R/pkg_reports_functions.R

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

# # Functions from `reports` package used in datelife
# # Hosting reports functions here for now so we can submit to CRAN
# # reports package on github https://github.com/trinker/reports
# # all function from https://github.com/trinker/reports/blob/master/R/delete.R
# # https://raw.githubusercontent.com/trinker/reports/master/R/delete.R
#
#
# #' Easy File Handling
# #'
# #' \code{delete} - Deletes files and directories.
# #'
# #' @param file The name of the file in the working directory or the path to the
# #' file to be deleted.  If \code{NULL} provides a menu of files from the working
# #' directory.
# #' @param \ldots The name(s) of the folder to be created.  If both \ldots and
# #' \code{folder.name} are \code{NULL} creates a file in the working directory
# #' with the creation date and time stamp.
# #' @param folder.name A character vector of the name(s) of the folder to be
# #' created.  Default \code{NULL}  (if the \ldots  is \code{NULL} too) creates a
# #' file in the working directory with the creation date and time stamp.  Use
# #' this argument only if the directory names contain spaces.
# #' @return \code{delete} permanently removes a file/directory.
# #' @seealso  \code{\link[base]{unlink}},
# #' \code{\link[base]{file.remove}},
# #' \code{\link[base]{dir.create}}
# #' @keywords file, delete, folder
# #' @rdname file_handling
# #' @export
# #' @examples
# #' \dontrun{  # This is a flag for package development. You are welcome to run the example.
# #' (x <- folder("DELETE.ME"))
# #' which(dir() == "DELETE.ME")
# #' delete("DELETE.ME")
# #' which(dir() == "DELETE.ME")
# #'
# #' folder("the/next/big/thing", "hello world", "now/is/the/time")
# #'
# #' folder(cat, dog)
# #' lapply(c("cat", "dog"), delete)
# #' }
# delete <-
# function(file = NULL) {
#     x <- if (is.null(file)) {
#         menu(dir())
#     } else {
#         file
#     }
#     unlink(x, recursive = TRUE, force = FALSE)
# }
#
# #' Create Folder
# #'
# #' \code{folder} - Create a folder/directory.
# #'
# #' @return \code{folder} creates a folder/directory.
# #' @rdname file_handling
# #' @export
# folder <- function(..., folder.name = NULL) {
#     if (!is.null(folder.name)) {
#         x <- strsplit(folder.name, split = ", ")
#     } else {
#         x <- substitute(...())
#     }
#     if (!is.null(x)) {
#         x <- unblanker(scrubber(unlist(lapply(x, function(y) {
#             as.character(y)}))))
#     }
#     if (is.null(x)) {
#         hfolder()
#     } else {
#         if (length(x) == 1) {
#             hfolder(x)
#         } else {
#             lapply(x, function(z) {
#                 hfolder(z)
#             })
#         }
#     }
# }
#
# hfolder <- function(folder.name = NULL) {
#     if (is.null(folder.name)) {
#         FN <- mgsub(c(":", " "), c(".", "_"),
#             substr(Sys.time(), 1, 19))
#     } else {
#         FN <-folder.name
#     }
#     parts <- unlist(strsplit(FN, "/"))
#     if (length(parts) == 1) {
#         x <- paste(getwd(), "/", FN, sep = "")
#     } else {
#
#         ## If nested path (multiple directories created)
#         if (!file.exists(dirname(FN))) {
#
#             y <- FN
#             z <- length(parts)
#             for (i in rev(seq_along(parts))) {
#                 if(file.exists(y)) {
#                     z <- z + 1
#                     break
#                 }
#                 y <- dirname(paste(parts[1:i], collapse ="/"))
#                 z <- z - 1
#             }
#
#             for (i in z:(length(parts) - 1)) {
#                 suppressWarnings(dir.create(paste(parts[1:i], collapse ="/")))
#             }
#
#         }
#         x <- FN
#     }
#     dir.create(x)
#     return(x)
# }