Revision 5dd036ba
Added by Benoit Parmentier over 11 years ago
| climate/research/oregon/interpolation/Database_stations_extraction_raster_covariates_processing.R | ||
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################## Data preparation for interpolation ####################################### |
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############################ Extraction of station data ########################################## |
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### Parameters and arguments for the function |
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db.name <- "ghcn" #name of the Postgres database |
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var <- "TMAX" #name of the variables to keep: TMIN, TMAX or PRCP |
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range_years<-c("2010","2011") #right bound not included in the range!!
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range_years_clim<-c("2000","2011") #right bound not included in the range!!
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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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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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infile3<-"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script |
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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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in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
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out_prefix<-"_365d_GAM_fus5_all_lstd_03012013" #User defined output prefix |
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#qc_flags<- flags allowe for the query from the GHCND?? |
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#The names of covariates can be changed...these names should be output/input from 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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#list of 11 parameters for input in the function... |
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list_param_prep<-list(db.name,var,range_years,range_years_clim,infile1,infile2,infile3,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","infile3","CRS_locs_WGS84","in_path","covar_names","out_prefix")
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names(list_param_prep)<-cnames |
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database_covaratiates_preparation<-function(list_param_prep){
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#This function performs queries on the Postgres ghcnd database for stations matching the |
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# 4) range_years_clim: range of records used in the monthly climatology interpolation, note that upper bound is not included |
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# 5) infile1: region outline as a shape file - used in the interpolation stage too |
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# 6) infile2: ghcnd stations locations as a textfile name with lat-long fields |
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# 7) infile3: tif file of raser covariates for the interpolation area: it should have a local projection
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# 7) infile_covarariates: tif file of raser covariates for the interpolation area: it should have a local projection
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# 8) CRS_locs_WGS84: longlat EPSG 4326 used as coordinates reference system (proj4)for stations locations |
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# 9) in_path: input path for covariates data and other files, this is also the output? |
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# 10) covar_names: names of covariates used for the interpolation --may be removed later? (should be stored in the brick) |
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year_start_clim <-list_param_prep$range_years_clim[1] #right bound not included in the range!! starting year for monthly query to calculate clime |
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infile1<- list_param_prep$infile1 #This is the shape file of outline of the study area #It is an input/output of the covariate script |
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infile2<-list_param_prep$infile2 #"/home/layers/data/climate/ghcn/v2.92-upd-2012052822/ghcnd-stations.txt" #This is the textfile of station locations from GHCND |
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infile3<-list_param_prep$infile3 #"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script
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infile3<-list_param_prep$infile_covariates #"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script
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CRS_locs_WGS84<-list_param_prep$CRS_locs_WGS84 #Station coords WGS84: same as earlier |
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in_path <- list_param_prep$in_path #CRS_locs_WGS84"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
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out_prefix<-list_param_prep$out_prefix #"_365d_GAM_fus5_all_lstd_03012013" #User defined output prefix |
Also available in: Unified diff
Data preparation, moving input parameters, call from other script