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4719fdd7
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Benoit Parmentier
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runGAMFusion <- function(i) { # loop over dates
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#date<-strptime(dates[i], "%Y%m%d") # interpolation date being processed
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date<-strptime(sampling_dat$date[i], "%Y%m%d") # interpolation date being processed
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month<-strftime(date, "%m") # current month of the date being processed
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LST_month<-paste("mm_",month,sep="") # name of LST month to be matched
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#Adding layer LST to the raster stack
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55056785
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Benoit Parmentier
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pos<-match("LST",layerNames(s_raster)) #Find column with name "LST"
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s_raster<-dropLayer(s_raster,pos) # If it exists drop layer
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4719fdd7
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Benoit Parmentier
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pos<-match(LST_month,layerNames(s_raster)) #Find column with the current month for instance mm12
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r1<-raster(s_raster,layer=pos) #Select layer from stack
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layerNames(r1)<-"LST"
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55056785
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Benoit Parmentier
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s_raster<-addLayer(s_raster,r1) #Adding current month as "LST"
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4719fdd7
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Benoit Parmentier
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###Regression part 1: Creating a validation dataset by creating training and testing datasets
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mod_LST <-ghcn.subsets[[i]][,match(LST_month, names(ghcn.subsets[[i]]))] #Match interpolation date and monthly LST average
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ghcn.subsets[[i]] = transform(ghcn.subsets[[i]],LST = mod_LST) #Add the variable LST to the subset dataset
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55056785
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Benoit Parmentier
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dst$LST<-dst[[LST_month]]
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4719fdd7
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Benoit Parmentier
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#n<-nrow(ghcn.subsets[[i]])
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#ns<-n-round(n*prop) #Create a sample from the data frame with 70% of the rows
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#nv<-n-ns #create a sample for validation with prop of the rows
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#ind.training <- sample(nrow(ghcn.subsets[[i]]), size=ns, replace=FALSE) #This selects the index position for 70% of the rows taken randomly
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ind.training<-sampling[[i]]
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ind.testing <- setdiff(1:nrow(ghcn.subsets[[i]]), ind.training)
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data_s <- ghcn.subsets[[i]][ind.training, ] #Training dataset currently used in the modeling
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data_v <- ghcn.subsets[[i]][ind.testing, ] #Testing/validation dataset using input sampling
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ns<-nrow(data_s)
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nv<-nrow(data_v)
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#i=1
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date_proc<-sampling_dat$date[i]
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date_proc<-strptime(sampling_dat$date[i], "%Y%m%d") # interpolation date being processed
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mo<-as.integer(strftime(date_proc, "%m")) # current month of the date being processed
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day<-as.integer(strftime(date_proc, "%d"))
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year<-as.integer(strftime(date_proc, "%Y"))
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datelabel=format(ISOdate(year,mo,day),"%b %d, %Y")
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###########
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# STEP 1 - LST 10 year monthly averages
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###########
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themolst<-raster(molst,mo) #current month being processed saved in a raster image
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plot(themolst)
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###########
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# STEP 2 - Weather station means across same days: Monthly mean calculation
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###########
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55056785
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Benoit Parmentier
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modst<-dst[dst$month==mo,] #Subsetting dataset for the relevant month of the date being processed
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4719fdd7
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Benoit Parmentier
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##########
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55056785
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Benoit Parmentier
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# STEP 3 - get LST at stations
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4719fdd7
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Benoit Parmentier
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##########
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sta_lola=modst[,c("lon","lat")] #Extracting locations of stations for the current month..
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proj_str="+proj=lcc +lat_1=43 +lat_2=45.5 +lat_0=41.75 +lon_0=-120.5 +x_0=400000 +y_0=0 +ellps=GRS80 +units=m +no_defs";
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lookup<-function(r,lat,lon) {
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xy<-project(cbind(lon,lat),proj_str);
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cidx<-cellFromXY(r,xy);
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return(r[cidx])
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}
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sta_tmax_from_lst=lookup(themolst,sta_lola$lat,sta_lola$lon) #Extracted values of LST for the stations
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#########
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# STEP 4 - bias at stations
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#########
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sta_bias=sta_tmax_from_lst-modst$TMax; #That is the difference between the monthly LST mean and monthly station mean
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#Added by Benoit
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modst$LSTD_bias<-sta_bias #Adding bias to data frame modst containning the monthly average for 10 years
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bias_xy=project(as.matrix(sta_lola),proj_str)
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png(paste("LST_TMax_scatterplot_",sampling_dat$date[i],"_",sampling_dat$prop[i],"_",sampling_dat$run_samp[i], out_prefix,".png", sep=""))
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plot(modst$TMax,sta_tmax_from_lst,xlab="Station mo Tmax",ylab="LST mo Tmax",main=paste("LST vs TMax for",datelabel,sep=" "))
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abline(0,1)
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dev.off()
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#added by Benoit
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#x<-ghcn.subsets[[i]] #Holds both training and testing for instance 161 rows for Jan 1
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x<-data_v
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d<-data_s
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pos<-match("value",names(d)) #Find column with name "value"
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#names(d)[pos]<-c("dailyTmax")
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names(d)[pos]<-y_var_name
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names(x)[pos]<-y_var_name
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#names(x)[pos]<-c("dailyTmax")
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d$dailyTmax=(as.numeric(d$dailyTmax))/10 #stored as 1/10 degree C to allow integer storage
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x$dailyTmax=(as.numeric(x$dailyTmax))/10 #stored as 1/10 degree C to allow integer storage
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pos<-match("station",names(d)) #Find column with name "value"
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names(d)[pos]<-c("id")
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names(x)[pos]<-c("id")
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names(modst)[1]<-c("id") #modst contains the average tmax per month for every stations...
