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Revision a156c854

Added by Benoit Parmentier almost 9 years ago

adding sourcing of relevant script for stage 6 assessment and debugging

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climate/research/oregon/interpolation/master_script_stage_6.R
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#STAGE 6: Assessement of predictions by tiles and regions with mosaicing of predictions and accuracy
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#AUTHOR: Benoit Parmentier
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#CREATED ON: 12/29/2015
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#MODIFIED ON: 12/31/2015
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#MODIFIED ON: 01/03/2015
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#PROJECT: NCEAS INPLANT: Environment and Organisms
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## TODO:


  		




  ......




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#CALLED FROM MASTER SCRIPT:


  		




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script_path <- "/nobackupp8/bparmen1/env_layers_scripts" #path to script


  		




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function_assessment_part1_script <- "global_run_scalingup_assessment_part1_functions_02112015.R" #PARAM12


  		




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function_assessment_part1a <-"global_run_scalingup_assessment_part1a_12312015.R"


  		




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source(file.path(script_path,function_assessment_part1_script)) #source all functions used in this script 


  		




  
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function_assessment_part1_functions <- "global_run_scalingup_assessment_part1_functions_02112015.R" #PARAM12


  		




  
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function_assessment_part1a <-"global_run_scalingup_assessment_part1a_01042016.R"


  		




  
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function_assessment_part2 <- "global_run_scalingup_assessment_part2_01042016.R"


  		




  
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function_assessment_part2_functions <- "global_run_scalingup_assessment_part2_functions_01032016.R"


  		




  
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source(file.path(script_path,function_assessment_part1_functions)) #source all functions used in this script 


  		




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source(file.path(script_path,function_assessment_part1a)) #source all functions used in this script 


  		




  
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source(file.path(script_path,function_assessment_part2)) #source all functions used in this script 


  		




  
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source(file.path(script_path,function_assessment_part2_functions)) #source all functions used in this script 


  		




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### Parameters and arguments ###


  		




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var<-"TMAX" # variable being interpolated


  		




  
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if (var == "TMAX") {


  		




  
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  y_var_name <- "dailyTmax"


  		




  
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  y_var_month <- "TMax"


  		




  
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}


  		




  
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if (var == "TMIN") {


  		




  
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  y_var_name <- "dailyTmin"


  		




  
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  y_var_month <- "TMin"


  		




  
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}


  		




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#interpolation_method<-c("gam_fusion") #other otpions to be added later


  		




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interpolation_method<-c("gam_CAI")


  		




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#/nobackupp6/aguzman4/climateLayers/out_15x45/1982


  		




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#region_names <- c("reg23","reg4") #selected region names, #PARAM2


  		




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region_name <- c("reg4") #run assessment by region


  		




  
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region_name <- c("reg4") #run assessment by region, this is a unique region only


  		




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#region_names <- c("reg1","reg2","reg3","reg4","reg5","reg6") #selected region names, #PARAM2


  		




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interpolation_method <- c("gam_CAI") #PARAM4


  		




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out_prefix <- "run_global_analyses_pred_12282015" #PARAM5


  		




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#CRS_interp <-"+proj=lcc +lat_1=43 +lat_2=45.5 +lat_0=41.75 +lon_0=-120.5 +x_0=400000 +y_0=0 +ellps=GRS80 +units=m +no_defs";


  		




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CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84


  		




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list_year_predicted <- 1984:2004


  		




  
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#list_year_predicted <- 1984:2004


  		




  
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list_year_predicted <- c("2014")


  		




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#year_predicted <- list_year_predicted[1]


  		




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file_format <- ".tif" #format for mosaiced files #PARAM10


  		




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NA_flag_val <- -9999  #No data value, #PARAM11


  		




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num_cores <- 6 #number of cores used #PARAM13


  		




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list_param_run_assessment_prediction <- list(in_dir1,region_name,interpolation_method,out_prefix,


  		




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                                          out_dir,create_out_dir_param,CRS_locs_WGS84,


  		




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                                             list_year_predicted,file_format,NA_flag_val,num_cores)


  		




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list_names <- c("in_dir1","region_name","interpolation_method","out_prefix",


  		




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                                      "out_dir","create_out_dir_param","CRS_locs_WGS84",


  		




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                                      "list_year_predicted","file_format","NA_flag_val","num_cores")


  		




  
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plotting_figures <- TRUE #running part2 of assessment to generate figures...


  		




  
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##Additional parameters used in part 2, some these may be removed as code is simplified


  		




  
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mosaic_plot <- FALSE #PARAM14


  		




  
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day_to_mosaic <- c("19920102","19920103","19920103") #PARAM15


  		




  
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multiple_region <- TRUE #PARAM16


  		




  
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countries_shp <- "/nobackupp8/bparmen1/NEX_data/countries.shp" #PARAM17


  		




  
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#countries_shp <-"/data/project/layers/commons/NEX_data/countries.shp" #Atlas


  		




  
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plot_region <- TRUE  #PARAM18


  		




  
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threshold_missing_day <- c(367,365,300,200)#PARAM19


  		




  
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list_param_run_assessment_prediction <- list(in_dir1,region_name,y_var_name,interpolation_method,out_prefix,


  		




  
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                                  out_dir,create_out_dir_param,CRS_locs_WGS84,list_year_predicted,


  		




  
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                                  file_format,NA_flag_val,num_cores,plotting_figures,


  		




  
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                                  mosaic_plot,day_to_mosaic,multiple_region,countries_shp,plot_region)


  		




  
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list_names <- c("in_dir1","region_name","y_var_name","interpolation_method","out_prefix",


  		




  
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                                  "out_dir","create_out_dir_param","CRS_locs_WGS84","list_year_predicted",


  		




  
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                                  "file_format","NA_flag_val","num_cores","plotting_figures",


  		




  
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                                  "mosaic_plot","day_to_mosaic","multiple_region","countries_shp","plot_region")


  		




  
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names(list_param_run_assessment_prediction)<-list_names


  		




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  assessment_prediction_obj <- run_assessment_prediction_fun(i,list_param_run_assessment_prediction)


  		




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}


  		




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## Add stage 7 (mosaicing) here??


  		




  
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#i <- 1 #this select the first year of list_year_predicted


  		




  
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#if (stages_to_run[7]==7){


  		




  
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#  assessment_prediction_obj <- run_assessment_prediction_fun(i,list_param_run_assessment_prediction)


  		




  
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#}


  		




  
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###############   END OF SCRIPT   ###################


  		




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#####################################################


  		




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