).",
            "insight: A unified interface to access information from model objects in R.",
            "Journal of Open Source Software, 4(38), 1412. https://doi.org/10.21105/joss.01412"
          ),
          package = sprintf(
            paste(
              "L\u00fcdecke, D., Makowski, D., Patil, I., Waggoner,",
              "P., Ben-Shachar, M. S., Wiernik, B. M., & Arel-Bundock, V. (2022).",
              "insight: Easy access to model information for various model objects (%s) [R package].",
              "https://CRAN.R-project.org/package=insight (Original work published 2019)"
            ),
            installed_packages["insight"]
          )
        ),
        datawizard = sprintf(
          paste(
            "Makowski, D., L\u00fcdecke, D., Patil, I., Ben-Shachar, M. S., & Wiernik, B. M. (2022).",
            "datawizard: Easy data wrangling (%s) [R package].",
            "https://CRAN.R-project.org/package=datawizard (Original work published 2021)"
          ),
          installed_packages["datawizard"]
        ),
        bayestestR = c(
          article = paste(
            "Makowski, D., Ben-Shachar, M., & L\u00fcdecke, D. (2019).",
            "bayestestR: Describing effects and their uncertainty, existence",
            "and significance within the Bayesian framework.",
            "Journal of Open Source Software, 4(40), 1541. https://doi.org/10.21105/joss.01541"
          ),
          package = sprintf(
            paste(
              "Makowski, D., L\u00fcdecke, D., Ben-Shachar, M. S., Patil, I.,",
              "Wilson, M. D., & Wiernik, B. M. (2021).",
              "bayestestR: Understand and describe Bayesian models and posterior distributions (%s) [R package].",
              "https://CRAN.R-project.org/package=bayestestR (Original work published 2019)"
            ),
            installed_packages["bayestestR"]
          )
        ),
        performance = c(
          article = paste(
            "L\u00fcdecke, D., Ben-Shachar, M., Patil, I., Waggoner, P., & Makowski, D. (2021).",
            "performance: An R package for assessment, comparison and testing of statistical models.",
            "Journal of Open Source Software, 6(60), 3139. https://doi.org/10.21105/joss.03139"
          ),
          package = sprintf(
            paste(
              "L\u00fcdecke, D., Makowski, D., Ben-Shachar, M. S., Patil,",
              "I., Waggoner, P., & Wiernik, B. M. (2021).",
              "performance: Assessment of regression models performance (%s) [R package].",
              "https://CRAN.R-project.org/package=performance (Original work published 2019)"
            ),
            installed_packages["performance"]
          )
        ),
        parameters = c(
          article = paste(
            "L\u00fcdecke, D., Ben-Shachar, M., Patil, I., & Makowski, D. (2020).",
            "Extracting, computing and exploring the parameters of statistical models using R.",
            "Journal of Open Source Software, 5(53), 2445. https://doi.org/10.21105/joss.02445"
          ),
          package = sprintf(
            paste(
              "L\u00fcdecke, D., Makowski, D., Ben-Shachar, M. S., Patil, I.,",
              "H\u00F8jsgaard, S., & Wiernik, B. M. (2022).",
              "parameters: Processing of model parameters (%s) [R package].",
              "https://CRAN.R-project.org/package=parameters (Original work published 2019)"
            ),
            installed_packages["parameters"]
          )
        ),
        effectsize = c(
          article = paste(
            "Ben-Shachar, M. S., L\u00fcdecke, D., & Makowski, D. (2020).",
            "effectsize: Estimation of effect size indices and standardized parameters.",
            "Journal of Open Source Software, 5(56), 2815. https://doi.org/10.21105/joss.02815"
          ),
          package = sprintf(
            paste(
              "Ben-Shachar, M. S., Makowski, D., L\u00fcdecke, D., Patil, I., & Wiernik, B. M. (2022).",
              "effectsize: Indices of effect size and standardized parameters (%s) [R package].",
              "https://CRAN.R-project.org/package=effectsize (Original work published 2019)"
            ),
            installed_packages["effectsize"]
          )
        ),
        correlation = c(
          article = paste(
            "Makowski, D., Ben-Shachar, M., Patil, I., & L\u00fcdecke, D. (2020).",
            "Methods and algorithms for correlation analysis in R.",
            "Journal of Open Source Software, 5(51), 2306. https://doi.org/10.21105/joss.02306"
          ),
          package = sprintf(
            paste(
              "Makowski, D., Wiernik, B. M., Patil, I., L\u00fcdecke, D., & Ben-Shachar, M. S. (2022).",
              "correlation: Methods for correlation analysis (%s) [R package].",
              "https://CRAN.R-project.org/package=correlation (Original work published 2020)"
            ),
            installed_packages["correlation"]
          )
        ),
        modelbased = sprintf(
          paste(
            "Makowski, D., L\u00fcdecke, D., Ben-Shachar, M. S., & Patil, I. (2022).",
            "modelbased: Estimation of model-based predictions, contrasts and means (%s) [R package].",
            "https://CRAN.R-project.org/package=modelbased (Original work published 2020)"
          ),
          installed_packages["modelbased"]
        ),
        see = c(
          article = paste(
            "L\u00fcdecke, D., Patil, I., Ben-Shachar, M. S., Wiernik,",
            "B. M., Waggoner, P., & Makowski, D. (2021).",
            "see: An R package for visualizing statistical models.",
            "Journal of Open Source Software, 6(64), 3393. https://doi.org/10.21105/joss.03393"
          ),
          package = sprintf(
            paste(
              "L\u00fcdecke, D., Makowski, D., Patil, I., Ben-Shachar, M. S., Wiernik,",
              "B. M., & Waggoner, P. (2022).",
              "see: Visualisation toolbox for 'easystats' (%s) [R package].",
              "https://CRAN.R-project.org/package=see (Original work published 2019)"
            ),
            installed_packages["see"]
          )
        ),
        report = sprintf(
          paste(
            "Makowski, D., L\u00fcdecke, D., Patil, I., Th\U00E9riault, R., Ben-Shachar, M. S.,",
            "& Wiernik, B. M. (2023).",
            "report: Automated reporting of results and statistical models (%s) [R package].",
            "https://easystats.github.io/easystats/ (Original work published 2021)"
          ),
          installed_packages["report"]
        )
      )[packages])),
      "\n"
    )
  } else if (format == "markdown") {
    ref_packages <- readLines(system.file("easystats_bib.yaml", package = "report"))
    ref_packages[ref_packages == "  version: %s"] <- sprintf(
      ref_packages[ref_packages == "  version: %s"],
      c(
        installed_packages["bayestestR"], installed_packages["correlation"],
        installed_packages["datawizard"], installed_packages["easystats"],
        installed_packages["effectsize"], installed_packages["insight"],
        installed_packages["modelbased"], installed_packages["parameters"],
        installed_packages["performance"], installed_packages["report"],
        installed_packages["see"]
      )
    )
    ref_packages <- list(
      ref_packages[1:2],
      ref_packages[-c(1:2, length(ref_packages))],
      ref_packages[length(ref_packages)]
    )
    ref_packages[[2]] <- split(ref_packages[[2]], cumsum(ref_packages[[2]] == ""))
    ref_packages.index <- grep(paste0("id: ((", paste0(packages, collapse = ")|("), "))"), ref_packages[[2]])
    ref_packages[[2]] <- unlist(ref_packages[[2]][ref_packages.index], use.names = FALSE)
    ref_packages <- paste0(unlist(ref_packages, use.names = FALSE), collapse = "\n")
  } else {
    ref_packages <- readLines(system.file("easystats_bib.bib", package = "report"))
    ref_packages[ref_packages == "  version = {%s}"] <- sprintf(
      ref_packages[ref_packages == "  version = {%s}"],
      c(
        installed_packages["bayestestR"], installed_packages["correlation"],
        installed_packages["datawizard"], installed_packages["easystats"],
        installed_packages["effectsize"], installed_packages["insight"],
        installed_packages["modelbased"], installed_packages["parameters"],
        installed_packages["performance"], installed_packages["report"],
        installed_packages["see"]
      )
    )
    ref_packages <- split(ref_packages, cumsum(ref_packages == ""))
    ref_packages.index <- grep(paste0(
      "((article)|(software))\\{((",
      paste0(packages, collapse = ")|("), "))"
    ), ref_packages)
    ref_packages <- unlist(ref_packages[ref_packages.index], use.names = FALSE)
    ref_packages <- paste0(unlist(ref_packages, use.names = FALSE), collapse = "\n")
  }