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55056785
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Benoit Parmentier
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dmoday=merge(modst,d,by="id",suffixes=c("",".y2")) #LOOSING DATA HERE!!! from 113 t0 103
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xmoday=merge(modst,x,by="id",suffixes=c("",".y2")) #LOOSING DATA HERE!!! from 48 t0 43
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mod_pat<-glob2rx("*.y2")
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var_pat<-grep(mod_pat,names(dmoday),value=FALSE) # using grep with "value" extracts the matching names
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dmoday<-dmoday[,-var_pat]
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mod_pat<-glob2rx("*.y2")
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var_pat<-grep(mod_pat,names(xmoday),value=FALSE) # using grep with "value" extracts the matching names
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xmoday<-xmoday[,-var_pat] #Removing duplicate columns
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4719fdd7
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Benoit Parmentier
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data_v<-xmoday
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###
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#dmoday contains the daily tmax values for training with TMax being the monthly station tmax mean
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#xmoday contains the daily tmax values for validation with TMax being the monthly station tmax mean
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png(paste("Daily_tmax_monthly_TMax_scatterplot_",sampling_dat$date[i],"_",sampling_dat$prop[i],
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"_",sampling_dat$run_samp[i],out_prefix,".png", sep=""))
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plot(dailyTmax~TMax,data=dmoday,xlab="Mo Tmax",ylab=paste("Daily for",datelabel),main="across stations in OR")
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dev.off()
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########
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# STEP 5 - interpolate bias
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########
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125 |
55056785
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Benoit Parmentier
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# ?? include covariates like elev, distance to coast, cloud frequency, tree heig
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126 |
4719fdd7
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Benoit Parmentier
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#fitbias<-Tps(bias_xy,sta_bias) #use TPS or krige
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55056785
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Benoit Parmentier
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#Adding options to use only training stations : 07/11/2012
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4719fdd7
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Benoit Parmentier
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bias_xy=project(as.matrix(sta_lola),proj_str)
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#bias_xy2=project(as.matrix(c(dmoday$lon,dmoday$lat),proj_str)
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if(bias_val==1){
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sta_bias<-dmoday$LSTD_bias
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bias_xy<-cbind(dmoday$x_OR83M,dmoday$y_OR83M)
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}
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fitbias<-Krig(bias_xy,sta_bias,theta=1e5) #use TPS or krige
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#The output is a krig object using fields
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mod9a<-fitbias
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55056785
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Benoit Parmentier
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140 |
4719fdd7
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Benoit Parmentier
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##########
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# STEP 7 - interpolate delta across space
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##########
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daily_sta_lola=dmoday[,c("lon","lat")] #could be same as before but why assume merge does this - assume not
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daily_sta_xy=project(as.matrix(daily_sta_lola),proj_str)
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daily_delta=dmoday$dailyTmax-dmoday$TMax
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147 |
55056785
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Benoit Parmentier
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148 |
4719fdd7
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Benoit Parmentier
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#fitdelta<-Tps(daily_sta_xy,daily_delta) #use TPS or krige
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fitdelta<-Krig(daily_sta_xy,daily_delta,theta=1e5) #use TPS or krige
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#Kriging using fields package
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mod9b<-fitdelta
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152 |
55056785
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Benoit Parmentier
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153 |
4719fdd7
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Benoit Parmentier
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png(paste("Delta_surface_LST_TMax_",sampling_dat$date[i],"_",sampling_dat$prop[i],
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"_",sampling_dat$run_samp[i],out_prefix,".png", sep=""))
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surface(fitdelta,col=rev(terrain.colors(100)),asp=1,main=paste("Interpolated delta for",datelabel,sep=" "))
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dev.off()
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#
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#### Added by Benoit on 06/19
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data_s<-dmoday #put the
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data_s$daily_delta<-daily_delta
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#data_s$y_var<-daily_delta #y_var is the variable currently being modeled, may be better with BIAS!!
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#data_s$y_var<-data_s$LSTD_bias
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#### Added by Benoit ends
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#########
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# STEP 8 - assemble final answer - T=LST+Bias(interpolated)+delta(interpolated)
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#########
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bias_rast=interpolate(themolst,fitbias) #interpolation using function from raster package
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#themolst is raster layer, fitbias is "Krig" object from bias surface
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#plot(bias_rast,main="Raster bias") #This not displaying...
