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read_write_option.R
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read_write_option.R
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#' Define default read/write options and add items to it
#'
#' @param new_type A data.frame with four columns: `type`, `read_fun`,
#' `read_header` and `write_fun` containing each a single character string or
#' `NA`. `type` is the usual extension for this type of file, e.g., `png` for
#' PNG images, `read_fun`, `read_header` and `write_fun` are character strings
#' with "pkg::fun" format ("pkg" is the package containing the function and
#' "fun" is the function name), or just "fun" if the function
#' is visible on the search path.
#'
#' @description Define the functions that [read()] or write() must call to
#' import or export data for the different types (formats).
#'
#' @return The data.frame with all known formats is returned invisibly. The same
#' data.frame is also saved in the `read_write`` option, and can be retrieved
#' directly with `getOption("read_write")`.
#' @author Philippe Grosjean <phgrosjean@sciviews.org>
#' @export
#' @seealso [read()], [getOption()]
#' @keywords utilities
#' @concept labeling objects
#' @examples
#' # The default options
#' (read_write_option())
#' # To add a new type:
#' tail(read_write_option(data.frame(type = "png", read_fun = "png::readPNG",
#' read_header = NA, write_fun = "png::writePNG", comment = "PNG image")))
read_write_option <- function(new_type) {
opts <- getOption("read_write", default = tibble::tribble(
~type, ~read_fun, ~read_header,
~write_fun, ~comment,
"csv", "readr::read_csv", "data.io::hread_text",
"readr::write_csv", "comma separated values",
"csv2", "readr::read_csv2", "data.io::hread_text",
NA, "semicolon separated values",
"xlcsv", "readr::read_csv", "data.io::hread_text",
"readr::write_excel_csv", "write a CSV file more easily readable by Excel",
"tsv", "readr::read_tsv", "data.io::hread_text",
"readr::write_tsv", "tab separated values",
"fwf", "readr::read_fwf", "data.io::hread_text",
NA, "fixed width file", # TODO: a writer here!
"log", "readr::read_log", NA,
NA, "standard log file", # TODO: a writer here!
"rds", "readr::read_rds", NA,
"readr::write_rds", "R data file (no compression by default)",
"txt", "readr::read_file", NA,
"readr::write_file", "text file (as length 1 character vector)",
"raw", "readr::read_file_raw", NA,
NA, "binary file (read as raw vector)",
# TODO: a writer here!
"ssv", "readr::read_table", "data.io::hread_text",
NA, "space separated values (strict)",
"ssv2", "readr::read_table2", "data.io::hread_text",
NA, "space separated values (relaxed)",
"csv.gz", "readr::read_csv", "data.io::hread_text",
"readr::write_csv", "gz compressed comma separated values",
"csv2.gz", "readr::read_csv2", "data.io::hread_text",
NA, "gz compressed semicolon separated values",
"tsv.gz", "readr::read_tsv", "data.io::hread_text",
"readr::write_tsv", "gz compressed tab separated values",
"txt.gz", "readr::read_file", NA,
"readr::write_file", "gz compressed text file",
"csv.bz2", "readr::read_csv", "data.io::hread_text",
"readr::write_csv", "bz2 compressed comma separated values",
"csv2.bz2","readr::read_csv2", "data.io::hread_text",
NA, "bz2 compressed semicolon separated values",
"tsv.bz2", "readr::read_tsv", "data.io::hread_text",
"readr::write_tsv", "bz2 compressed tab separated values",
"txt.bz2", "readr::read_file", "data.io::hread_text",
"readr::write_file", "bz2 compressed text file",
"csv.xz", "readr::read_csv", "data.io::hread_text",
"readr::write_csv", "xz compressed comma separated values",
"csv2.xz", "readr::read_csv2", "data.io::hread_text",
NA, "xz compressed semicolon separated values",
"tsv.xz", "readr::read_tsv", "data.io::hread_text",
"readr::write_tsv", "xz compressed tab separated values",
"txt.xz", "readr::read_file", NA,
"readr::write_file", "xz compressed text file",
# Buggy right now!! "csvy", "csvy::read_csvy", NA, "csvy::write_csvy",
# "comma separated value with YAML header",
"xls", "readxl::read_excel", "data.io::hread_xls",
"WriteXLS::WriteXLS", "Excel old .xls format",
"xlsx", "readxl::read_excel", "data.io::hread_xlsx",
"writexl::write_xlsx", "Excel new .xlsx format", #"openxlsx::write.xlsx",
"dta", "haven::read_dta", NA,
"haven::write_dta", "Stata DTA format",
# read_dta() = read_stata()
"sas", "haven::read_sas", NA,
"haven::write_sas", "SAS format",
"sas7bdat","haven::read_sas", NA,
"haven::write_sas", "SAS format (sas7bdat)",
"sav", "haven::read_sav", NA,
"haven::write_sav", "SPSS .sav format",
"zsav", "haven::read_sav", NA,
"haven::write_sav", "SPSS .zsav format",
"por", "haven::read_por", NA,
NA, "SPSS .por format",
# read_por()/read_sav() = read_spss()
"xpt", "haven::read_xpt", NA,
"haven::write_xpt", "SPSS transport format (FDA compliant)"#,
#"feather", "feather::read_feather",NA,
#"feather::write_feather", "transportable feather format"
))
if (!missing(new_type)) {
# Check it is in a correct format
if (!is.data.frame(new_type))
stop("new_type must be a data.frame")
if (ncol(new_type) != 5)
stop("new_type must contain 5 columns",
" (type, read_fun, read_header, write_fun & comment")
names(new_type) <- names(opts)
opts <- rbind(opts, new_type)
}
options(read_write = opts)
invisible(opts)
}
# TODO: check foreign fst, data.table, import and rio
# TODO: there is a xlsx writer in writexl, but does not support sheets!
# Note: csvy is csv with YAML header. It offers more configuration
#.import.rio_png <- function(file, native = FALSE, info = FALSE, ...) {
# readPNG(file, native = native, info = info)
#}