R/lstExtractTime.R

In NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

##' Extract run time from output control stream
##'
##' @param file path to output control stream
##' @param tz.lst The time zone of the time stamp from Nonmem. The
##'     default ("as.is") is to try to extract it or take it from the
##'     system on which this function is run. See details.
##' @details Time zones are system specific. See \code{OlsonNames()}
##'     for a list of what time zones are available on the system.
##' @return A POSIXct date-time object
##' @examples
##' file <- system.file("examples/nonmem/xgxr003.lst",package="NMdata")
##' NMdata:::lstExtractTime(file)
##' file <- system.file("examples/nonmem/xgxr003.mod",package="NMdata")
##' NMdata:::lstExtractTime(file)
##'
##' \dontrun{
##' all.lsts <- list.files(
##'   system.file("examples/nonmem",package="NMdata"),
##'   pattern="\\.lst",full.names=TRUE)
##' lapply(all.lsts,NMdata:::lstExtractTime)
##' }
##' @keywords internal

lstExtractTime <- function(file,tz.lst="as.is"){

    if(!is.null(tz.lst) && ( !is.character(tz.lst) || !length(tz.lst)) ){
        stop("tz.lst must be a character vector of length one.")
    }

### the time stamp must be before any $ blocks
    lines <- readLines(file)
    last.pre <- min(grep(" *\\$",lines))-1
    if(last.pre<1) return(NA)
    lines <- lines[1:last.pre]

    ## must be first line
    time.char <- lines[1]

    ## extract timestamp and time zone
    time.char <- sub("^... ","",time.char)
    if(tz.lst=="as.is"){
        tz <- sub(".+ ([^ ]+) [0-9]{4}$","\\1",time.char)
        if(!tz%in%OlsonNames()){
            tz.sys <- Sys.timezone()
            message(sprintf("Identified tz %s not recognized on system. System timezone (%s) used instead.",tz,tz.sys))
            tz <- tz.sys
        }
    } else {
        tz <- tz.lst
    }
    
    timedate <- sub("(.+) [^ ]+ ([0-9]{4})$","\\1 \\2",time.char)
    time.file <- as.POSIXct(timedate,format="%b %d %H:%M:%S %Y",tz=tz)
    time.file

}