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bc59c6bb
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Benoit Parmentier
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####################Interpolation of Tmax for 10 dates.#####################
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d7b0ef36
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Benoit Parmentier
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#This script interpolates station values for the Oregon case study. This program loads the station data from a csv file
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7f643c83
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Benoit Parmentier
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#and perform two types of regression: multiple linear model and general additive model (GAM). Note that this program:
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e2d673e4
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Benoit Parmentier
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#1)assumes that the csv file is in the current working
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#2)extract relevant variables from raster images before performing the regressions.
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7f643c83
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Benoit Parmentier
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#The user must provide the list of raster images in a textile.
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2a89fa5f
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Benoit Parmentier
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#Script created by Benoit Parmentier on March 3, 2012.
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89c6eee2
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Benoit Parmentier
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e2d673e4
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Benoit Parmentier
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###Loading r library and packages # loading the raster package
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92c36e33
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Benoit Parmentier
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library(gtools) # loading ...
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89c6eee2
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Benoit Parmentier
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library(mgcv)
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###Parameters and arguments
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4180b123
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Benoit Parmentier
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#infile1<-"ghcn_or_b_02122012_OR83M.csv"
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infile1<-"ghcn_or_tmax_b_03032012_OR83M.csv"
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fbc95c44
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Benoit Parmentier
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#path<-"C:/Data/Benoit/NCEAS/window_Oregon_data
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path<-"/data/computer/parmentier/Data/IPLANT_project/data_Oregon_stations"
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e2d673e4
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Benoit Parmentier
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setwd(path)
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2a89fa5f
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Benoit Parmentier
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#infile2<-"dates_interpolation_03012012.txt" # list of 10 dates for the regression
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25a68ae3
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Benoit Parmentier
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infile2<-"dates_interpolation_03052012.txt"
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2a89fa5f
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Benoit Parmentier
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prop<-0.3 #Proportion of testing retained for validation
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fbc95c44
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Benoit Parmentier
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out_prefix<-"_03042012_interaction_r1"
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aac7c36c
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Benoit Parmentier
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infile3<-"models_interpolation_03052012.txt"
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89c6eee2
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Benoit Parmentier
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7f643c83
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Benoit Parmentier
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#######START OF THE SCRIPT #############
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2a89fa5f
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Benoit Parmentier
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###Reading the station data and setting up for models' comparison
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e2d673e4
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Benoit Parmentier
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ghcn<-read.csv(paste(path,"/",infile1, sep=""), header=TRUE) #The "paste" function concatenates the path and file name in common string.
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25a68ae3
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Benoit Parmentier
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ghcn = transform(ghcn,Northness = cos(ASPECT)) #Adding a variable to the dataframe
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ghcn = transform(ghcn,Eastness = sin(ASPECT)) #adding variable to the dataframe.
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4180b123
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Benoit Parmentier
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ghcn = transform(ghcn,Northness_w = sin(slope)*cos(ASPECT)) #Adding a variable to the dataframe
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ghcn = transform(ghcn,Eastness_w = sin(slope)*sin(ASPECT)) #adding variable to the dataframe.
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set.seed(100)
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bc59c6bb
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Benoit Parmentier
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dates <-readLines(paste(path,"/",infile2, sep=""))
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aac7c36c
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Benoit Parmentier
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models <-readLines(paste(path,"/",infile3, sep=""))
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ec229367
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Benoit Parmentier
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25a68ae3
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Benoit Parmentier
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results <- matrix(1,length(dates),14) #This is a matrix containing the diagnostic measures from the GAM models.
