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1cd7ecf2
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Benoit Parmentier
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######################### Raster prediction GAM FUSION ####################################
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############################ Interpolation of temperature for given processing region ##########################################
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#This script interpolates temperature values using MODIS LST, covariates and GHCND station data.
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#It requires the text file of stations and a shape file of the study area.
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fb039a6b
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Benoit Parmentier
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#Note that the projection for both GHCND and study area is lonlat WGS84.
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#Options to run this program are:
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#1) Multisampling: vary the porportions of hold out and use random samples for each run
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#2)Constant sampling: use the same sample over the runs
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#3)over dates: run over for example 365 dates without mulitsampling
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#4)use seed number: use seed if random samples must be repeatable
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1508a57e
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Benoit Parmentier
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#5)GAM fusion: possibilty of running GAM+FUSION or GAM+CAI and other options added
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12 |
0f602e87
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Benoit Parmentier
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#The interpolation is done first at the monthly time scale then delta surfaces are added.
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13 |
fb039a6b
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Benoit Parmentier
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#AUTHOR: Benoit Parmentier
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1cd7ecf2
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Benoit Parmentier
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#DATE: 03/12/2013
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1508a57e
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Benoit Parmentier
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#568--
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e7bf2d1b
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Benoit Parmentier
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###################################################################################################
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###Loading R library and packages
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library(gtools) # loading some useful tools
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library(mgcv) # GAM package by Simon Wood
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library(sp) # Spatial pacakge with class definition by Bivand et al.
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library(spdep) # Spatial pacakge with methods and spatial stat. by Bivand et al.
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library(rgdal) # GDAL wrapper for R, spatial utilities
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library(gstat) # Kriging and co-kriging by Pebesma et al.
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0163d0e2
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Benoit Parmentier
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library(fields) # NCAR Spatial Interpolation methods such as kriging, splines
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e7bf2d1b
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Benoit Parmentier
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library(raster) # Hijmans et al. package for raster processing
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library(rasterVis)
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library(parallel) # Urbanek S. and Ripley B., package for multi cores & parralel processing
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fb039a6b
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Benoit Parmentier
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library(reshape)
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library(plotrix)
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0f602e87
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Benoit Parmentier
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library(maptools)
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c1e1cc30
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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### Parameters and arguments
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972ac6af
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Benoit Parmentier
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## output param from previous script: Database_stations_covariates_processing_function
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33095a53
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Benoit Parmentier
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#infile_monthly<-"monthly_covariates_ghcn_data_TMAXy2010_2010_VE_02082013.shp"
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#infile_daily<-"daily_covariates_ghcn_data_TMAXy2010_2010_VE_02082013.shp"
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#infile_locs<-"stations_venezuela_region_y2010_2010_VE_02082013.shp"
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infile_covariates<-"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script
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972ac6af
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Benoit Parmentier
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var<-"TMAX"
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1cd7ecf2
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Benoit Parmentier
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#out_prefix<-"_365d_GAM_fus5_all_lstd_02202013" #User defined output prefix should be defined in master script
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972ac6af
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Benoit Parmentier
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CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84: same as earlier
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e7bf2d1b
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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infile_monthly<-list_outfiles$monthly_covar_ghcn_data #outile4 from database_covar script
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infile_daily<-list_outfiles$daily_covar_ghcn_data #outfile3 from database_covar script
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infile_locs<- list_outfiles$loc_stations_ghcn #outfile2? from database covar script
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rnames <-c("x","y","lon","lat","N","E","N_w","E_w","elev","slope","aspect","CANHEIGHT","DISTOC")
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lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12")
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lst_names<-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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"nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08",
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"nobs_09","nobs_10","nobs_11","nobs_12")
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covar_names<-c(rnames,lc_names,lst_names)
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972ac6af
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Benoit Parmentier
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###
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#Input for sampling function...
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c1e1cc30
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Benoit Parmentier
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seed_number<- 100 #if seed zero then no seed?
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fb039a6b
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Benoit Parmentier
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nb_sample<-1 #number of time random sampling must be repeated for every hold out proportion
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step<-0
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0766370d
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Benoit Parmentier
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constant<-0 #if value 1 then use the same samples as date one for the all set of dates
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33095a53
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Benoit Parmentier
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prop_minmax<-c(0.3,0.3) #if prop_min=prop_max and step=0 then predicitons are done for the number of dates...
