R/eggdata.r

In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.

eggdata = function( data.loc=".", redo.data=F, data.file ) {

  if (redo.data) {

    # Data from Jae Jan 14
    load(file.path("det.rdata"))
    load(file.path("set_biologicals.rdata"))

    # Need to add time back into the SNCRABDETAILS data set
    set$sdate = set$t0     #'sdate' is 't0' in new data set
    set.with.time = set[ , c("trip", "set", "sdate", "t") ]  # trip and set act as 'markers' to align data
    det = merge( det, set.with.time, by=c("trip", "set"), all.x=T, all.y=F)

    sc=set
    sdt=det

    # There are NA's in the date, this fixes the problem
    xyr = (substring( sdt$trip, 6, 9))
    xmon =  (substring( sdt$trip, 4, 5))
    xday =  (substring( sdt$trip, 2, 3))
    date.string = paste( xyr, xmon, xday, sep="/")

    date.from.trip = lubridate::ymd( date.string)

    i = which(!is.finite(sdt$sdate))
    # sdt$timestamp = as.POSIXct(sdt$sdate, origin=lubridate::origin )
    sdt$timestamp[i] = date.from.trip[i]

    sdt$yr = lubridate::year(sdt$timestamp)
    sdt$month = lubridate::month(sdt$timestamp)
    sdt$julianday =  lubridate::yday( sdt$timestamp )
    sdt$dummy = 1

    sc$timestamp = as.POSIXct(sc$sdate, origin=lubridate::origin)
    sc$yr = lubridate::year( sc$timestamp )
    sc$month = lubridate::month(sc$timestamp)
    sc$day = lubridate::day(sc$timestamp)
    sc$dummy = 1     # This is to use with 'xtabs'
    sc$julianday = lubridate::yday( sc$timestamp )
    sdt=sdt[!is.na(sdt$sex),]   # Takes all good data, i.e. that which is not NA
    sdt=sdt[!is.na(sdt$cw),]

    save( sc, file= file.path(data.loc, "sc.rdata"), compress=T )
    save( sdt, file =file.path(data.loc, "sdt.rdata"), compress=T )
    rm(set,det)
    return ("Files saved to work directory")
  }

  if (data.file =="sc") {
    load( file.path(data.loc, "sc.rdata") )
    return( sc )
  }

  if( data.file== "sdt" ) {
    load( file.path(data.loc, "sdt.rdata") )
    return(sdt)
  }

}