R/TempModel.r

In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes

#' @export
TempModel = function(areas = 'subarea', annual.by.area=F, redo.data=F){

	require(mgcv)

	# read in temperature data        
 	#TempData1 = read.csv(file.path( project.datadirectory("bio.lobster"),"Temperature Data","TempData.csv"))
 	#TempData$subarea[TempData$subarea==311] = "31A"
 	#TempData$subarea[TempData$subarea==312] = "31B"
 	#write.csv(TempData,file.path( project.datadirectory("bio.lobster"),"Temperature Data","TempData.csv"),row.names=F)
  
  TempData = TempModelData(redo=F)
  
	# create time and harmonic variables
	TempData$y = decimal_date(as.Date(TempData$DATE))
	TempData$cos.y = cos(2*pi*TempData$y)
	TempData$sin.y = sin(2*pi*TempData$y)
	
	if(areas == 'subarea')	TempData$area = as.factor(TempData$subarea)
	if(areas == 'lfa')		TempData$area = as.factor(TempData$LFA)

		# fit GAM model 
		if(annual.by.area==F)TempModel <- gam(TEMPERATURE ~ sin.y + cos.y + s(y) + area + s(DEPTH, cos.y, sin.y), data=TempData)
		if(annual.by.area==T)TempModel <- gam(TEMPERATURE ~ sin.y + cos.y + s(y) + s(y,by=area) + area + s(DEPTH, cos.y, sin.y), data=TempData)
	
		print(summary(TempModel))

	return(list(Model=TempModel,Data=TempData))
}