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infile_dates<-"list_365_dates_04212012.txt"
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fb039a6b
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Benoit Parmentier
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c1e1cc30
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Benoit Parmentier
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#Models to run...this can be change for each run
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list_models<-c("y_var ~ s(elev_1)",
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"y_var ~ s(LST)",
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"y_var ~ s(elev_1,LST)",
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"y_var ~ s(lat) + s(lon)+ s(elev_1)",
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"y_var ~ s(lat,lon,elev_1)",
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"y_var ~ s(lat,lon) + s(elev_1) + s(N_w,E_w) + s(LST)",
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"y_var ~ s(lat,lon) + s(elev_1) + s(N_w,E_w) + s(LST) + s(LC2)",
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"y_var ~ s(lat,lon) + s(elev_1) + s(N_w,E_w) + s(LST) + s(LC6)",
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"y_var ~ s(lat,lon) + s(elev_1) + s(N_w,E_w) + s(LST) + s(DISTOC)")
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972ac6af
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Benoit Parmentier
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#Choose interpolation method...
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interpolation_method<-c("gam_fusion","gam_CAI") #other otpions to be added later
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c1e1cc30
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Benoit Parmentier
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#Default name of LST avg to be matched
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lst_avg<-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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972ac6af
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Benoit Parmentier
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in_path<-"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data"
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#Create on the fly output folder...
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out_path<-"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data"
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script_path<-"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/"
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setwd(in_path)
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33095a53
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Benoit Parmentier
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1cd7ecf2
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Benoit Parmentier
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#PARSING INPUTS/ARGUMENTS
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list_param_data_prep<-c(infile_monthly,infile_daily,infile_locs,infile_covariates,covar_names,var,out_prefix,CRS_locs_WGS84)
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33095a53
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Benoit Parmentier
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list_param_raster_prediction<-c(list_param_data_prep,
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seed_number,nb_sample,step,constant,prop_minmax,infile_dates,
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list_models,lst_avg,in_path,out_path,script_path,
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interpolation_method)
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1cd7ecf2
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Benoit Parmentier
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#9 parameters used in the data preparation stage and input in the current script
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list_param_data_prep<-list_param_raster_prediction$list_param_data_prep
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infile_monthly<-list_param_data_prep$infile_monthly
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infile_daily<-list_param_data_prep$infile_daily
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infile_locs<-list_param_data_prep$infile_locs
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infile_covariates<-list_param_data_prep$infile_covariates
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covar_names<- list_param_data_prep$covar_names
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var<-list_param_data_prep$var
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out_prefix<-list_param_data_prep$out_prefix
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CRS_locs_WGS84<-list_param_data_prep$CRS_locs_WGS84
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#6 parameters for sampling function
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seed_number<-list_param_raster_prediction$seed_number
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nb_sample<-list_param_raster_prediction$nb_sample
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step<-list_param_raster_prediction$step
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constant<-list_param_raster_prediction$constant
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prop_minmax<-list_param_raster_prediction$prop_minmax
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infile_dates<-list_param_raster_prediction$infile_dates
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#6 additional parameters for monthly climatology and more
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list_models<-list_param_raster_prediction$list_models
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lst_avg<-list_param_raster_prediction$lst_avg
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in_path<-list_param_raster_prediction$in_path
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out_path<-list_param_raster_prediction$out_path
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script_path<-list_param_raster_prediction$script_path
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interpolation_method<-list_param_raster_prediction$interpolation_method
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33095a53
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Benoit Parmentier
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source(file.path(script_path,"sampling_script_functions_03052013.R"))
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1cd7ecf2
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Benoit Parmentier
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source(file.path(script_path,"GAM_fusion_function_multisampling_03122013.R"))
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1508a57e
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Benoit Parmentier
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source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_02262013.R"))
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33095a53
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Benoit Parmentier
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fb039a6b
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Benoit Parmentier
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###################### START OF THE SCRIPT ########################
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e7bf2d1b
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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if (var=="TMAX"){
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y_var_name<-"dailyTmax"
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}
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if (var=="TMIN"){
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y_var_name<-"dailyTmin"
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}
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1508a57e
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Benoit Parmentier
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################# CREATE LOG FILE #####################
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#create log file to keep track of details such as processing times and parameters.
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c1e1cc30
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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log_fname<-paste("R_log_raster_prediction",out_prefix, ".log",sep="")
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c1e1cc30
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Benoit Parmentier
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if (file.exists(log_fname)){ #Stop the script???
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file.remove(log_fname)
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log_file<-file(log_fname,"w")
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}
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if (!file.exists(log_fname)){
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log_file<-file(log_fname,"w")
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}
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time1<-proc.time() #Start stop watch
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writeLines(paste("Starting script at this local Date and Time: ",as.character(Sys.time()),sep=""),
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con=log_file,sep="\n")
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writeLines("Starting script process time:",con=log_file,sep="\n")
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writeLines(as.character(time1),con=log_file,sep="\n")
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33095a53
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Benoit Parmentier
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############### READING INPUTS: DAILY STATION DATA AND OTEHR DATASETS #################
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1508a57e
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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ghcn<-readOGR(dsn=in_path,layer=sub(".shp","",basename(infile_daily)))
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96c5053f
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Benoit Parmentier
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CRS_interp<-proj4string(ghcn) #Storing projection information (ellipsoid, datum,etc.)
