R/variable.recode.r

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

  variable.recode = function( x, variable, direction="forward", rm.na=F, lookup.table=NULL, p=NULL ) {

    if (is.null(lookup.table)) lookup.table = snowcrab.db( DS="data.transforms", p=p)

    ii = which( lookup.table$varname == variable )
    if (length(ii) == 0 ) { # missing from list .. print error message and stop to figure out why
      # print( paste("Recode:", variable, "is missing from database, assuming no transformation"))
      # tmp = lookup.table[1,]
      # tmp[1,] = c(variable, "none", 0, 1 )
      return( x )
    } else if ( length(ii) > 1 ) {
      print(paste( "Error in recode:", variable, "has too many incidences in database"))
      stop()
    }

    TF = lookup.table[ii ,]
    if ( TF$transform %in% c("", "none") ) {
      B = x
    }

    if ( TF$transform == "log10") {
      if (direction =="forward") {
        B = log10( x + TF$offset )
      } else if (direction =="backward") {
        B = 10^x - TF$offset
      }
    }

    if ( TF$transform == "scaled+centered") {
      if (direction =="forward") {
        B = scale( x, center=TF$offset, scale=TF$scaling )
      } else if (direction=="backward" ) {
        B = fields::unscale( x, x.center=TF$offset, x.scale=TF$scaling )
      }
    }

    if (rm.na) B = B[which(is.finite(B))]

    return (B)
  }