FreesearchR/R/helpers.R

#' Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()'
#'
#' @description
#' This function follows the idea from this comment: https://stackoverflow.com/questions/38983179/do-call-a-function-in-r-without-loading-the-package
#' @param x function or function name
#'
#' @return function or character vector
#' @export
#'
#' @examples
#' getfun("stats::lm")
getfun <- function(x) {
  if ("character" %in% class(x)) {
    if (length(grep("::", x)) > 0) {
      parts <- strsplit(x, "::")[[1]]
      requireNamespace(parts[1])
      getExportedValue(parts[1], parts[2])
    }
  } else {
    x
  }
}

#' Wrapper to save data in RDS, load into specified qmd and render
#'
#' @param data list to pass to qmd
#' @param ... Passed to `quarto::quarto_render()`
#'
#' @return output file name
#' @export
#'
write_quarto <- function(data,...) {
  # Exports data to temporary location
  #
  # I assume this is more secure than putting it in the www folder and deleting
  # on session end

  # temp <- base::tempfile(fileext = ".rds")
  # readr::write_rds(data, file = here)

  readr::write_rds(data, file = "www/web_data.rds")

  ## Specifying a output path will make the rendering fail
  ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
  ## Outputs to the same as the .qmd file
  quarto::quarto_render(
    execute_params = list(data.file = "web_data.rds"),
    # execute_params = list(data.file = temp),
    ...
  )
}

write_rmd <- function(data,...) {
  # Exports data to temporary location
  #
  # I assume this is more secure than putting it in the www folder and deleting
  # on session end

  # temp <- base::tempfile(fileext = ".rds")
  # readr::write_rds(data, file = here)

  readr::write_rds(data, file = "www/web_data.rds")

  ## Specifying a output path will make the rendering fail
  ## Ref: https://github.com/quarto-dev/quarto-cli/discussions/4041
  ## Outputs to the same as the .qmd file
  rmarkdown::render(
    params = list(data.file = "web_data.rds"),
    # execute_params = list(data.file = temp),
    ...
  )
}

#' Flexible file import based on extension
#'
#' @param file file name
#' @param consider.na character vector of strings to consider as NAs
#'
#' @return tibble
#' @export
#'
#' @examples
#' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
read_input <- function(file, consider.na = c("NA", '""', "")) {
  ext <- tools::file_ext(file)

  if (ext == "csv") {
    df <- readr::read_csv(file = file, na = consider.na)
  } else if (ext %in% c("xls", "xlsx")) {
    df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
  } else if (ext == "dta") {
    df <- haven::read_dta(file = file)
  } else if (ext == "ods") {
    df <- readODS::read_ods(path = file)
  } else if (ext == "rds") {
    df <- readr::read_rds(file = file)
  } else {
    stop("Input file format has to be on of:
             '.csv', '.xls', '.xlsx', '.dta', '.ods' or '.rds'")
  }

  df
}

#' Convert string of arguments to list of arguments
#'
#' @description
#' Idea from the answer: https://stackoverflow.com/a/62979238
#'
#' @param string string to convert to list to use with do.call
#'
#' @return list
#' @export
#'
argsstring2list <- function(string) {
  eval(parse(text = paste0("list(", string, ")")))
}


#' Factorize variables in data.frame
#'
#' @param data data.frame
#' @param vars variables to force factorize
#'
#' @return data.frame
#' @export
factorize <- function(data, vars) {
  if (!is.null(vars)) {
    data |>
      dplyr::mutate(
        dplyr::across(
          dplyr::all_of(vars),
          REDCapCAST::as_factor
        )
      )
  } else {
    data
  }
}

dummy_Imports <- function() {
  list(
    MASS::as.fractions(),
    broom::augment(),
    broom.helpers::all_categorical(),
    here::here(),
    cardx::all_of(),
    parameters::ci(),
    DT::addRow(),
    bslib::accordion()
  )
  # https://github.com/hadley/r-pkgs/issues/828
}


#' Title
#'
#' @param data data
#' @param output.format output
#' @param filename filename
#' @param ... passed on
#'
#' @returns data
#' @export
#'
file_export <- function(data, output.format = c("df", "teal", "list"), filename, ...) {
  output.format <- match.arg(output.format)

  filename <- gsub("-", "_", filename)

  if (output.format == "teal") {
    out <- within(
      teal_data(),
      {
        assign(name, value |>
          dplyr::bind_cols(.name_repair = "unique_quiet") |>
          default_parsing())
      },
      value = data,
      name = filename
    )

    datanames(out) <- filename
  } else if (output.format == "df") {
    out <- data |>
      default_parsing()
  } else if (output.format == "list") {
    out <- list(
      data = data,
      name = filename
    )

    out <- c(out, ...)
  }

  out
}


#' Default data parsing
#'
#' @param data data
#'
#' @returns data.frame or tibble
#' @export
#'
#' @examples
#' mtcars |> str()
#' mtcars |>
#'   default_parsing() |>
#'   str()
default_parsing <- function(data) {
  name_labels <- lapply(data,\(.x) REDCapCAST::get_attr(.x,attr = "label"))

  out <- data |>
    REDCapCAST::parse_data() |>
    REDCapCAST::as_factor() |>
    REDCapCAST::numchar2fct()

  purrr::map2(out,name_labels,\(.x,.l){
    if (!(is.na(.l) | .l=="")) {
      REDCapCAST::set_attr(.x, .l, attr = "label")
    } else {
      attr(x = .x, which = "label") <- NULL
      .x
    }
    # REDCapCAST::set_attr(data = .x, label = .l,attr = "label", overwrite = FALSE)
  }) |> dplyr::bind_cols()
}

#' Remove NA labels
#'
#' @param data data
#'
#' @returns data.frame
#' @export
#'
#' @examples
#' ds <- mtcars |> lapply(\(.x) REDCapCAST::set_attr(.x,label=NA,attr = "label"))
#' ds |> remove_na_attr() |> str()
remove_na_attr <- function(data,attr="label"){
  out <- data |> lapply(\(.x){
    ls <- REDCapCAST::get_attr(data = .x,attr = attr)
    if (is.na(ls) | ls == ""){
      attr(x = .x, which = attr) <- NULL
    }
    .x
  })

  dplyr::bind_cols(out)
}