  out <- list(
    intext = intext,
    refs = ref_packages
  )

  class(out) <- c("cite_easystats", class(out))
  out
}


#' @export
#' @rdname cite_easystats
summary.cite_easystats <- function(object, what = "all", ...) {
  what <- match.arg(what, choices = c("all", "cite", "intext", "bib", "refs"))
  what <- switch(what,
    all = "all",
    cite = ,
    intext = "intext",
    bib = ,
    refs = "refs"
  )
  if (what == "all") {
    insight::print_colour("\nCitations\n----------\n\n", "blue")
    cat(strwrap(object$intext, exdent = 0, width = 0.95 * getOption("width")), sep = "\n")
    cat("\n")
    insight::print_colour("\nReferences\n----------\n\n", "blue")
    cat(unlist(lapply(object$refs, strwrap, exdent = 4, width = 0.95 * getOption("width"))), sep = "\n")
    cat("\n")
  } else if (what == "intext") {
    cat(strwrap(object$intext, exdent = 0, width = 0.95 * getOption("width")), sep = "\n")
  } else if (what == "refs") {
    cat(unlist(lapply(object$refs, strwrap, exdent = 4, width = 0.95 * getOption("width"))), sep = "\n")
  }
}


#' @export
#' @rdname cite_easystats
print.cite_easystats <- function(x, what = "all", ...) {
  what <- match.arg(what, choices = c("all", "cite", "intext", "bib", "refs"))
  what <- switch(what,
    all = "all",
    cite = ,
    intext = "intext",
    bib = ,
    refs = "refs"
  )
  if (what == "all") {
    insight::print_colour(sprintf(
      "Thanks for crediting us! %s You can cite the easystats ecosystem as follows:",
      ifelse(.support_unicode, "\U1F600", ":)")
    ), "blue")
    cat("\n")
  }
  summary(x, what = what, ...)
}


.disamguation_letters <- function(x) {
  if (!is.logical(x)) {
    stop("`x` must be a logical vector.", call. = FALSE)
  }
  count <- sum(x)
  x[!x] <- ""
  x[x != ""] <- letters[seq_len(count)]
  x
}