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#Saving kriged surface in raster images
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data_name<-paste("bias_LST_",sampling_dat$date[i],"_",sampling_dat$prop[i],
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"_",sampling_dat$run_samp[i],sep="")
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raster_name<-paste("fusion_",data_name,out_prefix,".rst", sep="")
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writeRaster(bias_rast, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
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daily_delta_rast=interpolate(themolst,fitdelta) #Interpolation of the bias surface...
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#plot(daily_delta_rast,main="Raster Daily Delta")
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#Saving kriged surface in raster images
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data_name<-paste("daily_delta_",sampling_dat$date[i],"_",sampling_dat$prop[i],
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"_",sampling_dat$run_samp[i],sep="")
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raster_name<-paste("fusion_",data_name,out_prefix,".rst", sep="")
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writeRaster(daily_delta_rast, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
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tmax_predicted=themolst+daily_delta_rast-bias_rast #Final surface as a raster layer...
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#tmax_predicted=themolst+daily_delta_rast+bias_rast #Added by Benoit, why is it -bias_rast
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#plot(tmax_predicted,main="Predicted daily")
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#Saving kriged surface in raster images
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data_name<-paste("tmax_predicted_",sampling_dat$date[i],"_",sampling_dat$prop[i],
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"_",sampling_dat$run_samp[i],sep="")
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raster_name<-paste("fusion_",data_name,out_prefix,".rst", sep="")
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writeRaster(tmax_predicted, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
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########
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# check: assessment of results: validation
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########
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RMSE<-function(x,y) {return(mean((x-y)^2)^0.5)}
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MAE_fun<-function(x,y) {return(mean(abs(x-y)))}
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#ME_fun<-function(x,y){return(mean(abs(y)))}
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#FIT ASSESSMENT
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sta_pred_data_s=lookup(tmax_predicted,data_s$lat,data_s$lon)
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rmse_fit=RMSE(sta_pred_data_s,data_s$dailyTmax)
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mae_fit=MAE_fun(sta_pred_data_s,data_s$dailyTmax)
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sta_pred=lookup(tmax_predicted,data_v$lat,data_v$lon)
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#sta_pred=lookup(tmax_predicted,daily_sta_lola$lat,daily_sta_lola$lon)
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#rmse=RMSE(sta_pred,dmoday$dailyTmax)
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#pos<-match("value",names(data_v)) #Find column with name "value"
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#names(data_v)[pos]<-c("dailyTmax")
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tmax<-data_v$dailyTmax
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#data_v$dailyTmax<-tmax
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rmse=RMSE(sta_pred,tmax)
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mae<-MAE_fun(sta_pred,tmax)
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r2<-cor(sta_pred,tmax)^2 #R2, coef. of var
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me<-mean(sta_pred-tmax)
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223 |
55056785
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Benoit Parmentier
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224 |
4719fdd7
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Benoit Parmentier
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png(paste("Predicted_tmax_versus_observed_scatterplot_",sampling_dat$date[i],"_",sampling_dat$prop[i],
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"_",sampling_dat$run_samp[i],out_prefix,".png", sep=""))
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plot(sta_pred~tmax,xlab=paste("Actual daily for",datelabel),ylab="Pred daily",main=paste("RMSE=",rmse))
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abline(0,1)
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dev.off()
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#resid=sta_pred-dmoday$dailyTmax
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resid=sta_pred-tmax
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###BEFORE GAM prediction the data object must be transformed to SDF
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coords<- data_v[,c('x_OR83M','y_OR83M')]
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coordinates(data_v)<-coords
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proj4string(data_v)<-CRS #Need to assign coordinates...
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coords<- data_s[,c('x_OR83M','y_OR83M')]
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coordinates(data_s)<-coords
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proj4string(data_s)<-CRS #Need to assign coordinates..
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55056785
|
Benoit Parmentier
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coords<- modst[,c('x_OR83M','y_OR83M')]
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coordinates(modst)<-coords
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proj4string(modst)<-CRS #Need to assign coordinates..
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243 |
4719fdd7
|
Benoit Parmentier
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ns<-nrow(data_s) #This is added to because some loss of data might have happened because of the averaging...
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nv<-nrow(data_v)
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###GAM PREDICTION
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249 |
55056785
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Benoit Parmentier
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if (bias_prediction==1){
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data_s$y_var<-data_s$LSTD_bias #This shoudl be changed for any variable!!!
