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Revision 1230ccc6

Added by Benoit Parmentier over 11 years ago

data preparation, addtional modifications to allow for Oregon and any regions

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climate/research/oregon/interpolation/Database_stations_covariates_processing_function.R
27 27 
  #6) monthly_covar_ghcn_data: ghcn monthly averaged data with covariates for the year range of interpolation (locally projected)
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  #AUTHOR: Benoit Parmentier
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  #DATE: 03/28/2013
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  #DATE: 04/05/2013
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  #PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363--
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  #Comments and TODO
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  #-Add buffer option...
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  #-Add output path argument option
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  #-Add qc flag options
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  #-Add screening for value predicted: var
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  ##################################################################################################
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  ###Loading R library and packages: should it be read in before???
......
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  coordinates(dat_stat)<-coords
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  proj4string(dat_stat)<-CRS_locs_WGS84 #this is the WGS84 projection
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  #proj4string(dat_stat)<-CRS_interp
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  dat_stat2<-spTransform(dat_stat,CRS(CRS_interp))         # Project from WGS84 to new coord. system
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  interp_area_WGS84 <-spTransform(interp_area,CRS_locs_WGS84)         # Project from WGS84 to new coord. system
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  # Spatial query to find relevant stations
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  inside <- !is.na(over(dat_stat2, as(interp_area, "SpatialPolygons")))  #Finding stations contained in the current interpolation area
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  stat_reg<-dat_stat2[inside,]              #Selecting stations contained in the current interpolation area
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  inside <- !is.na(over(dat_stat, as(interp_area_WGS84, "SpatialPolygons")))  #Finding stations contained in the current interpolation area
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  stat_reg<-dat_stat[inside,]              #Selecting stations contained in the current interpolation area
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  ####
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  ##TODO: Add buffer option?
......
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  data_d <-data_reg  #data_d: daily data containing the query without screening
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  #data_reg <-subset(data_d,mflag=="0" | mflag=="S") #should be input arguments!!
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  data_reg <-subset(data_d,mflag==qc_flags_stations[1] | mflag==qc_flags_stations[2]) #screening using flags
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  #Transform the query to be depending on the number of flags
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  data_reg <-subset(data_d, mflag %in% qc_flags_stations) #screening using flags
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  #data_reg2 <-subset(data_d,mflag==qc_flags_stations[1] | mflag==qc_flags_stations[2]) #screening using flags
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  ##################################################################
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  ### STEP 3: Save results and outuput in textfile and a shape file
......
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  #In Venezuela and other regions where there are not many stations...mflag==S should be added..see Durenne etal.2010.
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  228
  
  
    
  #d<-subset(data_m,mflag=="0" | mflag=="S") #should be input arguments!!


  		




  229
  
  
    
  d<-subset(data_m,mflag==qc_flags_stations[1] | mflag==qc_flags_stations[2])


  		




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  #May need some screeing??? i.e. range of temp and elevation...


  		




  
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  #d<-subset(data_m,mflag==qc_flags_stations[1] | mflag==qc_flags_stations[2])


  		




  
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  d<-subset(data_m,mflag %in% qc_flags_stations)


  		




  
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  #Add screening here ...May need some screeing??? i.e. range of temp and elevation...


  		




  
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  d1<-aggregate(value~station+month, data=d, mean)  #Calculate monthly mean for every station in OR


  		




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  #d2<-aggregate(value~station+month, data=d, length)  #Calculate monthly mean for every station in OR


  		




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  is_not_na_fun<-function(x) sum(!is.na(x)) #count the number of available observation


  		




  ......




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  stations_val<-extract(s_raster,dst_month,df=TRUE)  #extraction of the information at station location in a data frame


  		




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  #dst_extract<-spCbind(dst_month,stations_val) #this is in sinusoidal from the raster stack


  		




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  dst_extract<-cbind(dst_month,stations_val) #this is in sinusoidal from the raster stack


  		




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  dst<-dst_extract


  		




  
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  dst<-dst_extract #problem!!! two column named elev!!! use elev_s??


  		




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  #browser()


  		




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  coords<- dst[c('x','y')]              #Define coordinates in a data frame, this is the local x,y


  		




  ......




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  dst<-dst[index,]


  		




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  coords<- dst[c('x','y')]              #Define coordinates in a data frame, this is the local x,y


  		




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  coordinates(dst)<-coords                    #Assign coordinates to the data frame


  		




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  proj4string(dst)<-projection(s_raster)        #Assign coordinates reference system in PROJ4 format


  		




  
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  proj4string(dst)<-CRS_interp        #Assign coordinates reference system in PROJ4 format


  		




  
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  ### ADD SCREENING HERE BEFORE WRITING OUT DATA


  		




  
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  #Covariates ok since screening done in covariate script


  		




  
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  #screening on var i.e. value, TMIN, TMAX...


  		




  
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  ####


  		




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  ####


  		




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  #write out a new shapefile (including .prj component)


  		












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