Files in Burke-Lauenroth-Lab/SoilWat_R_Wrapper
Simulation Framework for SOILWAT2
.Rbuildignore
.appveyor_clear_cache.txt
.gitattributes
.gitignore
.lintr
.travis.yml
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
R/Aggregation_Functions.R
R/ExtractData_ClimateDownscaling.R
R/ExtractData_Elevation.R
R/ExtractData_MeanMonthlyClimate.R
R/ExtractData_Soils.R
R/IO_databases.R
R/IO_datafiles.R
R/Indices.R
R/Mathematical_Functions.R
R/Miscellaneous_Functions.R
R/OutputDatabase.R
R/OutputDatabase_DataAccess.R
R/OutputDatabase_Ensembles.R
R/Parallel.R
R/PriorCalculations.R
R/RandomNumberGenerator.R
R/Simulation_Project.R
R/Simulation_Run.R
R/Soils_Functions.R
R/Spatial_Functions.R
R/Status_Trackers.R
R/Synchronicity.R
R/Testproject_Functions.R
R/Time_SimulationWorld.R
R/Timing_Calls.R
R/WeatherDB.R
R/WeatherDB_Check.R
R/WorkDatabase.R
R/netCDF_prepare_climatedata_files.R
R/rSFSW2-package.R
R/rSOILWAT2_DataAccess.R
R/sysdata.rda
R/upgraders.R
R/zzz.R
README.md
appveyor.yml
data-raw/1_Input/SWRuns_InputData_ExperimentalDesign_v10.csv
data-raw/1_Input/SWRuns_InputData_SoilLayers_v9.csv
data-raw/1_Input/SWRuns_InputData_TreatmentDesign_v18.csv
data-raw/1_Input/SWRuns_InputMaster_YOURPROJECT_v12.csv
data-raw/1_Input/datafiles/SWRuns_InputData_ClimateScenarios_Change_v11.csv
data-raw/1_Input/datafiles/SWRuns_InputData_ClimateScenarios_Values_v11.csv
data-raw/1_Input/datafiles/SWRuns_InputData_cloud_v10.csv
data-raw/1_Input/datafiles/SWRuns_InputData_prod_v11.csv
data-raw/1_Input/datafiles/SWRuns_InputData_siteparam_v15.csv
data-raw/1_Input/datafiles/SWRuns_InputData_soils_v12.csv
data-raw/1_Input/datafiles/SWRuns_InputData_weathersetup_v10.csv
data-raw/1_Input/regeneration/ArtemisiaTridentataNotSpecifiedSubspecies.csv
data-raw/1_Input/treatments/LookupCO2data/AtmosCO2.csv
data-raw/1_Input/treatments/LookupCO2data/README.txt
data-raw/1_Input/treatments/LookupClimatePPT/climate_ppt.csv
data-raw/1_Input/treatments/LookupClimateTemp/climate_temp.csv
data-raw/1_Input/treatments/LookupEvapCoefs/EvaporationCoefs_v2.csv
data-raw/1_Input/treatments/LookupShiftedPPT/shifted_ppt.csv
data-raw/1_Input/treatments/LookupSnowDensity/SnowDensities_v2.csv
data-raw/1_Input/treatments/LookupTranspCoefs/TranspirationCoefs_v2.csv
data-raw/1_Input/treatments/LookupTranspRegions/TranspirationRegions.csv
data-raw/1_Input/treatments/LookupVegBiomass/Vegetation_MeanMonthly_v5.csv
data-raw/1_Input/treatments/LookupWeatherFolder/Weather_Test/weath.2010
data-raw/1_Input/treatments/tr_cloudin/climate.in
data-raw/1_Input/treatments/tr_prodin/veg.in
data-raw/1_Input/treatments/tr_siteparamin/siteparam.in
data-raw/1_Input/treatments/tr_soilsin/soils.in
data-raw/1_Input/treatments/tr_weathersetupin/weathsetup.in
data-raw/prepare_default_project_infrastructure.R
data-raw/update_test_project_infrastructure.R
demo/00Index