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33095a53
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Benoit Parmentier
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stat_loc<-readOGR(dsn=in_path,layer=sub(".shp","",basename(infile_locs)))
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dates <-readLines(file.path(in_path,infile_dates)) #dates to be predicted
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161 |
e7bf2d1b
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Benoit Parmentier
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162 |
972ac6af
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Benoit Parmentier
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#Reading of covariate brick covariates can be changed...
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33095a53
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Benoit Parmentier
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s_raster<-brick(infile_covariates) #read in the data brck
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96c5053f
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Benoit Parmentier
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names(s_raster)<-covar_names #Assigning names to the raster layers: making sure it is included in the extraction
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33095a53
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Benoit Parmentier
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pos<-match("elev",names(s_raster))
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names(s_raster)[pos]<-"elev_1"
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#Screen for extreme values": this needs more thought, min and max val vary with regions
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#min_val<-(-15+273.16) #if values less than -15C then screen out (note the Kelvin units that will need to be changed later in all datasets)
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#r1[r1 < (min_val)]<-NA
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96c5053f
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Benoit Parmentier
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972ac6af
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Benoit Parmentier
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#Reading monthly data
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33095a53
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Benoit Parmentier
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data3<-readOGR(dsn=in_path,layer=sub(".shp","",basename(infile_monthly)))
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760957d7
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Benoit Parmentier
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dst_all<-data3
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dst<-data3
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972ac6af
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Benoit Parmentier
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### TO DO -important ###
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33095a53
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Benoit Parmentier
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#Cleaning/sceerniging functions for daily stations, monthly stations and covariates?? do this during the preparation stage!!!??
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###
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181 |
e7bf2d1b
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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########### CREATE SAMPLING -TRAINING AND TESTING STATIONS ###########
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183 |
e7bf2d1b
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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#Input for sampling function...
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e7bf2d1b
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Benoit Parmentier
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186 |
33095a53
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Benoit Parmentier
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#dates #list of dates for prediction
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#ghcn_name<-"ghcn" #infile daily data
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e7bf2d1b
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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list_param_sampling<-list(seed_number,nb_sample,step,constant,prop_minmax,dates,ghcn)
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#list_param_sampling<-list(seed_number,nb_sample,step,constant,prop_minmax,dates,ghcn_name)
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names(list_param_sampling)<-c("seed_number","nb_sample","step","constant","prop_minmax","dates","ghcn")
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#run function
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sampling_obj<-sampling_training_testing(list_param_sampling)
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fb039a6b
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Benoit Parmentier
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196 |
e7bf2d1b
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Benoit Parmentier
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33095a53
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Benoit Parmentier
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########### PREDICT FOR MONTHLY SCALE ##################
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198 |
e7bf2d1b
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Benoit Parmentier
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199 |
0f602e87
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Benoit Parmentier
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#First predict at the monthly time scale: climatology
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c1e1cc30
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Benoit Parmentier
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writeLines("Predictions at monthly scale:",con=log_file,sep="\n")
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t1<-proc.time()
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1cd7ecf2
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Benoit Parmentier
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j=12
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list_param_runClim_KGFusion<-list(j,s_raster,covar_names,list_models,dst,var,y_var_name, out_prefix)
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names(list_param_runClim_KGFusion)<-c("list_index","covar_rast","covar_names","list_models","dst","var","y_var_name","out_prefix")
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source(file.path(script_path,"GAM_fusion_function_multisampling_03122013.R"))
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gamclim_fus_mod<-mclapply(1:6, list_param=list_param_runClim_KGFusion, runClim_KGFusion,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement
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33095a53
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Benoit Parmentier
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#gamclim_fus_mod<-mclapply(1:6, runClim_KGFusion,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement
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0f602e87
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Benoit Parmentier
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save(gamclim_fus_mod,file= paste("gamclim_fus_mod",out_prefix,".RData",sep=""))
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c1e1cc30
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Benoit Parmentier
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t2<-proc.time()-t1
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writeLines(as.character(t2),con=log_file,sep="\n")
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212 |
e7bf2d1b
|
Benoit Parmentier
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213 |
0f602e87
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Benoit Parmentier
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#now get list of raster clim layers
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214 |
e7bf2d1b
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Benoit Parmentier
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215 |
0f602e87
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Benoit Parmentier
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list_tmp<-vector("list",length(gamclim_fus_mod))
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for (i in 1:length(gamclim_fus_mod)){
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tmp<-gamclim_fus_mod[[i]]$clim
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list_tmp[[i]]<-tmp
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219 |
e7bf2d1b
|
Benoit Parmentier
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}
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221 |
1508a57e
|
Benoit Parmentier
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################## PREDICT AT DAILY TIME SCALE #################
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223 |
0f602e87
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Benoit Parmentier
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#put together list of clim models per month...