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fbc95c44
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Benoit Parmentier
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results_AIC<- matrix(1,length(dates),length(models)+2)
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results_GCV<- matrix(1,length(dates),length(models)+2)
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results_DEV<- matrix(1,length(dates),length(models)+2)
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results_RMSE<- matrix(1,length(dates),length(models)+2)
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#Screening for bad values
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#tmax~ lon + lat + ELEV_SRTM + Eastness + Northness + DISTOC
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#tmax range: min max)
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ghcn_all<-ghcn
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ghcn_test<-subset(ghcn,ghcn$tmax>0 & ghcn$tmax<400)
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ghcn_test2<-subset(ghcn_test,ghcn_test$ELEV_SRTM>0)
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ghcn<-ghcn_test2
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#lon range
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#lat range
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#ELEV_SRTM
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#Eastness
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#Northness
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aac7c36c
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Benoit Parmentier
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4180b123
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Benoit Parmentier
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ghcn.subsets <-lapply(dates, function(d) subset(ghcn, date==d)) #this creates a list of 10 subsets data
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#note that compare to the previous version date_ column was changed to date
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ec229367
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Benoit Parmentier
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2a89fa5f
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Benoit Parmentier
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## looping through the dates...
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aac7c36c
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Benoit Parmentier
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#Change this into a nested loop, looping through the number of models
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bc59c6bb
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Benoit Parmentier
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fbc95c44
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Benoit Parmentier
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2a89fa5f
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Benoit Parmentier
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for(i in 1:length(dates)){ # start of the for loop #1
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###Regression part 1: Creating a validation dataset by creating training and testing datasets
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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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#ns<-n-round(n*prop) #Create a sample from the data frame with 70% 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.testing <- setdiff(1:nrow(ghcn.subsets[[i]]), ind.training)
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data_s <- ghcn.subsets[[i]][ind.training, ]
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data_v <- ghcn.subsets[[i]][ind.testing, ]
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####Regression part 2: GAM models
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aac7c36c
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Benoit Parmentier
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mod1<-gam(tmax~ s(lat) + s (lon) + s (ELEV_SRTM), data=data_s)
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fbc95c44
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Benoit Parmentier
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mod2<- gam(tmax~ s(lat,lon) + s(ELEV_SRTM), data=data_s)
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aac7c36c
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Benoit Parmentier
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mod3<-gam(tmax~ s(lat) + s (lon) + s (ELEV_SRTM) + s (Northness)+ s (Eastness) + s(DISTOC), data=data_s)
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mod4<-gam(tmax~ s(lat) + s (lon) + s (ELEV_SRTM) + s (Northness_w)+ s (Eastness_w) + s(DISTOC), data=data_s)
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fbc95c44
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Benoit Parmentier
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mod5<- gam(tmax~ s(lat) + s (lon) + s (ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC), data=data_s)
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mod6<- gam(tmax~ s(lat,lon) + s (ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC), data=data_s)
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4180b123
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Benoit Parmentier
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2a89fa5f
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Benoit Parmentier
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####Regression part 3: Calculating and storing diagnostic measures
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aac7c36c
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Benoit Parmentier
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results_AIC[i,1]<- dates[i] #storing the interpolation dates in the first column
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results_AIC[i,2]<- ns #number of stations used in the training stage
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results_AIC[i,3]<- AIC (mod1)
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results_AIC[i,4]<- AIC (mod2)
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results_AIC[i,5]<- AIC (mod3)
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results_AIC[i,6]<- AIC (mod4)
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results_AIC[i,7]<- AIC (mod5)
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results_AIC[i,8]<- AIC (mod6)
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2a89fa5f
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Benoit Parmentier
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aac7c36c
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Benoit Parmentier
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results_GCV[i,1]<- dates[i] #storing the interpolation dates in the first column
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results_GCV[i,2]<- ns #number of stations used in the training stage
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results_GCV[i,3]<- mod1$gcv.ubre
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results_GCV[i,4]<- mod2$gcv.ubre
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results_GCV[i,5]<- mod3$gcv.ubre
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results_GCV[i,6]<- mod4$gcv.ubre
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results_GCV[i,7]<- mod5$gcv.ubre
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results_GCV[i,8]<- mod6$gcv.ubre
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25a68ae3
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Benoit Parmentier
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aac7c36c
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Benoit Parmentier
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results_DEV[i,1]<- dates[i] #storing the interpolation dates in the first column
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results_DEV[i,2]<- ns #number of stations used in the training stage
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results_DEV[i,3]<- mod1$deviance
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results_DEV[i,4]<- mod2$deviance
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results_DEV[i,5]<- mod3$deviance
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results_DEV[i,6]<- mod4$deviance
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results_DEV[i,7]<- mod5$deviance
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results_DEV[i,8]<- mod6$deviance
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2a89fa5f
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Benoit Parmentier
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#####VALIDATION: Prediction checking the results using the testing data########
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aac7c36c
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Benoit Parmentier
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y_mod1<- predict(mod1, newdata=data_v, se.fit = TRUE) #Using the coeff to predict new values.
