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24eedf3a
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Benoit Parmentier
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####################Interpolation of Tmax for 10 dates.#####################
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75151566
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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 shapefile
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#and perform 8 regressions using the general additive model (GAM). Note that this program:
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#1)assumes that the shapefile in the current working
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24eedf3a
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Benoit Parmentier
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#2)extract relevant variables from raster images before performing the regressions.
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63d8201d
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Benoit Parmentier
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#This scripts predicts tmas xsing GAM and LST derived from MOD11A1.
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24eedf3a
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Benoit Parmentier
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#Interactions terms are also included and assessed using the RMSE from validation dataset.
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#There are 10 dates used for the GAM interpolation. The dates must be provided as a textfile.
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#Script created by Benoit Parmentier on April 4, 2012.
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63d8201d
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Benoit Parmentier
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###Loading r library and packages # loading the raster package
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24eedf3a
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Benoit Parmentier
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library(gtools) # loading ...
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library(mgcv)
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library(sp)
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library(spdep)
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library(rgdal)
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###Parameters and arguments
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63d8201d
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Benoit Parmentier
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infile1<-"ghcn_or_tmax_b_04142012_OR83M.shp"
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f042de0f
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Benoit Parmentier
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path<-"/data/computer/parmentier/Data/IPLANT_project/data_Oregon_stations"
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#path<-"H:/Data/IPLANT_project/data_Oregon_stations"
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63d8201d
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Benoit Parmentier
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setwd(path)
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infile2<-"dates_interpolation_03052012.txt" #List of 10 dates for the regression
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f042de0f
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Benoit Parmentier
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infile2<-"list_365_dates_04212012.txt"
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24eedf3a
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Benoit Parmentier
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prop<-0.3 #Proportion of testing retained for validation
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f042de0f
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Benoit Parmentier
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out_prefix<-"_05012012_mod8_LST"
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24eedf3a
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Benoit Parmentier
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infile3<-"LST_dates_var_names.txt"
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80402fdf
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Benoit Parmentier
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infile4<-"models_interpolation_04032012b.txt"
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24eedf3a
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Benoit Parmentier
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#######START OF THE SCRIPT #############
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###Reading the station data and setting up for models' comparison
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63d8201d
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Benoit Parmentier
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filename<-sub(".shp","",infile1) #Removing the extension from file.
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ghcn<-readOGR(".", filename) #reading shapefile
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9c848d7a
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Benoit Parmentier
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f042de0f
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Benoit Parmentier
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proj4string(ghcn) #This retrieves the coordinate system for the SDF
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CRS_ghcn<-proj4string(ghcn) #this can be assigned to mean_LST!!!
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9c848d7a
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Benoit Parmentier
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24eedf3a
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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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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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63d8201d
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Benoit Parmentier
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24eedf3a
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Benoit Parmentier
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set.seed(100)
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dates <-readLines(paste(path,"/",infile2, sep=""))
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LST_dates <-readLines(paste(path,"/",infile3, sep=""))
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models <-readLines(paste(path,"/",infile4, sep=""))
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f042de0f
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Benoit Parmentier
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results <- matrix(1,length(dates),15) #This is a matrix containing the diagnostic measures from the GAM models.
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24eedf3a
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Benoit Parmentier
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f042de0f
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Benoit Parmentier
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results_AIC<- matrix(1,length(dates),length(models)+3)
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results_GCV<- matrix(1,length(dates),length(models)+3)
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results_DEV<- matrix(1,length(dates),length(models)+3)
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results_RMSE<- matrix(1,length(dates),length(models)+3)
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cor_LST_LC1<-matrix(1,length(dates),1) #correlation LST-LC1
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cor_LST_LC3<-matrix(1,length(dates),1) #correlation LST-LC3
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cor_LST_tmax<-matrix(1,length(dates),1) #correlation LST-tmax
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24eedf3a
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Benoit Parmentier
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#Screening for bad values
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ghcn_all<-ghcn
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ghcn_test<-subset(ghcn,ghcn$tmax>-150 & ghcn$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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63d8201d
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Benoit Parmentier
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month_var<-c("mm_01","mm_02","mm_03","mm_04","mm_05","mm_06","mm_07","mm_08","mm_09", "mm_10", "mm_11", "mm_12")
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24eedf3a
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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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## looping through the dates...