demo/SFSW2_project_code.R
demo/SFSW2_project_descriptions.R
demo/SFSW2_project_settings.R
demo/SFSW2_project_xMaintenance_dbOutputTemp.R
inst/WORDLIST
man/ExtractClimateChangeScenarios.Rd
man/ExtractClimateWizard.Rd
man/ExtractData_Elevation.Rd
man/ExtractData_MeanMonthlyClimate.Rd
man/ExtractData_Soils.Rd
man/ExtractDayMet.Rd
man/ExtractGriddedDailyWeatherFromMaurer2002_NorthAmerica.Rd
man/ExtractGriddedDailyWeatherFromNRCan_10km_Canada.Rd
man/GriddedDailyWeatherFromNCEPCFSR_Global.Rd
man/ISRICWISE_extract_SUIDs.Rd
man/PrepareClimateScenarios.Rd
man/SFSW2_read_csv.Rd
man/SFSW2_read_inputfile.Rd
man/add_delta_to_PPT.Rd
man/add_granular_dbWork.Rd
man/add_status_dbWork.Rd
man/adjust.WindspeedHeight.Rd
man/adjustLayersDepth.Rd
man/align_with_target_grid.Rd
man/align_with_target_res.Rd
man/applyDeltas.Rd
man/applyPPTdelta_detailed.Rd
man/applyPPTdelta_simple.Rd
man/assign_aggregation_soillayers.Rd
man/calcDeltas.Rd
man/calc_BareSoilEvapCoefs.Rd
man/calc_DailyScenarioWeather.Rd
man/calc_Days_withLoweredPPT.Rd
man/calc_MonthlyScenarioWeather.Rd
man/calc_RequestedSoilLayers.Rd
man/calc_cell_ISRICWISE.Rd
man/calc_drylandindices.Rd
man/calc_timeSlices.Rd
man/check_aggregated_output.Rd
man/check_cltool.Rd
man/check_dbWeather_version.Rd
man/check_intracker_design.Rd
man/check_outputDB_completeness.Rd
man/check_rSFSW2_project_input_data.Rd
man/check_rSW2_version.Rd
man/check_soilco.Rd
man/check_weatherDB.Rd
man/clean_SFSW2_cluster.Rd
man/clean_worker.Rd
man/climscen_determine_sources.Rd
man/climscen_metadata.Rd
man/compare_test_output.Rd
man/compare_two_dbOutput.Rd
man/compile_overall_timer.Rd
man/controlExtremePPTevents.Rd
man/create_dbWork.Rd
man/crs_units.Rd
man/dbConnect2.Rd
man/dbExecute2.Rd
man/dbOut_check_values.Rd
man/dbOut_read_variables_from_scenario.Rd
man/dbOut_update_values.Rd
man/dbOutput_ListDesignTables.Rd
man/dbOutput_ListInternalTables.Rd
man/dbOutput_ListOutputTables.Rd
man/dbOutput_Tables_have_SoilLayers.Rd
man/dbOutput_add_calculated_field.Rd
man/dbOutput_subset.Rd
man/dbOutput_update_OverallAggregationTable.Rd
man/dbVacuumRollack.Rd
man/dbWork_Ntodo.Rd
man/dbWork_agg_timing.Rd
man/dbWork_check_design.Rd
man/dbWork_check_granular.Rd
man/dbWork_check_run.Rd
man/dbWork_check_status.Rd
man/dbWork_checkpoint.Rd
man/dbWork_clean.Rd
man/dbWork_redo.Rd
man/dbWork_report_completion.Rd
man/dbWork_timing.Rd
man/dbWork_todos.Rd
man/dbWork_update_IncludeYN.Rd
man/dbWork_update_granular.Rd
man/dbWork_update_job.Rd
man/dbWork_update_status.Rd
man/delete_test_output.Rd
man/determine_simulation_size.Rd
man/dir_safe_create.Rd
man/doQmapQUANT.Rd
man/do_OneSite.Rd
man/do_compare_nc.Rd
man/do_prior_TableLookups.Rd
man/downscale.Rd
man/downscale.delta.Rd
man/downscale.deltahybrid.Rd
man/downscale.deltahybrid3mod.Rd
man/downscale.periods.Rd
man/downscale.raw.Rd
man/dw_determine_sources.Rd
