mcs-acc: Raw Accelerometer Data Analysis

g.shell.GGIR = function(mode=c(1,2),datadir=c(),outputdir=c(),studyname=c(),f0=1,f1=0,
                        do.report=c(2),overwrite=FALSE,visualreport=FALSE,viewingwindow=1,...) {
  #get input variables
  input = list(...)
  if (length(input) > 0) {
    for (i in 1:length(names(input))) {
      txt = paste(names(input)[i],"=",input[i],sep="")
      if (class(unlist(input[i])) == "character") {
        txt = paste(names(input)[i],"='",unlist(input[i]),"'",sep="")
      }
      eval(parse(text=txt))
    }
  }
  if (length(which(ls() == "timewindow")) != 0) timewindow = input$timewindow
  # verify whether datadir is a directory or a list of files
  filelist = isfilelist(datadir)
  derivef0f1 = FALSE
  if (length(f0) == 0 | length(f1) == 0) {
    derivef0f1 = TRUE
  } else {
    if (f0 == 0 | f1 == 0) derivef0f1 = TRUE
  }
  if (derivef0f1 == TRUE) { # What file to start with?
    f0 = 1
    if (filelist == FALSE) {  # What file to end with?
      f1 <- length(dir(datadir, recursive = TRUE, pattern = "[.](csv|bin|Rda|wa)")) # modified by JH
    } else {
      f1 = length(datadir) #modified
    }
  }
  dopart1 = dopart2 = dopart3 = dopart4 = dopart5 = FALSE
  if (length(which(mode == 0)) > 0) {
    dopart1 = dopart2 = dopart3 = dopart4 = dopart5 = TRUE
  } else {
    # if (length(which(mode == 0)) > 0) dopart0 = TRUE
    if (length(which(mode == 1)) > 0) dopart1 = TRUE
    if (length(which(mode == 2)) > 0) dopart2 = TRUE
    if (length(which(mode == 3)) > 0) dopart3 = TRUE; do.anglez = TRUE
    if (length(which(mode == 4)) > 0) dopart4 = TRUE
    if (length(which(mode == 5)) > 0) dopart5 = TRUE
  }
  
  # test whether RData input was used and if so, use original outputfolder
  if (length(datadir) > 0) {
    # list of all csv and bin files
    fnames = datadir2fnames(datadir,filelist)
    # check whether these are RDA
    if (length(unlist(strsplit(fnames[1],"[.]RD"))) > 1) {
      useRDA = TRUE
    } else {
      useRDA = FALSE
    }
  } else {
    useRDA = FALSE
  }
  if (filelist == TRUE | useRDA == TRUE) {
    metadatadir = paste(outputdir,"/output_",studyname,sep="")
  } else {
    outputfoldername = unlist(strsplit(datadir,"/"))[length(unlist(strsplit(datadir,"/")))]
    metadatadir = paste(outputdir,"/output_",outputfoldername,sep="")
  }
  # obtain default parameter values if not provided:
  if (length(which(ls() == "selectdaysfile")) == 0)  selectdaysfile = c()
  if (length(which(ls() == "diaryfile")) == 0)  diaryfile = c()
  