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#Change this into a nested loop, looping through the number of models
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for(i in 1:length(dates)){ # start of the for loop #1
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63d8201d
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Benoit Parmentier
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date<-strptime(dates[i], "%Y%m%d")
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month<-strftime(date, "%m")
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LST_month<-paste("mm_",month,sep="")
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24eedf3a
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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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63d8201d
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Benoit Parmentier
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mod <-ghcn.subsets[[i]][,match(LST_month, names(ghcn.subsets[[i]]))]
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24eedf3a
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Benoit Parmentier
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ghcn.subsets[[i]] = transform(ghcn.subsets[[i]],LST = mod)
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80402fdf
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Benoit Parmentier
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#Screening LST values
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#ghcn.subsets[[i]]<-subset(ghcn.subsets[[i]],ghcn.subsets[[i]]$LST> 258 & ghcn.subsets[[i]]$LST<313)
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24eedf3a
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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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#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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#mod <-data_s[,match(LST_dates[i], names(data_s))]
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#data_s = transform(data_s,LST = mod)
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#data_v = transform(data_v,LST = mod)
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####Regression part 2: GAM models
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mod1<- gam(tmax~ s(lat) + s (lon) + s (ELEV_SRTM), data=data_s)
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f042de0f
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Benoit Parmentier
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#mod2<- gam(tmax~ s(lat,lon,ELEV_SRTM), data=data_s)
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mod2<- gam(tmax~ s(lat,lon) + s(ELEV_SRTM), data=data_s)
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24eedf3a
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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) + s (Eastness) + s(DISTOC) + s(LST), data=data_s)
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mod5<- gam(tmax~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST), data=data_s)
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mod6<- gam(tmax~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST,LC1), data=data_s)
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80402fdf
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Benoit Parmentier
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mod7<- gam(tmax~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST,LC3), data=data_s)
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f042de0f
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Benoit Parmentier
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mod8<- gam(tmax~ s(lat,lon) +s(ELEV_SRTM) + s(Northness,Eastness) + s(DISTOC) + s(LST) + s(LC1), data=data_s)
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24eedf3a
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Benoit Parmentier
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####Regression part 3: Calculating and storing diagnostic measures
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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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80402fdf
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Benoit Parmentier
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results_AIC[i,9]<- AIC (mod7)
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f042de0f
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Benoit Parmentier
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results_AIC[i,10]<- AIC (mod8)
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24eedf3a
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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$gcv.ubre
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80402fdf
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Benoit Parmentier
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results_GCV[i,9]<- mod7$gcv.ubre
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f042de0f
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Benoit Parmentier
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results_GCV[i,10]<- mod7$gcv.ubre
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24eedf3a
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Benoit Parmentier
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results_DEV[i,1]<- dates[i] #storing the interpolation dates in the first column
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results_DEV[i,2]<- ns #number of stations used in the training stage
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results_DEV[i,3]<- mod1$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$deviance
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f042de0f
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Benoit Parmentier
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results_DEV[i,9]<- mod7$deviance
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results_DEV[i,10]<- mod8$deviance
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24eedf3a
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Benoit Parmentier
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#####VALIDATION: Prediction checking the results using the testing data########
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y_mod1<- predict(mod1, newdata=data_v, se.fit = TRUE) #Using the coeff to predict new values.