man/enable_debug_dump.Rd
man/exit_SFSW2_cluster.Rd
man/export_objects_to_workers.Rd
man/extract_SFSW2_cells_from_raster.Rd
man/extract_SFSW2_cells_from_shp.Rd
man/extract_SFSW2_points_from_shp.Rd
man/extract_blocks.Rd
man/extract_climate_NCEPCFSR.Rd
man/extract_daily_weather_from_gridMET.Rd
man/extract_daily_weather_from_livneh.Rd
man/extract_from_external_raster_old.Rd
man/extract_rSFSW2.Rd
man/extract_soil_CONUSSOIL.Rd
man/extract_soil_ISRICWISE.Rd
man/find_gridMET_files.Rd
man/find_sites_with_bad_weather.Rd
man/fix_PPTdata_length.Rd
man/gather_objects_for_export.Rd
man/generate_OverallAggregation_fields.Rd
man/generate_RNG_streams.Rd
man/get.SeveralOverallVariables.Rd
man/get.SeveralOverallVariables_Ensemble.Rd
man/get.SeveralOverallVariables_Scenario.Rd
man/get.SeveralOverallVariables_Scenario_old.Rd
man/get.Table.Rd
man/get.Table_Ensemble.Rd
man/get.Table_Scenario.Rd
man/get_BareSoilEvapCoefs.Rd
man/get_DailyGCMdata_netCDF.Rd
man/get_GCMdata_NEX.Rd
man/get_MonthlyGCMdata_netCDF.Rd
man/get_Pid_from_temptxt.Rd
man/get_SoilLayerID_from_temptxt.Rd
man/get_fieldnames.Rd
man/get_fnames_dbTempOut.Rd
man/get_fnames_temporaryOutput.Rd
man/get_nc_time_axis.Rd
man/get_simulation_time.Rd
man/get_tablename_from_temptxt.Rd
man/global_args_do_OneSite.Rd
man/gridMET_download_and_check.Rd
man/gridMET_metadata.Rd
man/has_NAs_pooled_at_depth.Rd
man/indices.Rd
man/init_SFSW2_cluster.Rd
man/init_intracker.Rd
man/init_rSFSW2_project.Rd
man/init_timer.Rd
man/is_project_script_file_recent.Rd
man/isdone_intracker.Rd
man/list.dbTables.Rd
man/list.dbVariables.Rd
man/list.dbVariablesOfAllTables.Rd
man/load_preprocessed_inputs.Rd
man/load_project_description.Rd
man/local_weatherDirName.Rd
man/make_dbOutput.Rd
man/make_dbW.Rd
man/make_test_output_reference.Rd
man/merge_2soils.Rd
man/missing_Pids_outputDB.Rd
man/move_dbTempOut_to_dbOut.Rd
man/move_output_to_dbOutput.Rd
man/move_temporary_to_outputDB.Rd
man/mpi_last.Rd
man/mpi_work.Rd
man/obtain_CMIP5_MACAv2metdata_USA.Rd
man/populate_rSFSW2_project_with_data.Rd
man/pragmas.Rd
man/prepare_ExtractData_Soils.Rd
man/prepare_climatedata_netCDFs.Rd
man/process_inputs.Rd
man/quickprepare_dbOutput_dbWork.Rd
man/rSFSW2.Rd
man/rbind_2cols_nonoverlapping.Rd
man/read_SOILWAT2_DefaultInputs.Rd
man/read_time_netCDF.Rd
man/reaggregate_raster.Rd
man/reaggregate_shapefile.Rd
man/reconstitute_inputfile.Rd
man/recreate_dbWork.Rd
man/remove_from_onexit_expression.Rd
man/res_to_polygons.Rd
man/run_simulation_experiment.Rd
man/run_test_projects.Rd
man/save_to_rds_with_backup.Rd
man/select_suitable_CFs.Rd
man/set_RNG_stream.Rd
man/set_full_RNG.Rd
man/set_glovar.Rd
man/set_options_warn_error.Rd
man/setup_RNG.Rd
man/setup_SFSW2_cluster.Rd
man/setup_dbWork.Rd
man/setup_rSFSW2_project_infrastructure.Rd
man/setup_spatial_simulation.Rd
man/setup_time_simulation_project.Rd