  if (length(which(ls() == "overwrite")) == 0)  overwrite = FALSE
  if (length(which(ls() == "strategy")) == 0)  strategy = 1
  if (length(which(ls() == "maxdur")) == 0)  maxdur = 7
  if (length(which(ls() == "do.cal")) == 0)  do.cal = TRUE
  if (length(which(ls() == "hrs.del.start")) == 0)  hrs.del.start = 0
  if (length(which(ls() == "hrs.del.end")) == 0)  hrs.del.end = 0
  if (length(which(ls() == "loglocation")) == 0)  loglocation = c()
  if (length(which(ls() == "storefolderstructure")) == 0)  storefolderstructure = FALSE
  if (length(which(ls() == "windowsizes")) == 0)  windowsizes = c(5,900,3600)
  if (length(which(ls() == "minloadcrit")) == 0)  minloadcrit = 72
  if (length(which(ls() == "desiredtz")) == 0)  desiredtz = "Europe/London"
  if (length(which(ls() == "chunksize")) == 0)  chunksize = 1
  if (length(which(ls() == "do.enmo")) == 0)  do.enmo = TRUE
  if (length(which(ls() == "do.lfenmo")) == 0)  do.lfenmo = FALSE
  if (length(which(ls() == "do.en")) == 0)  do.en = FALSE
  if (length(which(ls() == "do.bfen")) == 0)  do.bfen = FALSE
  if (length(which(ls() == "do.hfen")) == 0)  do.hfen = FALSE
  if (length(which(ls() == "do.hfenplus")) == 0)  do.hfenplus = FALSE
  if (length(which(ls() == "do.anglex")) == 0)  do.anglex = FALSE
  if (length(which(ls() == "do.angley")) == 0)  do.angley = FALSE
  if (length(which(ls() == "do.anglez")) == 0)  do.anglez = FALSE
  if (length(which(ls() == "do.roll_med_acc_x")) == 0)  do.roll_med_acc_x=FALSE
  if (length(which(ls() == "do.roll_med_acc_y")) == 0)  do.roll_med_acc_y=FALSE
  if (length(which(ls() == "do.roll_med_acc_z")) == 0)  do.roll_med_acc_z=FALSE
  if (length(which(ls() == "do.dev_roll_med_acc_x")) == 0)  do.dev_roll_med_acc_x=FALSE
  if (length(which(ls() == "do.dev_roll_med_acc_y")) == 0)  do.dev_roll_med_acc_y=FALSE
  if (length(which(ls() == "do.dev_roll_med_acc_z")) == 0)  do.dev_roll_med_acc_z=FALSE
  if (length(which(ls() == "do.enmoa")) == 0)  do.enmoa = FALSE
  if (length(which(ls() == "printsummary")) == 0)  printsummary = FALSE
  if (length(which(ls() == "includedaycrit")) == 0)  includedaycrit = 16
  if (length(which(ls() == "L5M5window")) == 0)  L5M5window = c(0,24)
  if (length(which(ls() == "M5L5res")) == 0)  M5L5res = 10
  if (length(which(ls() == "winhr")) == 0)  winhr = 5
  if (length(which(ls() == "qwindow")) == 0)  qwindow = c(0,24)
  if (length(which(ls() == "qlevels")) == 0)  qlevels = c()
  if (length(which(ls() == "ilevels")) == 0)  ilevels = c()
  if (length(which(ls() == "mvpathreshold")) == 0)  mvpathreshold = 100
  if (length(which(ls() == "boutcriter")) == 0)  boutcriter = 0.8
  if (length(which(ls() == "ndayswindow")) == 0)  ndayswindow = 7
  if (length(which(ls() == "idloc")) == 0) idloc = 1
  if (length(which(ls() == "do.imp")) == 0) do.imp = TRUE
  if (length(which(ls() == "anglethreshold")) == 0)  anglethreshold = 5
  if (length(which(ls() == "timethreshold")) == 0)  timethreshold = 5
  if (length(which(ls() == "ignorenonwear")) == 0)  ignorenonwear = FALSE
  if (length(which(ls() == "idloc")) == 0)  idloc=1
  if (length(which(ls() == "coldid")) == 0)  colid=1
  if (length(which(ls() == "coln1")) == 0)  coln1=1
  if (length(which(ls() == "nnights")) == 0)  nnights=7
  if (length(which(ls() == "outliers.only")) == 0)  outliers.only=FALSE
  if (length(which(ls() == "excludefirstlast")) == 0)  excludefirstlast=FALSE
  if (length(which(ls() == "criterror")) == 0)  criterror=3
  if (length(which(ls() == "includenightcrit")) == 0)  includenightcrit=16
  if (length(which(ls() == "relyonsleeplog")) == 0)  relyonsleeplog=FALSE
  if (length(which(ls() == "sleeplogidnum")) == 0)  sleeplogidnum=TRUE
  if (length(which(ls() == "def.noc.sleep")) == 0)  def.noc.sleep=c()
  if (length(which(ls() == "do.visual")) == 0)  do.visual=FALSE
  if (length(which(ls() == "excludefirstlast")) == 0)  excludefirstlast = FALSE
  if (length(which(ls() == "viewingwindow")) == 0)  viewingwindow = 1
  if (length(which(ls() == "dofirstpage")) == 0)  dofirstpage = TRUE
  if (length(which(ls() == "visualreport")) == 0)  visualreport = FALSE
  if (length(which(ls() == "print.filename")) == 0)  print.filename = FALSE
  if (length(which(ls() == "backup.cal.coef")) == 0)  backup.cal.coef = c()
  if (length(which(ls() == "bout.metric")) == 0)  bout.metric = 1
  if (length(which(ls() == "closedbout")) == 0)  closedbout = FALSE
  
