Revision 2ba31980
Added by Benoit Parmentier over 11 years ago
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#STAGE 5: Output analyses-visualization of results for specific dates... |
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# |
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#AUTHOR: Benoit Parmentier |
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#DATE: 03/21/2013
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#DATE: 03/28/2013
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568-- |
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script_path<-"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/" |
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#list_script_files<- |
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stages_to_run<-c(1,2,3,4,5) #May decide on antoher strategy later on... |
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#stages_to_run<-c(1,2,3,4,5) #May decide on antoher strategy later on... |
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stages_to_run<-c(0,0,3,4,5) #May decide on antoher strategy later on... |
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#####SCRIPT USED FOR THE PREDICTIONS |
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#####SCRIPT USED FOR THE PREDICTIONS: Source all scripts here to avoid confusion on versions being run!!!!
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#master_script_temp_03192013.R
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#source(file.path(script_path,"master_script_temp_03282013.R")) #Master script can be run directly...
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#CALLED FROM MASTER SCRIPT: |
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#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_03192013.py |
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source(file.path(script_path,"covariates_production_temperatures_03212013.R")) |
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source(file.path(script_path,"Database_stations_covariates_processing_function_03132013.R")) |
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03182013.R")) |
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source(file.path(script_path,"results_interpolation_date_output_analyses_03182013.R")) |
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source(file.path(script_path,"Database_stations_covariates_processing_function_03242013.R")) |
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03272013.R")) |
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source(file.path(script_path,"results_interpolation_date_output_analyses_03272013.R")) |
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#source(file.path(script_path,"results_covariates_database_stations_output_analyses_03272013.R")) |
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#CALLED FROM GAM FUSION ANALYSIS RASTER PREDICTION
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#FUNCTIONS CALLED FROM GAM FUSION ANALYSIS RASTER PREDICTION ARE FOUND IN...
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source(file.path(script_path,"sampling_script_functions_03122013.R")) |
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source(file.path(script_path,"GAM_fusion_function_multisampling_03142013.R")) #Include GAM_CAI |
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source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_03182013.R")) |
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source(file.path(script_path,"GAM_fusion_function_multisampling_03192013.R")) #Include GAM_CAI |
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source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_03272013.R")) |
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############ STAGE 1: LST Climatology ############### |
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############ STAGE 2: Covariate production ################ |
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##Paths to inputs and output |
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var<-"TMIN" |
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#var<-"TMIN" |
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var<-"TMAX" |
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in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
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out_path<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data/" |
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############# STAGE 3: Data preparation ############### |
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#Setting up input argurments for script function... |
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#set up earlier |
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var <- "TMAX" # name of the variables to keep: TMIN, TMAX or PRCP --already set up earlier |
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infile_covariates<-"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script and used in stage 3 and stage 4 |
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#infile_covariates<-"covariates__venezuela_region_TMIN__VE_03192013.tif" #covariates stack for TMIN |
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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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infile1<- "outline_venezuela_region__VE_01292013.shp" #This is the shape file of outline of the study area #It is an input/output of the covariate script |
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#covar_names see stage 2 |
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var <- "TMAX" # name of the variables to keep: TMIN, TMAX or PRCP |
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#specific to this stage |
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db.name <- "ghcn" # name of the Postgres database |
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range_years<-c("2000","2001") #right bound not included in the range!!
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range_years_clim<-c("1980","2011") #right bound not included in the range!!
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range_years_clim<-c("1981","2011") #right bound not included in the range!!
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infile2<-"/home/layers/data/climate/ghcn/v2.92-upd-2012052822/ghcnd-stations.txt" #This is the textfile of station locations from GHCND |
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in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
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out_prefix<-"_365d_GAM_fus5_all_lstd_03182013" #User defined output prefix |
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#qc_flags<- flags allowe for the query from the GHCND?? |
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out_prefix<-"_365d_GAM_fus5_all_lstd_03282013" #User defined output prefix |
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qc_flags_stations<-c("0","S") #flags allowed for screening after the query from the GHCND??
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#list of 11 parameters for input in the function...
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#list of 12 parameters for input in the function...
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list_param_prep<-list(db.name,var,range_years,range_years_clim,infile1,infile2,infile_covariates,CRS_locs_WGS84,in_path,covar_names,out_prefix) |
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cnames<-c("db.name","var","range_years","range_years_clim","infile1","infile2","infile_covariates","CRS_locs_WGS84","in_path","covar_names","out_prefix")
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list_param_prep<-list(db.name,var,range_years,range_years_clim,infile1,infile2,infile_covariates,CRS_locs_WGS84,in_path,covar_names,qc_flags_stations,out_prefix)
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cnames<-c("db.name","var","range_years","range_years_clim","infile1","infile2","infile_covariates","CRS_locs_WGS84","in_path","covar_names","qc_flags_stations","out_prefix")
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names(list_param_prep)<-cnames |
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##### RUN SCRIPT TO GET STATION DATA WITH COVARIATES ##### |
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"list_models","lst_avg","in_path","out_path","script_path", |
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"interpolation_method") |
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#Source file |
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#Make the function call |
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#Make the function call--names to be change to raster_prediction_obj and raster_prediction_fun |
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raster_prediction_gam_fus_obj <-raster_prediction_gam_fusion(list_param_raster_prediction) |
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Also available in: Unified diff
run TMAX prediction Venezuela for year 2000 with 1981-2010 period and modifications in sourcing and input parameters