#5)GAM fusion: possibilty of running GAM+FUSION or GAM+CAI and other options added

#The interpolation is done first at the monthly time scale then delta surfaces are added.

#AUTHOR: Benoit Parmentier                                                                        

#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#568--     

#

# TO DO:

# 2) simplify and bundle validation steps, make it general--method_mod_validation

# 3) solve issues with log file recordings

# 4) output location folder on the fly???

  s_raster<-brick(infile_covariates)                   #read in the data brck

  names(s_raster)<-covar_names               #Assigning names to the raster layers: making sure it is included in the extraction

  #Screen for extreme values": this needs more thought, min and max val vary with regions

  #min_val<-(-15+273.16) #if values less than -15C then screen out (note the Kelvin units that will need to be changed later in all datasets)

  #r1[r1 < (min_val)]<-NA

  ########### CREATE SAMPLING -TRAINING AND TESTING STATIONS ###########

  #Input for sampling function...

  t1<-proc.time()

  j=12

  #browser()

  names(list_param_runClim_KGFusion)<-c("list_index","covar_rast","covar_names","lst_avg","list_models","dst","var","y_var_name","out_prefix")

  #source(file.path(script_path,"GAM_fusion_function_multisampling_03122013.R"))

  gamclim_fus_mod<-mclapply(1:12, list_param=list_param_runClim_KGFusion, runClim_KGFusion,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement

  #gamclim_fus_mod<-mclapply(1:6, list_param=list_param_runClim_KGFusion, runClim_KGFusion,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement

  #gamclim_fus_mod<-runClim_KGFusion(1,list_param=list_param_runClim_KGFusion) #This is the end bracket from mclapply(...) statement