  # # specific for part 5
  if (length(which(ls() == "boutcriter.in")) == 0)  boutcriter.in = 0.9
  if (length(which(ls() == "boutcriter.lig")) == 0)  boutcriter.lig = 0.8
  if (length(which(ls() == "boutcriter.mvpa")) == 0)  boutcriter.mvpa = 0.8
  if (length(which(ls() == "threshold.lig")) == 0)  threshold.lig = 40
  if (length(which(ls() == "threshold.mod")) == 0)  threshold.mod = 100
  if (length(which(ls() == "threshold.vig")) == 0)  threshold.vig = 400
  if (length(which(ls() == "timewindow")) == 0)  timewindow = c("MM","WW")
  if (length(which(ls() == "boutdur.mvpa")) == 0)  boutdur.mvpa = c(1,5,10)
  if (length(which(ls() == "boutdur.in")) == 0)  boutdur.in = c(10,20,30)
  if (length(which(ls() == "boutdur.lig")) == 0)  boutdur.lig = c(1,5,10)
  
  # part 2
  if (length(which(ls() == "mvpadur")) == 0)  mvpadur = c(1,5,10) # related to part 2 (functionality to anticipate part 5)
  if (length(which(ls() == "epochvalues2csv")) == 0)  epochvalues2csv = FALSE
  # if (length(which(ls() == "bout.metric")) == 0) bout.metric = 1
  if (length(which(ls() == "window.summary.size")) == 0) window.summary.size = 10
  if (length(which(ls() == "dayborder")) == 0)  dayborder = 0
  

  
  cat("\n   g.shell.GGIR {GGIR} by Vincent van Hees\n")
  if (dopart1 == TRUE) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nPart 1\n")
    g.part1(datadir=datadir,outputdir=outputdir,f0=f0,f1=f1,windowsizes = windowsizes, 
            desiredtz = desiredtz,chunksize=chunksize,studyname=studyname,minloadcrit=minloadcrit,
            do.enmo = do.enmo,
            do.lfenmo = do.lfenmo,do.en = do.en,
            do.bfen = do.bfen,do.hfen=do.hfen,
            do.hfenplus = do.hfenplus,
            do.anglex=do.anglex,do.angley=do.angley,do.anglez=do.anglez,
            do.roll_med_acc_x=do.roll_med_acc_x,do.roll_med_acc_y=do.roll_med_acc_y,do.roll_med_acc_z=do.roll_med_acc_z,
            do.dev_roll_med_acc_x=do.dev_roll_med_acc_x,do.dev_roll_med_acc_y=do.dev_roll_med_acc_y,do.dev_roll_med_acc_z=do.dev_roll_med_acc_z,
            do.enmoa = do.enmoa,printsummary=printsummary,
            do.cal = do.cal,print.filename=print.filename,
            overwrite=overwrite,backup.cal.coef=backup.cal.coef,selectdaysfile=selectdaysfile,dayborder=dayborder)
  }
  if (dopart2 == TRUE) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nPart 2\n")
    if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/basic",sep="")))
    g.part2(datadir =datadir,metadatadir=metadatadir,f0=f0,f1=f1,strategy = strategy, 
            hrs.del.start = hrs.del.start,hrs.del.end = hrs.del.end,
            maxdur =  maxdur, includedaycrit = includedaycrit,
            L5M5window = L5M5window, M5L5res = M5L5res, winhr = winhr,
            qwindow=qwindow, qlevels = qlevels,
            ilevels = ilevels, mvpathreshold = mvpathreshold,
            boutcriter = boutcriter,ndayswindow=ndayswindow,idloc=idloc,do.imp=do.imp,
            storefolderstructure=storefolderstructure,overwrite=overwrite,epochvalues2csv=epochvalues2csv,
            mvpadur=mvpadur,selectdaysfile=selectdaysfile,bout.metric=bout.metric,window.summary.size=window.summary.size,
            dayborder=dayborder,closedbout=closedbout,desiredtz=desiredtz)
  }
  if (dopart3 == TRUE) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nPart 3\n")
    if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/basic",sep="")))
    g.part3(metadatadir=metadatadir,f0=f0,
            f1=f1,anglethreshold=anglethreshold,timethreshold=timethreshold,
            ignorenonwear=ignorenonwear,overwrite=overwrite,desiredtz=desiredtz)
  }
  if (dopart4 == TRUE) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nPart 4\n")
    if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/ms3.out",sep="")))
    g.part4(datadir=datadir,metadatadir=metadatadir,loglocation = loglocation,
            f0=f0,f1=f1,idloc=idloc, colid = colid,coln1 = coln1,nnights = nnights,
            outliers.only = outliers.only,
            excludefirstlast=excludefirstlast,criterror = criterror,
            includenightcrit=includenightcrit,relyonsleeplog=relyonsleeplog,
            sleeplogidnum=sleeplogidnum,def.noc.sleep=def.noc.sleep,do.visual = do.visual, #
            storefolderstructure=storefolderstructure,overwrite=overwrite)
  }
  if (dopart5 == TRUE) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nPart 5\n")
    if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/ms4.out",sep="")))
    g.part5(datadir=datadir,metadatadir=metadatadir,f0=f0,f1=f1,strategy=strategy,maxdur=maxdur,
            hrs.del.start=hrs.del.start,
            hrs.del.end=hrs.del.end,
            loglocation=loglocation,excludefirstlast=excludefirstlast,
            windowsizes=windowsizes,boutcriter.in=boutcriter.in,boutcriter.lig=boutcriter.lig,
            boutcriter.mvpa=boutcriter.mvpa,storefolderstructure=storefolderstructure,
            threshold.lig = threshold.lig,
            threshold.mod = threshold.mod,
            threshold.vig = threshold.vig,timewindow=timewindow,
            boutdur.mvpa = boutdur.mvpa,
            boutdur.in = boutdur.in,
            boutdur.lig = boutdur.lig,
            winhr = winhr,M5L5res = M5L5res,
            overwrite=overwrite,desiredtz=desiredtz)
  }
  