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224 |
33095a53
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Benoit Parmentier
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#rast_clim_yearlist<-list_tmp
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clim_yearlist<-list_tmp
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226 |
0f602e87
|
Benoit Parmentier
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#Second predict at the daily time scale: delta
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#gam_fus_mod<-mclapply(1:1, runGAMFusion,mc.preschedule=FALSE,mc.cores = 1) #This is the end bracket from mclapply(...) statement
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writeLines("Predictions at the daily scale:",con=log_file,sep="\n")
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t1<-proc.time()
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#input a list:note that ghcn.subsets is not sampling_obj$data_day_ghcn
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list_param_runGAMFusion<-list(i,clim_yearlist,sampling_obj,dst,var,y_var_name, out_prefix)
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names(list_param_runGAMFusion)<-c("list_index","clim_yearlist","sampling_obj","dst","var","y_var_name","out_prefix")
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#test<-mclapply(1:18, runGAMFusion,list_param=list_param_runGAMFusion,mc.preschedule=FALSE,mc.cores = 9)
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gam_fus_mod<-mclapply(1:length(sampling_obj$ghcn_data_day),list_param=list_param_runGAMFusion,runGAMFusion,mc.preschedule=FALSE,mc.cores = 9) #This is the end bracket from mclapply(...) statement
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#gam_fus_mod<-mclapply(1:length(sampling_obj$ghcn_data_day),runGAMFusion,list_param_runGAMFusion,mc.preschedule=FALSE,mc.cores = 9) #This is the end bracket from mclapply(...) statement
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#gam_fus_mod<-mclapply(1:length(ghcn.subsets), runGAMFusion,mc.preschedule=FALSE,mc.cores = 9) #This is the end bracket from mclapply(...) statement
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save(gam_fus_mod,file= paste("gam_fus_mod",out_prefix,".RData",sep=""))
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t2<-proc.time()-t1
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writeLines(as.character(t2),con=log_file,sep="\n")
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############### NOW RUN VALIDATION #########################
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list_tmp<-vector("list",length(gam_fus_mod))
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for (i in 1:length(gam_fus_mod)){
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tmp<-gam_fus_mod[[i]][[y_var_name]] #y_var_name is the variable predicted (tmax or tmin)
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list_tmp[[i]]<-tmp
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}
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rast_day_yearlist<-list_tmp #list of predicted images
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writeLines("Validation step:",con=log_file,sep="\n")
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t1<-proc.time()
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#calculate_accuary_metrics<-function(i)
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gam_fus_validation_mod<-mclapply(1:length(gam_fus_mod), calculate_accuracy_metrics,mc.preschedule=FALSE,mc.cores = 9) #This is the end bracket from mclapply(...) statement
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#gam_fus_validation_mod<-mclapply(1:1, calculate_accuracy_metrics,mc.preschedule=FALSE,mc.cores = 1) #This is the end bracket from mclapply(...) statement
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save(gam_fus_validation_mod,file= paste("gam_fus_validation_mod",out_prefix,".RData",sep=""))
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t2<-proc.time()-t1
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writeLines(as.character(t2),con=log_file,sep="\n")
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#################### ASSESSMENT OF PREDICTIONS: PLOTS OF ACCURACY METRICS ###########
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##Create data.frame with valiation metrics for a full year
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tb_diagnostic_v<-extract_from_list_obj(gam_fus_validation_mod,"metrics_v")
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rownames(tb_diagnostic_v)<-NULL #remove row names
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#Call function to create plots of metrics for validation dataset
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metric_names<-c("rmse","mae","me","r","m50")
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summary_metrics<-boxplot_from_tb(tb_diagnostic_v,metric_names,out_prefix)
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names(summary_metrics)<-c("avg","median")
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##Write out information concerning accuracy and predictions
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outfile<-file.path(in_path,paste("assessment_measures_",out_prefix,".txt",sep=""))
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write.table(tb_diagnostic_v,file= outfile,row.names=FALSE,sep=",")
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write.table(summary_metrics[[1]], file= outfile, append=TRUE,sep=",") #write out avg
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write.table(summary_metrics[[2]], file= outfile, append=TRUE,sep=",") #write out median
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#################### CLOSE LOG FILE #############
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#close log_file connection and add meta data
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writeLines("Finished script process time:",con=log_file,sep="\n")
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time2<-proc.time()-time1
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writeLines(as.character(time2),con=log_file,sep="\n")
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#later on add all the paramters used in the script...
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writeLines(paste("Finished script at this local Date and Time: ",as.character(Sys.time()),sep=""),
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con=log_file,sep="\n")
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writeLines("End of script",con=log_file,sep="\n")
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close(log_file)
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############################################################
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######################## END OF SCRIPT #####################
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