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data_v$y_var<-data_v$LSTD_bias
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data_month<-modst
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data_month$y_var<-modst$LSTD_bias
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}
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if (bias_prediction==0){
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data_v$y_var<-data_v[[y_var_name]]
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data_s$y_var<-data_s[[y_var_name]]
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}
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260 |
4719fdd7
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Benoit Parmentier
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#Model and response variable can be changed without affecting the script
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formula1 <- as.formula("y_var ~ s(lat) + s(lon) + s(ELEV_SRTM)", env=.GlobalEnv)
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formula2 <- as.formula("y_var~ s(lat,lon)+ s(ELEV_SRTM)", env=.GlobalEnv)
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formula3 <- as.formula("y_var~ s(lat) + s (lon) + s (ELEV_SRTM) + s (Northness)+ s (Eastness) + s(DISTOC)", env=.GlobalEnv)
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formula4 <- as.formula("y_var~ s(lat) + s (lon) + s(ELEV_SRTM) + s(Northness) + s (Eastness) + s(DISTOC) + s(LST)", env=.GlobalEnv)
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|
formula5 <- as.formula("y_var~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST)", env=.GlobalEnv)
|
268 |
|
|
formula6 <- as.formula("y_var~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST)+s(LC1)", env=.GlobalEnv)
|
269 |
|
|
formula7 <- as.formula("y_var~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST)+s(LC3)", env=.GlobalEnv)
|
270 |
55056785
|
Benoit Parmentier
|
formula8 <- as.formula("y_var~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST) + s(LC1,LC3)", env=.GlobalEnv)
|
271 |
|
|
|
272 |
|
|
if (bias_prediction==1){
|
273 |
|
|
mod1<- try(gam(formula1, data=data_month))
|
274 |
|
|
mod2<- try(gam(formula2, data=data_month)) #modified nesting....from 3 to 2
|
275 |
|
|
mod3<- try(gam(formula3, data=data_month))
|
276 |
|
|
mod4<- try(gam(formula4, data=data_month))
|
277 |
|
|
mod5<- try(gam(formula5, data=data_month))
|
278 |
|
|
mod6<- try(gam(formula6, data=data_month))
|
279 |
|
|
mod7<- try(gam(formula7, data=data_month))
|
280 |
|
|
mod8<- try(gam(formula8, data=data_month))
|
281 |
|
|
|
282 |
|
|
} else if (bias_prediction==0){
|
283 |
|
|
|
284 |
|
|
mod1<- try(gam(formula1, data=data_s))
|
285 |
|
|
mod2<- try(gam(formula2, data=data_s)) #modified nesting....from 3 to 2
|
286 |
|
|
mod3<- try(gam(formula3, data=data_s))
|
287 |
|
|
mod4<- try(gam(formula4, data=data_s))
|
288 |
|
|
mod5<- try(gam(formula5, data=data_s))
|
289 |
|
|
mod6<- try(gam(formula6, data=data_s))
|
290 |
|
|
mod7<- try(gam(formula7, data=data_s))
|
291 |
|
|
mod8<- try(gam(formula8, data=data_s))
|
292 |
|
|
}
|
293 |
|
|
|
294 |
4719fdd7
|
Benoit Parmentier
|
#Added
|
295 |
|
|
#tmax_predicted=themolst+daily_delta_rast-bias_rast #Final surface?? but daily_rst
|
296 |
|
|
|
297 |
|
|
### Added by benoit
|
298 |
|
|
#Store results using TPS
|
299 |
|
|
j=nmodels+1
|
300 |
|
|
results_RMSE[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
301 |
|
|
results_RMSE[2]<- ns #number of stations used in the training stage
|
302 |
|
|
results_RMSE[3]<- "RMSE"
|
303 |
|
|
|
304 |
|
|
results_RMSE[j+3]<- rmse #Storing RMSE for the model j
|
305 |
|
|
|
306 |
|
|
results_RMSE_f[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
307 |
|
|
results_RMSE_f[2]<- ns #number of stations used in the training stage
|
308 |
|
|
results_RMSE_f[3]<- "RMSE_f"
|
309 |
|
|
results_RMSE_f[j+3]<- rmse_fit #Storing RMSE for the model j
|
310 |
|
|
|
311 |
|
|
results_MAE_f[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
312 |
|
|
results_MAE_f[2]<- ns #number of stations used in the training stage
|
313 |
|
|
results_MAE_f[3]<- "RMSE_f"
|
314 |
|
|
results_MAE_f[j+3]<- mae_fit #Storing RMSE for the model j
|
315 |
|
|
|
316 |
|
|
results_MAE[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
317 |
|
|
results_MAE[2]<- ns #number of stations used in the training stage
|
318 |
|
|
results_MAE[3]<- "MAE"
|
319 |
|
|
results_MAE[j+3]<- mae #Storing RMSE for the model j
|
320 |
|
|
|
321 |
|
|
results_ME[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
322 |
|
|
results_ME[2]<- ns #number of stations used in the training stage
|
323 |
|
|
results_ME[3]<- "ME"
|
324 |
|
|
results_ME[j+3]<- me #Storing RMSE for the model j
|
325 |
|
|
|
326 |
|
|
results_R2[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
327 |
|
|
results_R2[2]<- ns #number of stations used in the training stage
|
328 |
|
|
results_R2[3]<- "R2"
|
329 |
|
|
results_R2[j+3]<- r2 #Storing RMSE for the model j
|
330 |
|
|
|
331 |
|
|
#ns<-nrow(data_s) #This is added to because some loss of data might have happened because of the averaging...
