R/CreateGeoObject_BioGeoBEARS.R

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

CreateGeoObject_BioGeoBEARS<-function(full.phylo,trimmed.phylo=NULL,ana.events,clado.events,stratified=FALSE,simmap.out=FALSE){

	if(simmap.out){
		if(stratified){
			if(is.null(trimmed.phylo)){
				smap<-.stratified_BGB_to_tables(full.phylo,clado_events_tables,1)
				x<-.make.simmap.BGB(anc.phylo=full.phylo,subclade.phylo=full.phylo,ana.events=smap$ana.int,clado.events=smap$clado.int)
				return(x$geo.simmap)
			}else{
				smap<-.stratified_BGB_to_tables(full.phylo,clado_events_tables,1)
				x<-.make.simmap.BGB(anc.phylo=full.phylo,subclade.phylo=trimmed.phylo,ana.events=smap$ana.int,clado.events=smap$clado.int)
				return(x$geo.simmap)
			}	
		} else{
			if(is.null(trimmed.phylo)){
				x<-.make.simmap.BGB(anc.phylo=full.phylo,subclade.phylo=full.phylo,ana.events=ana.events,clado.events=clado.events)
				return(x$geo.simmap)
			}else{
				x<-.make.simmap.BGB(anc.phylo=full.phylo,subclade.phylo=trimmed.phylo,ana.events=ana.events,clado.events=clado.events)
				return(x$geo.simmap)
			}
		}
	} else {
		if(stratified){
			if(is.null(trimmed.phylo)){
				clado_events_tables<-list()
				clado_events_tables[[1]]<-clado.events
				smap<-.stratified_BGB_to_tables(full.phylo,clado_events_tables,1)
				x<-.CreateBioGeoB_Object_subclade(anc.phylo=full.phylo,subclade.phylo=full.phylo,ana.events=smap$ana.int,clado.events=smap$clado.int,nat.only=FALSE)
				return(x)
				}else{
				clado_events_tables<-list()
				clado_events_tables[[1]]<-clado.events
				smap<-.stratified_BGB_to_tables(full.phylo,clado_events_tables,1)
				x<-.CreateBioGeoB_Object_subclade(anc.phylo=full.phylo,subclade.phylo=trimmed.phylo,ana.events=smap$ana.int,clado.events=smap$clado.int,nat.only=FALSE)
				return(x)		
				}		
		} else{
			if(is.null(trimmed.phylo)){
				x<-.CreateBioGeoB_Object_subclade(anc.phylo=full.phylo,subclade.phylo=full.phylo,ana.events=ana.events,clado.events=clado.events,nat.only=FALSE)
				return(x)
			} else{
				x<-.CreateBioGeoB_Object_subclade(anc.phylo=full.phylo,subclade.phylo=trimmed.phylo,ana.events=ana.events,clado.events=clado.events,nat.only=FALSE)
				return(x)
			}
		}
	}
	
}