R/table2qmd.R

In inti: Tools and Statistical Procedures in Plant Science

#' Table to Quarto format
#'
#' Use Articul8 Add-ons from Google docs to build Rticles
#'
#' @param text Markdown text with table information (string)
#' @param type output file type [strig: "asis" "list", "listfull", "full"]
#'
#' @return string mutated
#' 
#' @export
#' 

table2qmd <- function(text, type = "asis") {
  
  # text <- ": Potato genotypes (Solanum tuberosum L.) used for water deficit experiment with two commercial varieties and 13 genotypes from an advanced breeding population developed by the International Potato Center (CIP). Source: CIP {#tbl:id.oxthgr87o9kv}"
  # text <- "Two commercial varieties and thirteen potato genotypes from the advanced breeding population at the International Potato Center (CIP) were used in this study ([Table  @tbl:id.b16ekvy5zs9n]:). The commercial varieties were UNICA (CIP392797.22) with a good yield in warm and dry environments [(Demirel et al., 2020; Gutiérrez-Rosales et al., 2007; Rolando et al., 2015)](https://www.zotero.org/google-docs/?LcYrXv); and Achirana INTA (CIP720088) known for its earliness and drought tolerance [(Schafleitner et al., 2007)](https://www.zotero.org/google-docs/?LkdMBJ). The plants were grown in a controlled greenhouse at 28/15°C average day/night temperature with 70±5% average relative humidity, monitored by a weather station ‘HOBO U12 Outdoor/Industrial model’ (Onset Computer Corporation, Bourne, MA, USA)."
  # text <- ": Reading list for the Journal Club (JC) implemented during two academic semesters in years 2021 and 2022 in the plant genetics lectures of the Agronomy Faculty at the Universidad Nacional Agraria La Molina (UNALM), Peru. {#tbl:id.85ly0lr9xnr1}"
  
  result <- if(isTRUE(grepl("#tbl\\:", text)) & !type == "asis") { 
    
    opt <- text %>% 
      tibble::enframe(name = "num") %>% 
      dplyr::mutate(id = gsub(".+?\\{\\#(.*)\\}", "\\1", .data$value) %>% gsub(":", "-", .)) %>% 
      dplyr::mutate(title = gsub("\\: (.*) \\{\\#(.+)", "\\1", .data$value)) %>% 
      dplyr::select(!c(.data$value)) %>% 
      tidyr::pivot_longer(!.data$num) %>% 
      dplyr::mutate(opt = dplyr::case_when(
        .data$name %in% "id" ~ paste0("#| label: ", .data$value)
        , .data$name %in% "title" ~ paste0("#| tbl-cap: '", .data$value, "'")
      )) %>% 
      dplyr::select(.data$opt) %>% 
      purrr::as_vector() %>% 
      paste0(collapse = "\n")
    
    chunk <- paste0(
      "```{r}\n"
      , opt
      , "\nknitr::kable(tibble::tibble(' ' = ''))"
      , "\n```"
    )

    # chunk %>% cat()
    
  } else if(isTRUE(grepl("tbl\\:", text))) {

    cite <- text %>%
      gsub("tbl\\:", "tbl-", .) %>%
      gsub("]:", "]", .) %>%
      gsub("Table  \\@", "\\@", .)
    
  } else {
    
    text
    
  }
  
  return(result)
  
}