|
332 |
|
|
#nv<-nrow(data_v)
|
333 |
|
|
|
334 |
55056785
|
Benoit Parmentier
|
pred_mod<-paste("pred_mod",j,sep="")
|
335 |
|
|
#Adding the results back into the original dataframes.
|
336 |
|
|
data_s[[pred_mod]]<-sta_pred_data_s
|
337 |
|
|
data_v[[pred_mod]]<-sta_pred
|
338 |
|
|
|
339 |
|
|
#Model assessment: RMSE and then krig the residuals....!
|
340 |
|
|
|
341 |
|
|
res_mod_s<- data_s$dailyTmax - data_s[[pred_mod]] #Residuals from kriging training
|
342 |
|
|
res_mod_v<- data_v$dailyTmax - data_v[[pred_mod]] #Residuals from kriging validation
|
343 |
|
|
|
344 |
|
|
name2<-paste("res_mod",j,sep="")
|
345 |
|
|
data_v[[name2]]<-as.numeric(res_mod_v)
|
346 |
|
|
data_s[[name2]]<-as.numeric(res_mod_s)
|
347 |
|
|
|
348 |
4719fdd7
|
Benoit Parmentier
|
|
349 |
|
|
for (j in 1:nmodels){
|
350 |
|
|
|
351 |
|
|
##Model assessment: specific diagnostic/metrics for GAM
|
352 |
|
|
|
353 |
|
|
name<-paste("mod",j,sep="") #modj is the name of The "j" model (mod1 if j=1)
|
354 |
|
|
mod<-get(name) #accessing GAM model ojbect "j"
|
355 |
|
|
|
356 |
|
|
#If mod "j" is not a model object
|
357 |
|
|
if (inherits(mod,"try-error")) {
|
358 |
|
|
results_AIC[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
359 |
|
|
results_AIC[2]<- ns #number of stations used in the training stage
|
360 |
|
|
results_AIC[3]<- "AIC"
|
361 |
|
|
results_AIC[j+3]<- NA
|
362 |
|
|
|
363 |
|
|
results_GCV[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
364 |
|
|
results_GCV[2]<- ns #number of stations used in the training
|
365 |
|
|
results_GCV[3]<- "GCV"
|
366 |
|
|
results_GCV[j+3]<- NA
|
367 |
|
|
|
368 |
|
|
results_DEV[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
369 |
|
|
results_DEV[2]<- ns #number of stations used in the training stage
|
370 |
|
|
results_DEV[3]<- "DEV"
|
371 |
|
|
results_DEV[j+3]<- NA
|
372 |
|
|
|
373 |
|
|
results_RMSE_f[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
374 |
|
|
results_RMSE_f[2]<- ns #number of stations used in the training stage
|
375 |
|
|
results_RMSE_f[3]<- "RSME_f"
|
376 |
|
|
results_RMSE_f[j+3]<- NA
|
377 |
|
|
|
378 |
|
|
results_MAE_f[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
379 |
|
|
results_MAE_f[2]<- ns #number of stations used in the training stage
|
380 |
|
|
results_MAE_f[3]<- "MAE_f"
|
381 |
|
|
results_MAE_f[j+3]<-NA
|
382 |
|
|
|
383 |
|
|
results_RMSE[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
384 |
|
|
results_RMSE[2]<- ns #number of stations used in the training stage
|
385 |
|
|
results_RMSE[3]<- "RMSE"
|
386 |
|
|
results_RMSE[j+3]<- NA #Storing RMSE for the model j
|
387 |
|
|
results_MAE[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
388 |
|
|
results_MAE[2]<- ns #number of stations used in the training stage
|
389 |
|
|
results_MAE[3]<- "MAE"
|
390 |
|
|
results_MAE[j+3]<- NA #Storing MAE for the model j
|
391 |
|
|
results_ME[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
392 |
|
|
results_ME[2]<- ns #number of stations used in the training stage
|
393 |
|
|
results_ME[3]<- "ME"
|
394 |
|
|
results_ME[j+3]<- NA #Storing ME for the model j
|
395 |
|
|
results_R2[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
396 |
|
|
results_R2[2]<- ns #number of stations used in the training stage
|
397 |
|
|
results_R2[3]<- "R2"
|
398 |
|
|
|
399 |
|
|
|
400 |
|
|
results_R2[j+3]<- NA #Storing R2 for the model j
|
401 |
|
|
|
402 |
|
|
}
|
403 |
|
|
|
404 |
|
|
#If mod is a modelobject
|
405 |
|
|
|
406 |
|
|
#If mod "j" is not a model object
|
407 |
|
|
if (inherits(mod,"gam")) {
|
408 |
|
|
|
409 |
|
|
results_AIC[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
410 |
|
|
results_AIC[2]<- ns #number of stations used in the training stage
|
411 |
|
|
results_AIC[3]<- "AIC"
|
412 |
|
|
results_AIC[j+3]<- AIC (mod)
|
413 |
|
|
|
414 |
|
|
results_GCV[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
415 |
|
|
results_GCV[2]<- ns #number of stations used in the training
|
416 |
|
|
results_GCV[3]<- "GCV"
|
417 |
|
|
results_GCV[j+3]<- mod$gcv.ubre
|
418 |
|
|
|
419 |
|
|
results_DEV[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