man/simulate_SOILWAT2_experiment.Rd
man/swOutput_access.Rd
man/synchronicity.Rd
man/todo_intracker.Rd
man/trewartha_climate.Rd
man/tryToGet_ClimDB.Rd
man/try_MonthlyScenarioWeather.Rd
man/try_cell_ISRICWISE.Rd
man/update_actions.Rd
man/update_intracker.Rd
man/update_runIDs_sites_by_dbW.Rd
man/update_todos.Rd
man/upgrade_datafile.Rd
man/vp0.Rd
man/vpd.Rd
man/weighted.agg.Rd
man/whereNearest.Rd
src/.gitignore
src/init.c
src/ncepcfsr_convert.c
tests/test_data/0_ReferenceOutput/dbOutput_TestPrj4_v4.3.0.sqlite3
tests/test_data/SWRuns_InputData_test.csv
tests/test_data/SWRuns_InputData_test1.rds
tests/test_data/SWRuns_InputData_test2.rds
tests/test_data/TestPrj4/1_Input/SWRuns_InputData_ExperimentalDesign_v10.csv
tests/test_data/TestPrj4/1_Input/SWRuns_InputData_SoilLayers_v9.csv
tests/test_data/TestPrj4/1_Input/SWRuns_InputData_TreatmentDesign_v18.csv
tests/test_data/TestPrj4/1_Input/SWRuns_InputMaster_Test_v12.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_ClimateScenarios_Change_v11.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_ClimateScenarios_Values_v11.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_cloud_v10.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_prod_v11.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_siteparam_v15.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_soils_v12.csv
tests/test_data/TestPrj4/1_Input/datafiles/SWRuns_InputData_weathersetup_v10.csv
tests/test_data/TestPrj4/1_Input/dbWeatherData3.sqlite3
tests/test_data/TestPrj4/1_Input/regeneration/ArtemisiaTridentataNotSpecifiedSubspecies.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupCO2data/AtmosCO2.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupCO2data/README.txt
tests/test_data/TestPrj4/1_Input/treatments/LookupClimatePPT/climate_ppt.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupClimateTemp/climate.temp.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupClimateTemp/climate_temp.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupEvapCoefs/EvaporationCoefs_v2.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupShiftedPPT/shifted_ppt.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupSnowDensity/SnowDensities_v2.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupTranspCoefs/TranspirationCoefs_v2.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupTranspRegions/TranspirationRegions.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupVegBiomass/Vegetation_MeanMonthly_v5.csv
tests/test_data/TestPrj4/1_Input/treatments/LookupWeatherFolder/Weather_Test/weath.2010
tests/test_data/TestPrj4/1_Input/treatments/tr_cloudin/climate.in
tests/test_data/TestPrj4/1_Input/treatments/tr_prodin/veg.in
tests/test_data/TestPrj4/1_Input/treatments/tr_siteparamin/siteparam.in
tests/test_data/TestPrj4/1_Input/treatments/tr_soilsin/soils.in
