added template for R scripts

misc/template_r_script.R

+#!/usr/bin/env Rscript
+
+##TODO: define title and objective
+#' # Report Title
+#' Objective: Analysis objective
+#'
+#' Created by: `r system("whoami", intern=T)`
+#'
+#' Created at: `r format(Sys.Date(), format="%B %d %Y")`
+
+#-----------------------------------------------------------------------------------------------------------------------
+
+#+ include=FALSE
+suppressMessages(require(docopt))
+
+##TODO: specify function of the script, usage (name of R script and required input data) and optional parameters with type (e.g. boolean, file, etc.), a description and the default setting
+doc = '
+Function of the script
+Usage: script_name.R [options] <required_input_1> <required_input_2>
+
+Options:
+--parameter_1 <parameter_type>    parameter description [default: parameter_default]
+--parameter_2 <parameter_type>    parameter description [default: parameter_default]
+'
+
+
+#commandArgs <- function(x) c("--argument_1", "argument_1_setting", "required_input_1", "required_input_2")
+opts = docopt(doc, commandArgs(TRUE))
+
+
+#-----------------------------------------------------------------------------------------------------------------------
+
+## REQUIRED PACKAGES
+devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/core_commons.R")
+#TODO: load all additionally required packages
+
+
+
+## NEWLY DEFINED FUNCTIONS
+#TODO: define new functions if required
+
+
+
+
+#-----------------------------------------------------------------------------------------------------------------------
+
+#TODO: write script with commented code
+
+
+
+
+
+#-----------------------------------------------------------------------------------------------------------------------
+
+## ADDITIONAL INFORMATION EXPORT
+## export R version and package infos
+writeLines(capture.output(devtools::session_info()), ".sessionInfo.txt")
+
+## save R session as hidden file
+#TODO: use the R script's name as a name for the session file
+session::save.session(".script_name.dat")
+# session::restore.session(".script_name.dat")
+