420 |
|
|
results_DEV[2]<- ns #number of stations used in the training stage
|
421 |
|
|
results_DEV[3]<- "DEV"
|
422 |
|
|
results_DEV[j+3]<- mod$deviance
|
423 |
|
|
|
424 |
|
|
y_var_fit= mod$fit
|
425 |
|
|
|
426 |
|
|
results_RMSE_f[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
427 |
|
|
results_RMSE_f[2]<- ns #number of stations used in the training stage
|
428 |
|
|
results_RMSE_f[3]<- "RSME_f"
|
429 |
|
|
#results_RMSE_f[j+3]<- sqrt(sum((y_var_fit-data_s$y_var)^2)/ns)
|
430 |
|
|
results_RMSE_f[j+3]<-sqrt(mean(mod$residuals^2,na.rm=TRUE))
|
431 |
|
|
|
432 |
|
|
results_MAE_f[1]<- sampling_dat$date[i] #storing the interpolation sampling_dat$date in the first column
|
433 |
|
|
results_MAE_f[2]<- ns #number of stations used in the training stage
|
434 |
|
|
results_MAE_f[3]<- "MAE_f"
|
435 |
|
|
#results_MAE_f[j+3]<-sum(abs(y_var_fit-data_s$y_var))/ns
|
436 |
|
|
results_MAE_f[j+3]<-mean(abs(mod$residuals),na.rm=TRUE)
|
437 |
|
|
|
438 |
|
|
##Model assessment: general diagnostic/metrics
|
439 |
|
|
##validation: using the testing data
|
440 |
|
|
if (predval==1) {
|
441 |
|
|
|
442 |
|
|
##Model assessment: specific diagnostic/metrics for GAM
|
443 |
|
|
|
444 |
|
|
name<-paste("mod",j,sep="") #modj is the name of The "j" model (mod1 if j=1)
|
445 |
|
|
mod<-get(name) #accessing GAM model ojbect "j"
|
446 |
|
|
|
447 |
|
|
s_sgdf<-as(s_raster,"SpatialGridDataFrame") #Conversion to spatial grid data frame
|
448 |
|
|
|
449 |
|
|
rpred<- predict(mod, newdata=s_sgdf, se.fit = TRUE) #Using the coeff to predict new values.
|
450 |
55056785
|
Benoit Parmentier
|
y_pred<-rpred$fit #rpred is a list with fit being and array
|
451 |
4719fdd7
|
Benoit Parmentier
|
raster_pred<-r1
|
452 |
|
|
layerNames(raster_pred)<-"y_pred"
|
453 |
|
|
values(raster_pred)<-as.numeric(y_pred)
|
454 |
55056785
|
Benoit Parmentier
|
|
455 |
|
|
if (bias_prediction==1){
|
456 |
|
|
data_name<-paste("predicted_mod",j,"_",sampling_dat$date[i],"_",sampling_dat$prop[i],
|
457 |
|
|
"_",sampling_dat$run_samp[i],sep="")
|
458 |
|
|
raster_name<-paste("GAM_bias_",data_name,out_prefix,".rst", sep="")
|
459 |
|
|
writeRaster(raster_pred, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
|
460 |
|
|
bias_rast<-raster_pred
|
461 |
|
|
|
462 |
|
|
raster_pred=themolst+daily_delta_rast-bias_rast #Final surface as a raster layer...
|
463 |
|
|
layerNames(raster_pred)<-"y_pred"
|
464 |
|
|
#=themolst+daily_delta_rast-bias_rast #Final surface as a raster layer...
|
465 |
|
|
|
466 |
|
|
data_name<-paste("predicted_mod",j,"_",sampling_dat$date[i],"_",sampling_dat$prop[i],
|
467 |
|
|
"_",sampling_dat$run_samp[i],sep="")
|
468 |
|
|
raster_name<-paste("GAM_bias_tmax_",data_name,out_prefix,".rst", sep="")
|
469 |
|
|
writeRaster(raster_pred, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
|
470 |
|
|
|
471 |
|
|
}
|
472 |
|
|
|
473 |
|
|
if (bias_prediction==0){
|
474 |
|
|
data_name<-paste("predicted_mod",j,"_",sampling_dat$date[i],"_",sampling_dat$prop[i],
|
475 |
|
|
"_",sampling_dat$run_samp[i],sep="")
|
476 |
|
|
raster_name<-paste("GAM_",data_name,out_prefix,".rst", sep="")
|
477 |
|
|
writeRaster(raster_pred, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
|
478 |
|
|
#writeRaster(r2, filename=raster_name,overwrite=TRUE) #Writing the data in a raster file format...(IDRISI)
|
479 |
|
|
|
480 |
|
|
}
|
481 |
|
|
|
482 |
4719fdd7
|
Benoit Parmentier
|
|
483 |
|
|
pred_sgdf<-as(raster_pred,"SpatialGridDataFrame") #Conversion to spatial grid data frame
|
484 |
|
|
#rpred_val_s <- overlay(raster_pred,data_s) #This overlays the kriged surface tmax and the location of weather stations
|
485 |
|
|
|
486 |
55056785
|
Benoit Parmentier
|
rpred_val_s <- overlay(pred_sgdf,data_s) #This overlays the interpolated surface tmax and the location of weather stations
|
487 |
|
|
rpred_val_v <- overlay(pred_sgdf,data_v) #This overlays the interpolated surface tmax and the location of weather stations
|
488 |
4719fdd7
|
Benoit Parmentier
|
|
489 |
|
|
pred_mod<-paste("pred_mod",j,sep="")
|
490 |
|
|
#Adding the results back into the original dataframes.