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y_mod2<- predict(mod2, newdata=data_v, se.fit = TRUE)
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y_mod3<- predict(mod3, newdata=data_v, se.fit = TRUE)
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y_mod4<- predict(mod4, newdata=data_v, se.fit = TRUE)
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y_mod5<- predict(mod5, newdata=data_v, se.fit = TRUE)
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y_mod6<- predict(mod6, newdata=data_v, se.fit = TRUE)
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80402fdf
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Benoit Parmentier
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y_mod7<- predict(mod7, newdata=data_v, se.fit = TRUE)
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f042de0f
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Benoit Parmentier
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y_mod8<- predict(mod8, newdata=data_v, se.fit = TRUE)
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24eedf3a
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Benoit Parmentier
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res_mod1<- data_v$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$fit
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80402fdf
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Benoit Parmentier
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res_mod7<- data_v$tmax - y_mod7$fit
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f042de0f
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Benoit Parmentier
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res_mod8<- data_v$tmax - y_mod8$fit
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24eedf3a
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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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80402fdf
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Benoit Parmentier
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RMSE_mod7 <- sqrt(sum(res_mod7^2)/nv)
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f042de0f
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Benoit Parmentier
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RMSE_mod8 <- sqrt(sum(res_mod8^2)/nv)
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24eedf3a
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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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80402fdf
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Benoit Parmentier
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results_RMSE[i,9]<- RMSE_mod7
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f042de0f
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Benoit Parmentier
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results_RMSE[i,10]<- RMSE_mod8
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9c848d7a
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Benoit Parmentier
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f042de0f
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Benoit Parmentier
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#Saving dataset in dataframes
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24eedf3a
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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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data_name<-paste("ghcn_s_",dates[[i]],sep="")
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assign(data_name,data_s)
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f042de0f
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Benoit Parmentier
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#ghcn_v<-ls(pattern="ghcn_v_")
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cor_LST_LC1[i]<-cor(ghcn.subsets[[i]]$LST,ghcn.subsets[[i]]$LC1)
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cor_LST_LC3[i]<-cor(ghcn.subsets[[i]]$LST,ghcn.subsets[[i]]$LC3)
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24eedf3a
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Benoit Parmentier
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f042de0f
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Benoit Parmentier
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#end of the for loop #1
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24eedf3a
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Benoit Parmentier
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}
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## Plotting and saving diagnostic measures
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results_RMSEnum <-results_RMSE
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80402fdf
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Benoit Parmentier
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results_AICnum <-results_AIC
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24eedf3a
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Benoit Parmentier
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mode(results_RMSEnum)<- "numeric"
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80402fdf
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Benoit Parmentier
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mode(results_AICnum)<- "numeric"
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24eedf3a
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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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results_table_RMSE<-as.data.frame(results_RMSEnum)
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80402fdf
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Benoit Parmentier
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results_table_AIC<-as.data.frame(results_AICnum)
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75151566
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Benoit Parmentier
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colnames(results_table_RMSE)<-c("dates","ns","mod1", "mod2","mod3", "mod4", "mod5", "mod6", "mod7", "mod8")
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colnames(results_table_AIC)<-c("dates","ns","mod1", "mod2","mod3", "mod4", "mod5", "mod6", "mod7", "mod8")
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24eedf3a
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Benoit Parmentier
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#results_table_RMSE
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80402fdf
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Benoit Parmentier
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write.table(results_table_RMSE, file= paste(path,"/","results_GAM_Assessment",out_prefix,".txt",sep=""), sep=",")
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write.table(results_table_AIC, file= paste(path,"/","results_GAM_Assessment",out_prefix,".txt",sep=""),sep=",", append=TRUE)
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24eedf3a
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Benoit Parmentier