  #==========================
  # Report generation:
  # check a few basic assumptions before continuing
  if (length(which(do.report==4 | do.report==5)) > 0 | visualreport==TRUE) {
    if (file.exists(paste(metadatadir,"/meta/ms4.out",sep=""))) {
    } else {
      cat("ERROR: First run g.shell.GGIR with mode = 4 to generate required milestone data\n")
      stop()
    }
  }  
  if (visualreport==TRUE & length(do.report) == 0) {
    if (file.exists(paste(metadatadir,"/meta/ms4.out",sep=""))) {
    } else {
      do.report=c(2,4) #visual report is impossible without creating quantitative reports first
    }
  }  
  if (length(which(do.report == 2)) > 0) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nReport part 2\n")
    N.files.ms2.out = length(dir(paste(metadatadir,"/meta/ms2.out",sep="")))
    if (N.files.ms2.out < f0) f0 = 1
    if (N.files.ms2.out < f1) f1 = N.files.ms2.out
    if (f1 == 0) f1 = N.files.ms2.out
    g.report.part2(metadatadir=metadatadir,f0=f0,f1=f1,maxdur=maxdur,selectdaysfile=selectdaysfile)
  }
  if (length(which(do.report == 4)) > 0) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nReport part 4\n")
    N.files.ms4.out = length(dir(paste(metadatadir,"/meta/ms4.out",sep="")))
    if (N.files.ms4.out < f0) f0 = 1
    if (N.files.ms4.out < f1) f1 = N.files.ms4.out
    if (f1 == 0) f1 = N.files.ms4.out
    g.report.part4(datadir=datadir,metadatadir=metadatadir,loglocation =loglocation,f0=f0,f1=f1,
                   storefolderstructure=storefolderstructure)
  }
  if (length(which(do.report == 5)) > 0) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nReport part 5\n")
    N.files.ms5.out = length(dir(paste(metadatadir,"/meta/ms5.out",sep="")))
    if (N.files.ms5.out < f0) f0 = 1
    if (N.files.ms5.out < f1) f1 = N.files.ms5.out
    if (f1 == 0) f1 = N.files.ms5.out
    g.part5.report(metadatadir=metadatadir,f0=f0,f1=f1,loglocation=loglocation,
                   includenightcrit=includenightcrit,includedaycrit=includedaycrit)
  }
  if (visualreport == TRUE) {
    cat('\n')
    cat(paste0(rep('_',options()$width),collapse=''))
    cat("\nGenerate visual reports\n")
    if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/ms4.out",sep="")))
    g.plot5(metadatadir=metadatadir,dofirstpage=dofirstpage,
            viewingwindow=viewingwindow,f0=f0,f1=f1,overwrite=overwrite)
  }
  
}