|
491 |
|
|
data_s[[pred_mod]]<-rpred_val_s$y_pred
|
492 |
|
|
|
493 |
|
|
data_v[[pred_mod]]<-rpred_val_v$y_pred
|
494 |
|
|
|
495 |
|
|
#Model assessment: RMSE and then krig the residuals....!
|
496 |
|
|
|
497 |
55056785
|
Benoit Parmentier
|
res_mod_s<-data_s[[y_var_name]] - data_s[[pred_mod]] #residuals from modeling training
|
498 |
|
|
res_mod_v<-data_v[[y_var_name]] - data_v[[pred_mod]] #residuals from modeling validation
|
499 |
4719fdd7
|
Benoit Parmentier
|
|
500 |
|
|
}
|
501 |
|
|
|
502 |
|
|
if (predval==0) {
|
503 |
|
|
|
504 |
|
|
y_mod<- predict(mod, newdata=data_v, se.fit = TRUE) #Using the coeff to predict new values.
|
505 |
|
|
|
506 |
|
|
pred_mod<-paste("pred_mod",j,sep="")
|
507 |
|
|
#Adding the results back into the original dataframes.
|
508 |
|
|
data_s[[pred_mod]]<-as.numeric(mod$fit)
|
509 |
|
|
data_v[[pred_mod]]<-as.numeric(y_mod$fit)
|
510 |
|
|
|
511 |
|
|
#Model assessment: RMSE and then krig the residuals....!
|
512 |
|
|
|
513 |
55056785
|
Benoit Parmentier
|
#res_mod_s<- data_s$y_var - data_s[[pred_mod]] #Residuals from modeling training
|
514 |
|
|
#res_mod_v<- data_v$y_var - data_v[[pred_mod]] #Residuals from modeling validation
|
515 |
|
|
res_mod_s<-data_s[[y_var_name]] - data_s[[pred_mod]]
|
516 |
|
|
res_mod_v<-data_v[[y_var_name]] - data_v[[pred_mod]]
|
517 |
|
|
|
518 |
4719fdd7
|
Benoit Parmentier
|
}
|
519 |
|
|
|
520 |
|
|
####ADDED ON JULY 20th
|
521 |
|
|
res_mod<-res_mod_v
|
522 |
|
|
|
523 |
|
|
#RMSE_mod <- sqrt(sum(res_mod^2)/nv) #RMSE FOR REGRESSION STEP 1: GAM
|
524 |
|
|
RMSE_mod<- sqrt(mean(res_mod^2,na.rm=TRUE))
|
525 |
|
|
#MAE_mod<- sum(abs(res_mod),na.rm=TRUE)/(nv-sum(is.na(res_mod))) #MAE from kriged surface validation
|
526 |
|
|
MAE_mod<- mean(abs(res_mod), na.rm=TRUE)
|
527 |
|
|
#ME_mod<- sum(res_mod,na.rm=TRUE)/(nv-sum(is.na(res_mod))) #ME, Mean Error or bias FOR REGRESSION STEP 1: GAM
|
528 |
|
|
ME_mod<- mean(res_mod,na.rm=TRUE) #ME, Mean Error or bias FOR REGRESSION STEP 1: GAM
|
529 |
|
|
#R2_mod<- cor(data_v$y_var,data_v[[pred_mod]])^2 #R2, coef. of var FOR REGRESSION STEP 1: GAM
|
530 |
|
|
R2_mod<- cor(data_v$y_var,data_v[[pred_mod]], use="complete")^2
|
531 |
|
|
results_RMSE[1]<- sampling_dat$date[i] #storing the interpolation sampling_dat$date in the first column
|
532 |
|
|
results_RMSE[2]<- ns #number of stations used in the training stage
|
533 |
|
|
results_RMSE[3]<- "RMSE"
|
534 |
|
|
results_RMSE[j+3]<- RMSE_mod #Storing RMSE for the model j
|
535 |
|
|
results_MAE[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
536 |
|
|
results_MAE[2]<- ns #number of stations used in the training stage
|
537 |
|
|
results_MAE[3]<- "MAE"
|
538 |
|
|
results_MAE[j+3]<- MAE_mod #Storing MAE for the model j
|
539 |
|
|
results_ME[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
540 |
|
|
results_ME[2]<- ns #number of stations used in the training stage
|
541 |
|
|
results_ME[3]<- "ME"
|
542 |
|
|
results_ME[j+3]<- ME_mod #Storing ME for the model j
|
543 |
|
|
results_R2[1]<- sampling_dat$date[i] #storing the interpolation dates in the first column
