#' Report for PVS - Global summary
#'
#' Produce a report for PVS data global summary sheet.
#' @param traits A list of traits to be included in the report.
#' @param dfr A data frame with data for a pvs global summary form.
#' @param title Report title.
#' @param subtitle Report subtitle.
#' @param author Report author.
#' @param format The output file format for the report, \code{"html"} by default.
#' Other options are \code{"word"} and \code{"pdf"}.
#' @param server Logical. If \code{"FALSE"} works with local machines.
#' Otherwise works in server environments.
#' @param server_dir_name If \code{"server = TRUE"}, this is the directory name in the server.
#' @param server_file_name If \code{"server = TRUE"}, this is the file name in the server.
#' @details It produces a report for global summary sheet of the Mother & Baby methodology
#' implemented by CIP.
#' @return It returns an automatic report.
#' @author Raul Eyzaguirre.
#' @examples
#' traits <- c("NMTP_Mean_mother", "TNTP_Mean_mother", "PPH_Mean_mother", "TTYA_Mean_mother")
#' repo.pvssg(traits, pvssg)
#' @import ggplot2
#' @importFrom factoextra fviz_pca
#' @importFrom magrittr %>%
#' @importFrom purrr map
#' @export
repo.pvssg <- function(traits,
dfr,
title = "Automatic report for PVS",
subtitle = "Global summary data",
author = "International Potato Center",
format = c("html", "word", "pdf"),
server = FALSE,
server_dir_name = "directory",
server_file_name = "filename") {
format <- paste0(match.arg(format), "_document")
dirfiles <- system.file(package = "pepa")
if (!server) {
fileRmd <- paste0(dirfiles, "/rmd/pvssg.Rmd")
fileURL <- paste0(dirfiles, "/rmd/pvssg.html")
fileDOCX <- paste0(dirfiles, "/rmd/pvssg.docx")
filePDF <- paste0(dirfiles, "/rmd/pvssg.pdf")
} else {
dirfiles <- server_dir_name
# Only Markdown and Word files
fileRmd <- paste0(dirfiles, "pvssg.Rmd")
fileRmd_server_name <- paste0(dirfiles, server_file_name, ".Rmd")
fileDOCX <- paste0(dirfiles, "pvssg.docx")
fileDOCX_server_name <- paste0(dirfiles, server_file_name, ".docx")
}
rmarkdown::render(fileRmd, output_format = format,
params = list(traits = traits,
dfr = dfr,
title = title,
subtitle = subtitle,
author = author))
if (!server) {
if (format == "html_document")
try(browseURL(fileURL))
if (format == "word_document")
try(system(paste("open", fileDOCX)))
if (format == "pdf_document")
try(system(paste("open", filePDF)))
} else {
file.copy(fileDOCX, fileDOCX_server_name, overwrite = TRUE)
}
}
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