Rscript for command line execution and --flagged arguments checks

Template_Rscript.R

#!/usr/bin/env Rscript
#
# Purpose: what this script does.
# Author: Renzo Bonifazi - dd-mm-yyyy
# Usage:
# # Rscript --vanilla myscript.R --file my_path/myfile.csv --output myoutput.csv
#
# Example:
# # Rscript --vanilla Make_pedigree.R --file Renzo/Documents/file.csv --output Output.csv
#
# Details:
#
# Versions:
# * 0.0 - initial script.
#
# Notes:
#
###################################################################################
Sys.time() # print starting time

# 0. Load packages --------
if (!require("pacman")) {install.packages("pacman", quiet = T)}
pacman::p_load(optparse, dplyr, tidyr, lubridate, data.table, dtplyr)
# [test usage only] pacman::p_load(tidylog)

# 1. Read cmd line arguments ---------------------------------------------------------------
# args parser # https://www.r-bloggers.com/2015/09/passing-arguments-to-an-r-script-from-command-lines/
option_list <- list(
  make_option(c("-f", "--file"),
    type = "character", default = NULL,
    help = "Input file name", metavar = "character"
  ),
  make_option(c("-o", "--output"),
    type = "character", default = NULL,
    help = "Output file name", metavar = "character"
  )
)
opt_parser <- OptionParser(option_list = option_list) # process list of args above
opt <- parse_args(opt_parser) # make args accessible in an object
if (is.null(opt$file) | is.null(opt$output)) {
  print_help(opt_parser)
  stop(cat("Input and output file name must be supplied! \n Current path is:", getwd(), "\n"), call. = FALSE)
}

# 2. Vars and set working directory --------
# ___ 2.1 Set variables and wd
infile <- opt$file
outfile <- opt$output
setwd(dirname(infile)) # set wd to input filename

# [test usage only] infile <- "myfile.csv"
# [test usage only] outfile <- "outfile.csv"
# [test usage only] setwd("C:/Users/Documents/mycodes/")

# ___ 2.2 Fixed vars
col_names <- c("col1", "col2", "col3", "col4")

# 3. Read files --------
file_proc <- fread(infile,
  sep = ";", header = F, stringsAsFactors = F,
  strip.white = T, col.names = col_names,
  colClasses = list(character = c(1:2), integer64 = c(3:4)) # first 2 cols as character, last 2 as integer64 (=large integer)
)

# 4. Edit files or any other operations --------
file_edited <- lazy_dt(file_proc) %>% # trigger R to use dtplyr for faster execution
  # [test usage only] file_proc %>% as.data.frame %>%
 your_lines_of_dplyr %>%
 as.data.frame() # convert back to readable data.frame
 
# 5. Checks ----------------------------------------

# 6. Save output  ------
fwrite(x = file_edited, file = outfile, quote = F, row.names = F, append = F, sep = ",")

Sys.time() # print ending time