|
544 |
|
|
results_R2[2]<- ns #number of stations used in the training stage
|
545 |
|
|
results_R2[3]<- "R2"
|
546 |
|
|
results_R2[j+3]<- R2_mod #Storing R2 for the model j
|
547 |
|
|
|
548 |
|
|
#Saving residuals and prediction in the dataframes: tmax predicted from GAM
|
549 |
|
|
|
550 |
|
|
name2<-paste("res_mod",j,sep="")
|
551 |
|
|
data_v[[name2]]<-as.numeric(res_mod_v)
|
552 |
|
|
data_s[[name2]]<-as.numeric(res_mod_s)
|
553 |
|
|
#end of loop calculating RMSE
|
554 |
|
|
}
|
555 |
|
|
}
|
556 |
|
|
|
557 |
|
|
#if (i==length(dates)){
|
558 |
|
|
|
559 |
|
|
#Specific diagnostic measures related to the testing datasets
|
560 |
|
|
|
561 |
|
|
results_table_RMSE<-as.data.frame(results_RMSE)
|
562 |
|
|
results_table_MAE<-as.data.frame(results_MAE)
|
563 |
|
|
results_table_ME<-as.data.frame(results_ME)
|
564 |
|
|
results_table_R2<-as.data.frame(results_R2)
|
565 |
|
|
results_table_RMSE_f<-as.data.frame(results_RMSE_f)
|
566 |
|
|
results_table_MAE_f<-as.data.frame(results_MAE_f)
|
567 |
|
|
|
568 |
|
|
results_table_AIC<-as.data.frame(results_AIC)
|
569 |
|
|
results_table_GCV<-as.data.frame(results_GCV)
|
570 |
|
|
results_table_DEV<-as.data.frame(results_DEV)
|
571 |
|
|
|
572 |
|
|
tb_metrics1<-rbind(results_table_RMSE,results_table_MAE, results_table_ME, results_table_R2,results_table_RMSE_f,results_table_MAE_f) #
|
573 |
|
|
tb_metrics2<-rbind(results_table_AIC,results_table_GCV, results_table_DEV)
|
574 |
|
|
cname<-c("dates","ns","metric","mod1", "mod2","mod3", "mod4", "mod5", "mod6", "mod7","mod8","mod9")
|
575 |
|
|
colnames(tb_metrics1)<-cname
|
576 |
|
|
cname<-c("dates","ns","metric","mod1", "mod2","mod3", "mod4", "mod5", "mod6", "mod7","mod8")
|
577 |
|
|
colnames(tb_metrics2)<-cname
|
578 |
|
|
#colnames(results_table_RMSE)<-cname
|
579 |
|
|
#colnames(results_table_RMSE_f)<-cname
|
580 |
|
|
#tb_diagnostic1<-results_table_RMSE #measures of validation
|
581 |
|
|
#tb_diagnostic2<-results_table_RMSE_f #measures of fit
|
582 |
|
|
|
583 |
|
|
#write.table(tb_diagnostic1, file= paste(path,"/","results_fusion_Assessment_measure1",out_prefix,".txt",sep=""), sep=",")
|
584 |
|
|
|
585 |
|
|
#}
|
586 |
|
|
print(paste(sampling_dat$date[i],"processed"))
|
587 |
|
|
# end of the for loop1
|
588 |
|
|
mod_obj<-list(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8,mod9a,mod9b)
|
589 |
|
|
names(mod_obj)<-c("mod1","mod2","mod3","mod4","mod5","mod6","mod7","mod8","mod9a","mod9b")
|
590 |
|
|
#results_list<-list(data_s,data_v,tb_metrics1,tb_metrics2)
|
591 |
55056785
|
Benoit Parmentier
|
results_list<-list(data_s,data_v,tb_metrics1,tb_metrics2,mod_obj,sampling_dat[i,],data_month)
|
592 |
|
|
names(results_list)<-c("data_s","data_v","tb_metrics1","tb_metrics2","mod_obj","sampling_dat","data_month")
|
593 |
4719fdd7
|
Benoit Parmentier
|
save(results_list,file= paste(path,"/","results_list_metrics_objects_",sampling_dat$date[i],"_",sampling_dat$prop[i],
|
594 |
|
|
"_",sampling_dat$run_samp[i],out_prefix,".RData",sep=""))
|
595 |
|
|
return(results_list)
|
596 |
|
|
#return(tb_diagnostic1)
|
597 |
|
|
}
|