R/gl.set.verbosity.r

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#' @name gl.set.verbosity
#' @title Sets the default verbosity level
#' @description
#' dartR functions have a verbosity parameter that sets the level of reporting
#'  during the execution of the function. The verbosity level, set by parameter
#'  'verbose' can be one of verbose 0, silent or fatal errors; 1, begin and end;
#'  2, progress log; 3, progress and results summary; 5, full report. The
#'  default value for verbosity is stored in the r environment. This script sets
#'  the default value.
#' @param value Set the default verbosity to be this value: 0, silent only fatal
#' errors; 1, begin and end; 2, progress log; 3, progress and results summary;
#' 5, full report [default 2]
#' @return verbosity value [set for all functions]
#' @export
#' @author Custodian: Arthur Georges (Post to
#' \url{https://groups.google.com/d/forum/dartr})
#' @examples
#' gl <- gl.set.verbosity(value=2)

gl.set.verbosity <- function(value = 2) {
    # FLAG SCRIPT START
    funname <- match.call()[[1]]
    utils.flag.start(func = funname,
                     build = "Jackson",
                     verbosity = value)
    
    # SET GLOBAL VERBOSITY
    if (!is.null(value) &
        is.numeric(value) & value >= 0 & value <= 5) {
        options(dartR_verbose = value)
    }
    if (value >= 2) {
        cat(report("  Global verbosity set to:", value, "\n"))
    }
    
    # FLAG SCRIPT END
    
    if (value >= 1) {
        cat(report("Completed:", funname, "\n"))
    }
    
    invisible(NULL)
}