Revision 9634f124
Added by Benoit Parmentier over 11 years ago
| climate/research/oregon/interpolation/master_script_temp.R | ||
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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: 04/05/2013
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#DATE: 04/21/2013
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568-- |
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#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_03192013.py |
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source(file.path(script_path,"covariates_production_temperatures_03212013.R")) |
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source(file.path(script_path,"Database_stations_covariates_processing_function_04042013.R")) |
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_04052013.R"))
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source(file.path(script_path,"results_interpolation_date_output_analyses_03272013.R"))
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_04162013.R"))
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#source(file.path(script_path,"results_interpolation_date_output_analyses_04162013.R"))
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#source(file.path(script_path,"results_covariates_database_stations_output_analyses_04012013.R")) |
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#FUNCTIONS CALLED FROM GAM FUSION ANALYSIS RASTER PREDICTION ARE FOUND IN...
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#FUNCTIONS CALLED FROM GAM ANALYSIS RASTER PREDICTION ARE FOUND IN... |
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source(file.path(script_path,"sampling_script_functions_03122013.R")) |
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source(file.path(script_path,"GAM_fusion_function_multisampling_04022013.R")) #Include GAM_CAI
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source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_03272013.R"))
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source(file.path(script_path,"GAM_fusion_function_multisampling_04162013.R")) #Include GAM_CAI
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source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_04162013.R"))
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############ STAGE 1: LST Climatology ############### |
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##Paths to inputs and output |
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var<-"TMAX" |
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#in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/"
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#out_path<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data/"
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in_path <-"/home/parmentier/Data/IPLANT_project/Oregon_interpolation/Oregon_03142013/input" |
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out_path<-"/home/parmentier/Data/IPLANT_project/Oregon_interpolation/Oregon_03142013/output"
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in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/"
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out_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data/"
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#in_path <-"/home/parmentier/Data/IPLANT_project/Oregon_interpolation/Oregon_03142013/input"
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#out_path <-"/home/parmentier/Data/IPLANT_project/Oregon_interpolation/Oregon_03142013/output"
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lc_path<-"/home/layers/data/land-cover/lc-consensus-global" |
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infile_elev<-"/home/layers/data/terrain/dem-cgiar-srtm-1km-tif/srtm_1km.tif" #this is the global file: replace later with the input produced by the DEM team |
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infile_canheight<-"/home/layers/data/land-cover/treeheight-simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif" #Canopy height |
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#list_tiles_modis <- c('h11v08','h11v07','h12v07','h12v08','h10v07','h10v08') #tile for Venezuel and surrounding area
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list_tiles_modis <- c("h08v04","h09v04") #tiles for Oregon
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list_tiles_modis <- c('h11v08','h11v07','h12v07','h12v08','h10v07','h10v08') #tile for Venezuel and surrounding area
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#list_tiles_modis <- c("h08v04","h09v04") #tiles for Oregon
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#infile_reg_outline="" #input region outline defined by polygon: none for Venezuel
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infile_reg_outline <- "OR83M_state_outline.shp" #input region outline defined by polygon: Oregon |
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infile_reg_outline="" #input region outline defined by polygon: none for Venezuel |
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#infile_reg_outline <- "OR83M_state_outline.shp" #input region outline defined by polygon: Oregon
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#CRS_interp<-"+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs";
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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_interp<-"+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs"; |
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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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out_region_name<-"_oregon_region" #generated on the fly
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out_suffix<-"_OR_04042013"
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#ref_rast_name<-"" #local raster name defining resolution, exent, local projection--. set on the fly??
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ref_rast_name<-"mean_day244_rescaled.rst" #local raster name defining resolution, exent: oregon |
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out_region_name<-"_venezuela_region" #generated on the fly
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out_suffix<-"_VE_04162013"
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ref_rast_name<-"" #local raster name defining resolution, exent, local projection--. set on the fly?? |
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#ref_rast_name<-"mean_day244_rescaled.rst" #local raster name defining resolution, exent: oregon
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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_s","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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lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10") #use older version for continuity check to be changed
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lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12")
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#lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10") #use older version for continuity check to be changed
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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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#set up earlier |
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#var <- "TMIN" # name of the variables to keep: TMIN, TMAX or PRCP --already set up earlier |
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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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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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#infile_covariates<-"covariates__venezuela_region_TMIN__VE_03192013.tif" #covariates stack for TMIN |
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infile_covariates<- "covariates_Oregon_region_TMAX__OR_04052013.tif" #Oregon covar TMAX from earlier codes...for continuity |
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#infile_covariates<- "covariates_Oregon_region_TMAX__OR_04052013.tif" #Oregon covar TMAX from earlier codes...for continuity
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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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#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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#CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84: same as earlier
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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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#infile_reg_outline <- "OR83M_state_outline.shp" #input region outline defined by polygon: Oregon |
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infile1 <-"OR83M_state_outline.shp" #remove this parameter!!! |
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#infile1 <-"OR83M_state_outline.shp" #remove this parameter!!!
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#covar_names see stage 2 |
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range_years_clim<-c("2000","2011") #right bound not included in the range!!
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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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#in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
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out_prefix<-"_365d_GAM_fus5_all_lstd_04042013" #User defined output prefix
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#qc_flags_stations<-c("0","S") #flags allowed for screening after the query from the GHCND??
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qc_flags_stations<-c("0") #flags allowed for screening after the query from the GHCND??
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out_prefix<-"_365d_GAM_CAI_all_lst_04162013" #User defined output prefix
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qc_flags_stations<-c("0","S") #flags allowed for screening after the query from the GHCND??
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#qc_flags_stations<-c("0") #flags allowed for screening after the query from the GHCND??
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#list of 12 parameters for input in the function... |
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"y_var ~ s(lat) + s(lon)+ s(elev_s)", |
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"y_var ~ s(lat,lon,elev_s)", |
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"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST)", |
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"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST) + s(LC1)",
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"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST) + s(LC2)",
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"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST) + s(LC2)",
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"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST) + s(LC6)",
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"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST) + s(DISTOC)") |
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#Choose interpolation method... |
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interpolation_method<-c("gam_fusion","gam_CAI") #other otpions to be added later
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#interpolation_method<-c("gam_fusion","gam_CAI") #other otpions to be added later
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interpolation_method<-c("gam_CAI") #other otpions to be added later
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#Default name of LST avg to be matched |
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lst_avg<-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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"interpolation_method") |
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#Make the function call--names to be change to raster_prediction_obj and raster_prediction_fun |
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raster_prediction_gam_fus_obj <-raster_prediction_gam_fusion(list_param_raster_prediction) |
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raster_prediction_obj <-raster_prediction_fun(list_param_raster_prediction) |
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############## STAGE 5: OUTPUT ANALYSES ################## |
Also available in: Unified diff
master script adding GAM CAI method and parameters for Venezuela region