R/logr.R

In flr/FLEDA: Exploratory Data Analysis for FLR

# logr (log ratio)

## class
setClass("logr", contains="FLQuant")

# logr (log ratio)
## OK !!

setGeneric("logr", function(object, ...){
	standardGeneric("logr")
	}
)

setMethod("logr", signature("FLQuant"), function(object, ...){
	if(!missing(...)){
		object <- trim(object, ...)
	} else {
		object <- object
	}
	dobj <- dim(object)
	flc <- FLCohort(object)
	dflc <- dim(flc)
	logr <- log(flc[-dobj[1],,,,,,drop=FALSE]/flc[-1,,,,,,drop=FALSE])
	logr <- logr[,-c(1, dflc[2]),,,,,drop=FALSE]
	#logr <- new("FLCohort", logr)
	logr <- as(logr,"FLQuant")
	new("logr", logr)
})

setMethod("logr", signature("missing"),
  function(...)
  {
    logr(
        FLQuant(...)
        )
  }
)