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y_mod2<- predict(mod2, newdata=data_v, se.fit = TRUE)
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y_mod3<- predict(mod3, newdata=data_v, se.fit = TRUE)
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y_mod4<- predict(mod4, newdata=data_v, se.fit = TRUE)
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y_mod5<- predict(mod5, newdata=data_v, se.fit = TRUE)
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fbc95c44
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Benoit Parmentier
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y_mod6<- predict(mod6, newdata=data_v, se.fit = TRUE)
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25a68ae3
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Benoit Parmentier
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aac7c36c
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Benoit Parmentier
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res_mod1<- data_v$tmax - y_mod1$fit #Residuals for GMA model that resembles the ANUSPLIN interpolation
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res_mod2<- data_v$tmax - y_mod2$fit #Residuals for GAM model that resembles the PRISM interpolation
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res_mod3<- data_v$tmax - y_mod3$fit
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res_mod4<- data_v$tmax - y_mod4$fit
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res_mod5<- data_v$tmax - y_mod5$fit
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res_mod6<- data_v$tmax - y_mod6$fit
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Benoit Parmentier
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aac7c36c
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Benoit Parmentier
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RMSE_mod1 <- sqrt(sum(res_mod1^2)/nv)
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RMSE_mod2 <- sqrt(sum(res_mod2^2)/nv)
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RMSE_mod3 <- sqrt(sum(res_mod3^2)/nv)
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RMSE_mod4 <- sqrt(sum(res_mod4^2)/nv)
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RMSE_mod5 <- sqrt(sum(res_mod5^2)/nv)
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RMSE_mod6 <- sqrt(sum(res_mod6^2)/nv)
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2a89fa5f
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Benoit Parmentier
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aac7c36c
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Benoit Parmentier
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results_RMSE[i,1]<- dates[i] #storing the interpolation dates in the first column
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results_RMSE[i,2]<- ns #number of stations used in the training stage
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results_RMSE[i,3]<- RMSE_mod1
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results_RMSE[i,4]<- RMSE_mod2
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results_RMSE[i,5]<- RMSE_mod3
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results_RMSE[i,6]<- RMSE_mod4
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results_RMSE[i,7]<- RMSE_mod5
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results_RMSE[i,8]<- RMSE_mod6
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25a68ae3
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Benoit Parmentier
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data_name<-paste("ghcn_v_",dates[[i]],sep="")
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assign(data_name,data_v)
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#ghcn_v<-ls(pattern="ghcn_v_")
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2a89fa5f
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Benoit Parmentier
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# end of the for loop #1
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}
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## Plotting and saving diagnostic measures
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aac7c36c
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Benoit Parmentier
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results_RMSEnum <-results_RMSE
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mode(results_RMSEnum)<- "numeric"
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2a89fa5f
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Benoit Parmentier
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# Make it numeric first
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# Now turn it into a data.frame...
