R/fun.Report.R

In leppott/ContDataQC: Quality Control (QC) of Continous Monitoring Data

#' Generate Reports
#'
#' Subfunction for generating reports.  Needs to be called from ContDataQC().
#' Requires knitr() and pandoc.
#' Different reports (in Word) are created using the RMD files in this package
#' depending on the input fun.myFile.Prefix.
#' Values are "QC", "DATA", or "STATS".
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Erik.Leppo@tetratech.com (EWL)
# 20151022
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Basic Operations:
# load all files in data directory
# find ones specified by user
# generate QC data summaries
# output to PDF
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## ideas
# load one file instead of all
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# library (load any required helper functions)
#library(waterData)
#library(knitr)

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# # 20151221
# # create MD file in myDir.BASE
# # then knit
# # then PANDOC to DOCX
# ##
# # 1. Create MD file
# # 2. Knit MD file
# knit('report_knit_.md')
# # 3. Pandoc, convert MD to DOCX
# pandoc(report.md,-0,"report.docx")
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 20150302, Change function to "Report"
# QC / Aggregate
#' @param fun.myData.SiteID Station/SiteID.
#' @param fun.myData.Type data type;
#' c("Air","Water","AW","Gage","AWG","AG","WG")
#' @param fun.myData.DateRange.Start Start date for requested data.
#' Format = YYYY-MM-DD.
#' @param fun.myData.DateRange.End End date for requested data.
#' Format = YYYY-MM-DD.
#' @param fun.myDir.import Directory for import data.
#' Default is current working directory.
#' @param fun.myDir.export Directory for export data.
#' Default is current working directory.
#' @param fun.myFile.Prefix Valid prefixes are "QC", "DATA", or "STATS".
#' This determines the RMD to use for the output.
#' @param fun.myReport.format Report format (docx or html).
#' Default is specified in config.R (docx).  Can be customized in config.R;
#' ContData.env$myReport.Format.
#' @param fun.myReport.Dir Report (rmd) template folder.
#' Default is the package rmd folder.  Can be customized in config.R;
#' ContData.env$myReport.Dir.
#'
#' @return Creates a Word file in the specified directory.
#'
#' @examples
#' #Not intended to be accessed indepedant of function ContDataQC().
#
# FUNCTION
#' @export
fun.Report <- function(fun.myData.SiteID
                         , fun.myData.Type
                         , fun.myData.DateRange.Start
                         , fun.myData.DateRange.End
                         , fun.myDir.import = getwd()
                         , fun.myDir.export = getwd()
                         , fun.myFile.Prefix
                         , fun.myReport.format
                         , fun.myReport.Dir) {##FUN.fun.Report.START
  #
  # global varible bindings ----
  data.plot <- NULL

  # Convert Data Type to proper case
  fun.myData.Type <- paste(toupper(substring(fun.myData.Type, 1, 1))
                           , tolower(substring(fun.myData.Type, 2
                                               , nchar(fun.myData.Type)))
                           , sep="")
  # QC, ensure inputs are in the proper case
  fun.myReport.format <- tolower(fun.myReport.format)
  #
  # data directories
  # myDir.data.import <- paste(fun.myDir.BASE,ifelse(fun.myDir.SUB.import=="",""
  #,paste("/",fun.myDir.SUB.import,sep="")),sep="")
  # myDir.data.export <- paste(fun.myDir.BASE,ifelse(fun.myDir.SUB.export=="",""
  #,paste("/",fun.myDir.SUB.export,sep="")),sep="")
  myDir.data.import <- fun.myDir.import
  myDir.data.export <- fun.myDir.export
  #
  myDate <- format(Sys.Date(),"%Y%m%d")
  myTime <- format(Sys.time(),"%H%M%S")
  #
  # Start Time (used to determine run time at end)
  myTime.Start <- Sys.time()
  #
    # 0. Load Single file
    # QC Check - delimiter for strsplit
    if(ContData.env$myDelim==".") {##IF.myDelim.START
      # special case for regex check to follow (20170531)
      myDelim.strsplit <- "\\."
    } else {
      myDelim.strsplit <- ContData.env$myDelim
    }##IF.myDelim.END
    strFile.Prefix     <- toupper(fun.myFile.Prefix) # DATA = Aggregate, QC = QC
    strFile.SiteID     <- fun.myData.SiteID
    strFile.DataType   <- fun.myData.Type
    strFile.Date.Start <- format(as.Date(fun.myData.DateRange.Start,"%Y-%m-%d")
                                 , "%Y%m%d")
    strFile.Date.End   <- format(as.Date(fun.myData.DateRange.End,"%Y-%m-%d")
                                 , "%Y%m%d")
    strFile <- paste(paste(strFile.Prefix
                           , strFile.SiteID
                           , fun.myData.Type
                           , strFile.Date.Start
                           , strFile.Date.End
                           , sep = ContData.env$myDelim)
                     , "csv"
                     , sep = ".")
    strFile.Base <- substr(strFile,1,nchar(strFile)-nchar(".csv"))
    strFile.parts <- strsplit(strFile.Base, myDelim.strsplit)