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75151566
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Benoit Parmentier
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###Analysing the results from the 365 days run: Summarize by month
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for(i in 1:nrow(results_table_RMSE)){
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date<-results_table_RMSE$dates[i]
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date<-strptime(date, "%Y%m%d")
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results_table_RMSE$month[i]<-as.integer(strftime(date, "%m"))
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}
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average<-aggregate(cbind(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8)~month,data=results_table_RMSE,mean, na.rm=TRUE)
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average<-aggregate(cbind(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8)~month,data=results_table_RMSE, FUN=mean)
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#average on all the data.frame
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averaget<-aggregate(results_table_RMSE, by=list(results_table_RMSE$month),FUN=mean, na.rm=TRUE)
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#mediant<-aggregate(results_table_RMSE, by=list(results_table_RMSE$month),FUN=median, na.rm=TRUE)
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#average_lowt<-aggregate(results_table_RMSE, by=list(results_table_RMSE$month), FUN=function(v) t.test(v)$conf.int[1])
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#average_up<-aggregate(cbind(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8)~month,data=results_table_RMSE, function(v) t.test(v)$conf.int[2])
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median<-aggregate(cbind(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8)~month,data=results_table_RMSE, median, na.rm=TRUE)
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average_low<-aggregate(cbind(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8)~month,data=results_table_RMSE, function(v) t.test(v)$conf.int[1])
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average_up<-aggregate(cbind(mod1,mod2,mod3,mod4,mod5,mod6,mod7,mod8)~month,data=results_table_RMSE, function(v) t.test(v)$conf.int[2])
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mod<-names(averaget)
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mod<-mod[4:11]
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#Saving graphic plots
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for(i in 1:length(mod)){
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X11(width=14,height=10)
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name<-mod[i]
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barplot2(average[[name]],plot.ci=TRUE, ci.l=average_low[[name]], ci.u=average_up[[name]],main="Mean RMSE per month", names.arg=c("Jan", "Feb", "Mar", "Apr", "May", "Jun","Jul", "Aug", "Sep","Oct", "Nov", "Dec"),ylim=c(20,30),ylab="RMSE in tenth deg C",xlab=name)
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#title(paste("Sampling RMSE for mod",i,sep=""))
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savePlot(paste("barplot_results_RMSE_month_",name,out_prefix,".png", sep=""), type="png")
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dev.off()
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}
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for(i in 1:length(mod)){
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X11(width=14,height=10)
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name<-mod[i]
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barplot2(average[[name]],plot.ci=TRUE, ci.l=average_low[[name]], ci.u=average_up[[name]],main=paste(" Mean RMSE per month ",name, sep=""), names.arg=c("Jan", "Feb", "Mar", "Apr", "May", "Jun","Jul", "Aug", "Sep","Oct", "Nov", "Dec"),ylim=c(20,30),ylab="RMSE in tenth deg C",xlab=name)
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#title(paste("Sampling RMSE for mod",i,sep=""))
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savePlot(paste("barplot_results_RMSE_month_",name,out_prefix,".png", sep=""), type="png")
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dev.off()
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X11(width=14,height=10)
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name<-mod[i]
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hist(results_table_RMSE[[name]],breaks=15, main=paste(" Histogram RMSE_",name, sep=""),xlab=paste("RMSE ",name, sep=""))
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savePlot(paste("Hist_results_RMSE_365_",name,out_prefix,".png", sep=""), type="png")
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dev.off()
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}
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for(i in 1:length(mod)){
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X11(width=14,height=10)
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name<-mod[i]
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hist(results_table_RMSE[[name]],breaks=15, main=paste(" Histogram RMSE_",name, sep=""),xlab=paste("RMSE ",name, sep=""))
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savePlot(paste("Hist_results_RMSE_365_",name,out_prefix,".png", sep=""), type="png")
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dev.off()
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}
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r<-(results_table_RMSE[,3:10]) #selecting only the columns related to models...
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mean_r<-mean(r)
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median_r<-sapply(r, median)
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sd_r<-sapply(r, sd)
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barplot(mean_r,ylim=c(23,26),ylab="RMSE in tenth deg C")
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barplot(median_r,ylim=c(23,26),ylab="RMSE in tenth deg C",add=TRUE,inside=FALSE,beside=TRUE) # put both on the same plot
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barplot(sd_r,ylim=c(6,8),ylab="RMSE in tenth deg C") # put both on the same plot
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height<-rbind(mean_r,median_r)
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barplot(height,ylim=c(23,26),ylab="RMSE in tenth deg C",beside=TRUE,legend=rownames(height))
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barplot(height,ylim=c(23,26),ylab="RMSE in tenth deg C",beside=TRUE, col=c("darkblue","red"),legend=rownames(height)) # put both on the same plot
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barplot2(mean_r,median_r,ylim=c(23,26),ylab="RMSE in tenth deg C") # put both on the same plot
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#Collect var explained and p values for each var...
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# End of script##########
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names(results_table_RMSE)
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