scripts/example_cmd_line_execution_script.R

In lmullany/iddplotting: Aids in plotting COVID-19 model results with empirical data

#function to generate cmd, given a named list of flags
gencmd <- function(script_args) {
  cmdstring <- "Rscript generate_idd_plots.R "
  for(flag in names(script_args)) {
    cmdstring <- paste0(cmdstring, flag, " \"", script_args[[flag]], "\" ")
  }
  return(cmdstring)
}

#manually construct list of flags
script_args <- list("-r"= "2020-07-22",
             "-g"= "us",
             "-s"= "<Put Caption Here>",
             "-e"= "../data/us_data_territories.csv",
             "-m"= "../data/q_summ_country.csv",
             "--modelend" = "2020-09-04",
             "--convertIDD" = TRUE)

#generate the cmd
mycmd <- gencmd(script_args)

#use the shell cmd to execute the cmd
shell(mycmd)