    #QC, make sure file exists
    if(strFile %in% list.files(path=myDir.data.import)==FALSE) {##IF.file.START
      #
      print("ERROR; no such file exits.  Cannot create QC Report.")
      print(paste("PATH = ", myDir.data.import, sep=""))
      print(paste("FILE = ", strFile, sep=""))
      utils::flush.console()
      stop("Bad file.")
      #
    }##IF.file.END

    #import the file
    #data.import <- utils::read.csv(paste(myDir.data.import,strFile,sep="/")
    #,as.is=TRUE,na.strings=c("","NA"))
    data.import <- utils::read.csv(file.path(myDir.data.import,strFile)
                                   , as.is = TRUE
                                   , na.strings = c("", "NA"))


    # pick 'report' based on prefix
    myPkg <- "ContDataQC"
    if (strFile.Prefix == "QC") {##IF.strFile.Prefix.START
      myReport.Name <- "Report_QC"
    } else if (strFile.Prefix == "DATA") {
      myReport.Name <- "Report_Aggregate"
    } else if (strFile.Prefix == "STATS") {
      myReport.Name <- "Report_Stats"
    }

    #RStudio help solution
    # use RMD with embedded code
    # much cleaner DOCX than the 2-step process; MD with knit to RMD with pandoc
    #strFile.RMD <- paste(myDir.BASE,"Scripts"
    #,paste(myReport.Name,"rmd",sep=".")
    # ,sep="/") #"QCReport.rmd"
    #strFile.RMD <- system.file(paste0("rmd/",myReport.Name,"_"
    # ,fun.myReport.format,".rmd"),package=myPkg)
    # use provided dir for template
    #strFile.RMD <- file.path(fun.myReport.Dir, paste0(myReport.Name, "_"
    # , fun.myReport.format, ".rmd"))
    strFile.RMD <- file.path(fun.myReport.Dir, paste0(myReport.Name, ".rmd"))
    strFile.out.ext <- paste0(".",fun.myReport.format) #".docx" # ".html"
    strFile.out <- paste(paste(strFile.Prefix
                               , strFile.SiteID
                               , fun.myData.Type
                               , strFile.Date.Start
                               , strFile.Date.End
                               , myReport.Name,sep = ContData.env$myDelim)
                         , strFile.out.ext
                         , sep = "")
    strFile.RMD.format <- paste0(ifelse(fun.myReport.format == "docx"
                                        , "word"
                                        , fun.myReport.format)
                                 ,"_document")
    #
    # 20180212
    # Test if RMD file exists
    if (file.exists(strFile.RMD)){##IF.file.exists.START
      #suppressWarnings(
      rmarkdown::render(strFile.RMD, output_format=strFile.RMD.format
                        , output_file=strFile.out, output_dir=fun.myDir.export
                        , quiet=TRUE)
      #)
    } else {
      Msg.Line0 <- "\n~~~~~~~~~~~~~~~~~~~~~~~~~~\n"
      Msg.Line1 <- "Provided report template file directory does not include the
      necessary RMD file to generate the report.
      So no report will be generated."
      Msg.Line2 <- "The default report directory can be modified in config.R
      (ContData.env$myReport.Dir) and used as input to the function
      (fun.myConfig)."
      Msg.Line3 <- paste0("file = ", paste0(myReport.Name, ".rmd"))
      Msg.Line4 <- paste0("directory = ", fun.myReport.Dir)
      Msg <- paste(Msg.Line0
                   , Msg.Line1
                   , Msg.Line2
                   , Msg.Line3
                   , Msg.Line4
                   , Msg.Line0
                   , sep = "\n\n")
      cat(Msg)
      utils::flush.console()
    }##IF.file.exists.END
    #


      #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    # Clean up
    rm(data.import)
    rm(data.plot)
    #


    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  #
  #print(paste("Processing of ",intCounter," of ",intCounter.Stop
    #," files complete.",sep=""))
 # files2process[intCounter] #use for troubleshooting if get error
  # inform user task complete with status
  myTime.End <- Sys.time()
#   print(paste("Processing of items (n=",intItems.Total,") finished.
  #Total time = ",format(difftime(myTime.End,myTime.Start)),".",sep=""))
#   print(paste("Items COMPLETE = ",myItems.Complete,".",sep=""))
#   print(paste("Items SKIPPPED = ",myItems.Skipped,".",sep=""))
    print(paste("Task COMPLETE. QC Report.  Total time = "
                , format(difftime(myTime.End, myTime.Start))
                , "."
                , sep = ""))
  # User defined parameters
  print(paste("User defined parameters: SiteID ("
              , fun.myData.SiteID
              , "), Data Type ("
              , fun.myData.Type
              , "), Date Range ("
              , fun.myData.DateRange.Start
              , " to "
              , fun.myData.DateRange.End
              , ")."
              , sep = ""))
  utils::flush.console()
  #
}##FUN.Report.END