tests/test_data/TestPrj4/1_Input/treatments/tr_weathersetupin/weathsetup.in
tests/test_data/TestPrj4/SFSW2_project_code.R
tests/test_data/TestPrj4/SFSW2_project_descriptions.R
tests/test_data/TestPrj4/SFSW2_project_settings.R
tests/test_data/TestPrj4/SFSW2_project_xMaintenance_dbOutputTemp.R
tests/test_data/dailySW.rds
tests/test_data/test_reference_applyPPTdelta_detailed_01.rds
tests/test_data/test_reference_applyPPTdelta_detailed_02.rds
tests/test_data/test_reference_applyPPTdelta_detailed_03.rds
tests/test_data/test_reference_applyPPTdelta_detailed_04.rds
tests/test_data/test_reference_applyPPTdelta_detailed_05.rds
tests/test_data/test_reference_applyPPTdelta_detailed_06.rds
tests/testthat.R
tests/testthat/helper_testthat.R
tests/testthat/setup_testthat.R
tests/testthat/teardown_testthat.R
tests/testthat/test_CO2.R
tests/testthat/test_ExtractData_ClimateDownscaling.R
tests/testthat/test_IO_SWSFinputfiles.R
tests/testthat/test_OutputDatabase.R
tests/testthat/test_OutputDatabase_DataAccess.R
tests/testthat/test_Status_Trackers.R
tests/testthat/test_Time_SimulationWorld.R
tests/testthat/test_WeatherDB_DayMet.R
tests/testthat/test_action_check.R
tests/testthat/test_dbWork.R
tests/testthat/test_downscaling_add_delta_to_PPT.R
tests/testthat/test_downscaling_applyPPTdelta.R
tests/testthat/test_downscaling_fix_PPTdata_length.R
tests/testthat/test_downscaling_quantile_mapping.R
tests/testthat/test_indices.R
tests/testthat/test_netCDF_functions.R
tests/testthat/test_projects.R
tests/testthat/test_rSFSW2_CodeStylePractices.R
tests/testthat/test_rSFSW2_Spelling.R
tests/testthat/test_soil_functions.R
tools/Database_Stuff/DBdumpTables.R
tools/Database_Stuff/DBdumpTables_EverythingInItsOwnSubFolder.R
tools/Database_Stuff/Database_Overhaul/DatabaseDesign/Database_Design.mwb
tools/Database_Stuff/Database_Overhaul/DatabaseDesign/Database_Design.mwb.bak
tools/Database_Stuff/Database_Overhaul/dbDesign.pdf
tools/Database_Stuff/Explanation_output_variables_overall_aggregation.xlsx
tools/Database_Stuff/Primer_SQLdatabase.docx
tools/Database_Stuff/Primer_SQLdatabase_v2.docx
tools/Rwrapper_Explanations/2_SWSF_p0of5_Notes_v51.R
tools/Rwrapper_Explanations/SoilDataInputLocationTracker.odt
tools/Scripts_Miscellaneous/ClimScen_ConvertCSV_fromV10ToV11.R
tools/Scripts_Miscellaneous/WeatherDatabase_Conversion_OldToNew.R
tools/Scripts_Miscellaneous/Windows_ScriptToRunRWrapper.bat
tools/Scripts_Miscellaneous/ncepcfsr/cfsr_convert.c
tools/Scripts_Miscellaneous/ncepcfsr/chopGrib.R
tools/Scripts_Miscellaneous/ncepcfsr/filefuncs2.c
tools/Scripts_Miscellaneous/ncepcfsr/filefuncs2.h
tools/Scripts_Miscellaneous/ncepcfsr/generic2.c
tools/Scripts_Miscellaneous/ncepcfsr/generic2.h
tools/Scripts_Miscellaneous/ncepcfsr/myMemory2.h
tools/Scripts_Miscellaneous/ncepcfsr/mymemory2.c
tools/rhub_package_checks.R
vignettes/rSFSW2_FAQs.Rmd