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aac7c36c
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Benoit Parmentier
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results_table_RMSE<-as.data.frame(results_RMSEnum)
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colnames(results_table_RMSE)<-c("dates","ns","mod1", "mod2","mod3", "mod4", "mod5", "mod6")
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2a89fa5f
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Benoit Parmentier
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fbc95c44
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Benoit Parmentier
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# win.graph()
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# barplot(results_table$RMSE_A1/10,main="RMSE for the A1 models",names.arg=results_table$dates,ylab="Temp (deg. C)",xlab="interpolated date")
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# savePlot(paste("GAM_ANUSPLIN1_RMSE",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$RMSE_P1/10,main="RMSE for the P1 models",names.arg=results_table$dates,ylab="Temp ( deg. C)",xlab="interpolated date")
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# savePlot(paste("GAM_PRISM1_RMSE",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$RMSE_P2/10,main="RMSE for the P2 models",names.arg=results_table$dates,ylab="Temp ( deg. C)",xlab="interpolated date")
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# savePlot(paste("GAM_PRISM1_RMSE",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$AIC_A1,main="AIC for the A1 models",names.arg=results_table$dates,ylab="Temp ( deg. C)",xlab="interpolated date")
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# savePlot(paste("GAM_PRISM1_RMSE",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$AIC_P1/10,main="AIC for the P1 models",names.arg=results_table$dates,ylab="Temp ( deg. C)",xlab="interpolated date")
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# savePlot(paste("GAM_PRISM1_RMSE",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$AIC_P2/10,main="AIC for the P2 models",names.arg=results_table$dates,ylab="Temp (10 X deg. C)",xlab="interolated date")
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# savePlot(paste("GAM_PRISM1_RMSE",out_prefix,".emf", s‰‰ep=""), type="emf")
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# win.graph()
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# barplot(results_table$Deviance_A1/10,main="Deviance for the A1 models",names.arg=results_table$dates,ylab="Temp (10 X deg. C)",xlab="interolated date")
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# savePlot(paste("GAM_ANUSPLIN1_Deviance",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$Deviance_P1/10,main="Deviance for the P1 models",names.arg=results_table$dates,ylab="Temp (10 X deg. C)",xlab="interolated date")
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# savePlot(paste("GAM_PRISM1_Deviance",out_prefix,".emf", sep=""), type="emf")
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# win.graph()
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# barplot(results_table$Deviance_P2/10,main="Deviance for the P2 models",names.arg=results_table$dates,ylab="Temp (10 X deg. C)",xlab="interolated date")
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# savePlot(paste("GAM_PRISM2_Deviance",out_prefix,".emf", sep=""), type="emf")
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#results_table_RMSE
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write.csv(results_table_RMSE, file= paste(path,"/","results_GAM_Assessment",out_prefix,".txt",sep=""))
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2a89fa5f
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Benoit Parmentier
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| 201 |
4180b123
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Benoit Parmentier
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2a89fa5f
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Benoit Parmentier
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# End of script##########
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# ###############################
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bc59c6bb
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Benoit Parmentier
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#
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# ############Diagnostic GAM plots#############
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# win.graph()
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# gam.check(GAM_ANUSPLIN1)
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# savePlot("GAM_ANUSPLIN1_diagnostic1.emf", type="emf")
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# win.graph()
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# gam.check(GAM_PRISM1) #This will produce basic plots of residuals
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# savePlot("GAM_PRISM_diagnostic1.emf", type="emf")
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# gam.check(GAM_ANUSPLIN1)
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# win.graph()
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# vis.gam(GAM_ANUSPLIN1)
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# savePlot("GAM_ANUSPLIN1_prediction.emf", type="emf")
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# win.graph()
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# vis.gam(GAM_PRISM1)
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# savePlot("GAM_PRISM1_prediction.emf", type="emf")
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# win.graph()
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# vis.gam(GAM_ANUSPLIN1, view=c("lat","ELEV_SRTM"))
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# #vis.gam(GAM_ANUSPLIN1, view=c("lat","ELEV_SRTM", theta=100,phi=200))
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# savePlot("GAM_ANUSPLIN1_prediction2.emf", type="emf")
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