Revision d7f715b5
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: 03/12/2013
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#DATE: 03/14/2013
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568-- |
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############# STAGE 3: Data preparation ############### |
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source(file.path(script_path,"Database_stations_covariates_processing_function_03052013.R"))
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source(file.path(script_path,"Database_stations_covariates_processing_function_03132013.R"))
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#Setting up input argurments for script 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<-c("2000","2001") #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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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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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_03052013" #User defined output prefix
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out_prefix<-"_365d_GAM_fus5_all_lstd_03142013" #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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names(list_param_prep)<-cnames |
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##### RUN SCRIPT TO GET STATION DATA WITH COVARIATES ##### |
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list_outfiles<-database_covaratiates_preparation(list_param_prep) |
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list_outfiles<-database_covariates_preparation(list_param_prep) |
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############### STAGE 4: RASTER PREDICTION ################# |
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infile_daily<-list_outfiles$daily_covar_ghcn_data #outfile3 from database_covar script |
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infile_locs<- list_outfiles$loc_stations_ghcn #outfile2? from database covar script |
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list_param_data_prep<-list(infile_monthly,infile_daily,infile_locs,infile_covariates,covar_names,var,out_prefix,CRS_locs_WGS84)
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#names(outfiles_obj)<- c("loc_stations","loc_stations_ghcn","daily_covar_ghcn_data","monthly_covar_ghcn_data")
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list_param_data_prep<-list(infile_monthly,infile_daily,infile_locs,infile_covariates,covar_names,var,out_prefix,CRS_locs_WGS84) |
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names(list_param_data_prep)<-c("infile_monthly","infile_daily","infile_locs","infile_covariates","covar_names","var","out_prefix","CRS_locs_WGS84")
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#Set additional parameters |
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step<-0 |
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constant<-0 #if value 1 then use the same samples as date one for the all set of dates |
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prop_minmax<-c(0.3,0.3) #if prop_min=prop_max and step=0 then predicitons are done for the number of dates... |
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infile_dates<-"list_365_dates_04212012.txt" |
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#dates_selected<-c("20100101","20100102","20100103","20100901") # Note that the dates set must have a specific format: yyymmdd
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dates_selected<-"" # if empty string then predict for the full year specified earlier |
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#Models to run...this can be change for each run |
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list_models<-c("y_var ~ s(elev_1)",
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#Collect all parameters in a list |
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list_param_raster_prediction<-list(list_param_data_prep, |
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seed_number,nb_sample,step,constant,prop_minmax,infile_dates,
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seed_number,nb_sample,step,constant,prop_minmax,dates_selected,
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list_models,lst_avg,in_path,out_path,script_path, |
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interpolation_method) |
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names(list_param_raster_prediction)<-c("list_param_data_prep",
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"seed_number","nb_sample","step","constant","prop_minmax","infile_dates",
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"seed_number","nb_sample","step","constant","prop_minmax","dates_selected",
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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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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03122013b.R"))
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03132013.R"))
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#Make the function call |
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raster_prediction_gam_fus_obj <-raster_prediction_gam_fusion(list_param_raster_prediction) |
Also available in: Unified diff
Master function, modification of date passing, run for tmax prediction for 2000 in Venezuela