Removed scaleWithOmega.

PopularSequences.R

@@ -719,101 +719,6 @@ setMethodS3(
   validators=getOption("R.methodsS3:validators:setMethodS3")
 );
 
-###########################################################################/**
-#
-# @RdocMethod scaleWithOmega
-# 
-# @title "Switch to PAML-style rate scaling" 
-# 
-# \description{ 
-#	@get "title".
-#
-#	This method sets the site-process specific rate multipliers ("rate.multiplier") in order to have
-#	the expected number of substitutions \emph{after selection} equal to one at equilibrium 
-#	(PAML-style scaling).
-#
-#	The scaling factor is calculated by the \code{\link{getOmegaScalingFactor.GY94}} method.
-#	The scaling factors are based on the actual values of the omega site-process specific parameters,
-#	so rescaling is needed after changing the omega values.
-# } 
-# 
-# @synopsis 
-# 
-# \arguments{ 
-# 	\item{this}{A CodonSequence object.} 
-#	\item{process}{A GY94 substitution process object.}
-# 	\item{...}{Not used.} 
-# } 
-# 
-# \value{ 
-# 	The sequences object (invisible).
-# } 
-# 
-# \examples{
-#	# construct a GY94 object
-#	p<-GY94(kappa=4)
-#	# construct a codon sequence object,
-#	# attach process p
-#	s<-CodonSequence(length=10,processes=list(list(p)))
-#	# sample omegas from a discrete model
-#	omegaVarM3(s,p,c(0.5,1,2),c(1/3,1/3,1/3));
-#	# set rate multipliers to obtain PAML-style scaling
-#	scaleWithOmega(s,p)
-#	# get omegas
-#	getOmegas(s,p)
-#	# get rate multipliers
-#	getRateMultipliers(s,p)
-# } 
-# 
-# @author 
-# 
-# \seealso{ 
-# 	@seeclass 
-# } 
-# 
-#*/###########################################################################
-setMethodS3(
-  "scaleWithOmega",
-  class="CodonSequence",
-  function(
-	this,
-	process,
-    	...
-  ){
-
-if(!exists("PSIM_FAST")){
-    if(missing(process)){
-      throw("No process specified!\n");
-    }
-    if(!is.GY94(process)){
-      throw("The sepcified process is not a GY94 codon substitution process!\n");
-    }
-}
-	cache<-list();
-	for(s in this$.sites){
-		omega<-s$.processes[[process$.id]]$site.params[["omega"]]$value;	
-		mul<-NA;
-
-		if(!is.null(cache[[as.character(omega)]])){
-			mul<-cache[[as.character(omega)]];
-		}
-		else {
-			mul<-getOmegaScalingFactor(process,omega);
-			cache[[as.character(omega)]]<-mul;
-		}
-
-		setParameterAtSite(process,s,"rate.multiplier",mul);
-	}
-		return(invisible(this));
-
-  },
-  private=FALSE,
-  protected=FALSE,
-  overwrite=FALSE,
-  conflict="warning",
-  validators=getOption("R.methodsS3:validators:setMethodS3")
-);
-
 ##  
 ## Method: omegaVarM0 - one ratio
 ##