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Revision d95d4617

Added by Benoit Parmentier over 11 years ago

covariates, fixing screening function to remove extreme values

View differences:

climate/research/oregon/interpolation/covariates_production_temperatures.R
180 180 
  tab_range <- strsplit(tab_range_list,",")
181 181 
  tab_range <-as.data.frame(do.call(rbind, tab_range))
182 182 
  names(tab_range)<-c("varname","vmin","vmax")
183 
  tab_range$vmin <- as.numeric(tab_range$vmin)
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  tab_range$vmax <- as.numeric(tab_range$vmax)
183 
  tab_range$vmin <- as.numeric(as.character(tab_range$vmin)) #transform to character first to avoid values being considered as factor
184 
  tab_range$vmax <- as.numeric(as.character(tab_range$vmax))
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  tab_range$varname <- as.character(tab_range$varname)
185 186 
  val_rst<-vector("list",nrow(tab_range)) #list of one row data.frame
186 187
187 188 
  for (k in 1:nrow(tab_range)){
......
196 197 
  }
197 198 
  #could be taken out of function for parallelization
198 199 
  s_rst_m<-stack(val_rst) #This a raster stack with valid range of values
199 
  retained_names<-setdiff(names(r_stack),as.character(tab_range$varname))
200 
  retained_names<-setdiff(names(r_stack),tab_range$varname)
200 201 
  r_stack <- dropLayer(r_stack,match(tab_range$varname,names(r_stack)))
201 202 
  names(r_stack) <-retained_names
202 203 
  r_stack <- addLayer(r_stack,s_rst_m) #add back layers that were screened out
......
539 540 
  #covar_names<-c(rnames,lc_names,lst_names)
540 541 
  names(s_raster)<-covar_names
541 542
542 
  ##Write function to screen data values...
543 
  #add screening here...
544 
  #browser()
545 
  #test <-screening_val_r_stack_fun(list_val_range,s_raster)
543 
  #Screen values given valid value ranges for specified variables
546 544 
  s_raster<-screening_val_r_stack_fun(list_val_range,s_raster)
547 545
548 546 
  #Write out stack of number of change
climate/research/oregon/interpolation/master_script_temp.R
45 45 

  		




  46
  46
  
    
##SCRIPT USED FOR THE PREDICTIONS: Source or list all scripts here to avoid confusion on versions being run!!!!


  		




  47
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  48
  
  
    
#source(file.path(script_path,"master_script_temp_06082013.R")) #Master script can be run directly...


  		




  
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#source(file.path(script_path,"master_script_temp_06272013.R")) #Master script can be run directly...


  		




  49
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  50
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#CALLED FROM MASTER SCRIPT:


  		




  51
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  ......




  53
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clim_script <- file.path(script_path,"climatology_05312013.py") # LST climatology python script


  		




  54
  54
  
    
grass_setting_script <- file.path(script_path,"grass-setup.R") #Set up system shell environment for python+GRASS


  		




  55
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source(file.path(script_path,"download_and_produce_MODIS_LST_climatology_05302013.R"))


  		




  56
  
  
    
source(file.path(script_path,"covariates_production_temperatures_06202013.R"))


  		




  
  56
  
    
source(file.path(script_path,"covariates_production_temperatures_06272013.R"))


  		




  57
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source(file.path(script_path,"Database_stations_covariates_processing_function_05212013.R"))


  		




  58
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_06082013.R"))


  		




  59
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source(file.path(script_path,"results_interpolation_date_output_analyses_06102013.R"))


  		




  60
  
  
    
#source(file.path(script_path,"results_covariates_database_stations_output_analyses_04012013.R"))


  		




  
  60
  
    
#source(file.path(script_path,"results_covariates_database_stations_output_analyses_04012013.R")) #to be completed


  		




  61
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  62
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#FUNCTIONS CALLED FROM GAM ANALYSIS RASTER PREDICTION ARE FOUND IN...


  		




  63
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  ......




  134
  134
  
    
               "nobs_09","nobs_10","nobs_11","nobs_12")


  		




  135
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covar_names<-c(rnames,lc_names,lst_names)


  		




  136
  136
  
    
  


  		




  137
  
  
    
list_val_range <-c("lon,180,180","lat,-90,90","N,-1,1","E,-1,1","N_w,-1,1","E_w,-1,1","elev_s,0,6000","slope,0,90",


  		




  
  137
  
    
list_val_range <-c("lon,-180,180","lat,-90,90","N,-1,1","E,-1,1","N_w,-1,1","E_w,-1,1","elev_s,0,6000","slope,0,90",


  		




  138
  138
  
    
                   "aspect,0,360","DISTOC,-0,10000000","CANHEIGHT,0,255","LC1,0,100","LC3,0,100","mm_01,-15,50",


  		




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                   "mm_02,-15,50","mm_03,-15,50","mm_04,-15,50","mm_05,-15,50","mm_06,-15,50","mm_07,-15,50",


  		




  140
  140
  
    
                   "mm_08,-15,50","mm_09,-15,50","mm_10,-15,50","mm_11,-15,50","mm_12,-15,50")


  		












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