R/utils_cli.R

In epi-sam/SamsElves: Helper functions for the data science at IHME

#' Convert a vector to a comma-separated string
#'
#' Useful for passing R vectors to a CLI arg-parser
#'
#' @param vec [vector] some R vector
#'
#' @return [chr] a comma-separated string
#' @export
#'
#' @examples
#' vec_to_comma_string(1:10) # '1,2,3,4,5,6,7,8,9,10'
vec_to_comma_string <- function(vec){
  return(paste(vec, collapse = ","))
}

#' Convert a comma-separated string to a vector
#'
#' Useful for passing comma-separated CLI args to an R script.
#' - WARNING: returned vector is character type - user is responsible for type conversions
#'
#' @param string [chr] a comma-separated string, e.g. 'arg1,arg2,arg3'
#'
#' @return [chr] a CHARACTER vector of the comma-separated string.
#' @export
#'
#' @examples
#' comma_string_to_vec("1,2,3,4,5") # c("1", "2", "3", "4", "5")
comma_string_to_vec <- function(string){
  return(strsplit(string, ",")[[1]])
}

#' Convert atomic list elements to comma strings
#'
#' Facilitates arg-parsing at the command line.
#'
#' @param lst [list] a list of (potentially) atomic vectors
#'
#' @return [list] a list with atomic elements converted to comma-separated strings
#' @export
#'
#' @examples
#' apply_comma_string_to_list(list(1:5, c("a")))
#' [[1]]
#' [1] "1,2,3,4,5"
#'
#' [[2]]
#' [1] "a"
apply_comma_string_to_list <- function(lst){
  # all list items must be atomic or NULL
  all_valid <- unlist(lapply(lst, function(x) is.atomic(x) || is.null(x)))
  if(!all(all_valid)) stop("All elements of the list must be atomic vectors or NULL - no nested lists allowed.")
  return(lapply(lst, vec_to_comma_string))
}

#' Are all elements of a vector contiguous integers?
#'
#' Useful for checking if a vector is a valid array task list.
#' - uses user-submitted order
#'
#' @param x [int] an integer vector
#'::
#' @return [lgl] TRUE if all elements are contiguous integers
#' @export
#'
#' @examples
#' is_contiguous_int_vec(1L:10L) # TRUE
#' is_contiguous_int_vec(c(1L, 3L, 2L)) # FALSE
is_sequential_int_vec <- function(x){
  stopifnot(is.vector(x, mode = "integer"))
  if(anyNA(x)) stop("NA values are not allowed")
  return(all(diff(x, lag = 1, differences = 1) == 1))
}