Files in Burke-Lauenroth-Lab/rSFSW2
Simulation Framework for SOILWAT2

.Rbuildignore
.appveyor_clear_cache.txt
.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/GISSM.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_Ensembles.R R/Parallel.R R/Pedotransfer_Functions.R R/PriorCalculations.R R/RandomNumberGenerator.R R/RcppExports.R R/Simulation_Project.R R/Simulation_Run.R R/SoilMTRegimes.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/Vegetation.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_v09.csv
data-raw/1_Input/SWRuns_InputData_SoilLayers_v9.csv
data-raw/1_Input/SWRuns_InputData_TreatmentDesign_v17.csv
data-raw/1_Input/SWRuns_InputMaster_YOURPROJECT_v11.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_v14.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/cloud.in
data-raw/1_Input/treatments/tr_prodin/prod.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/SMR_logic.Rd man/STMR.Rd man/STR_logic.Rd man/SeedlingRootingDepth.Rd man/SoilLayer_at_SoilDepth.Rd man/TranspCoeffByVegType.Rd man/add_delta_to_PPT.Rd man/add_granular_dbWork.Rd man/add_layer_to_soil.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/biomass.Rd man/calc.ScenarioWeather.Rd man/calcDeltas.Rd man/calc_BareSoilEvapCoefs.Rd man/calc_Days_withLoweredPPT.Rd man/calc_DurationFavorableConds.Rd man/calc_RequestedSoilLayers.Rd man/calc_SeedlingMortality.Rd man/calc_SiteClimate.Rd man/calc_TimeToGerminate.Rd man/calc_cell_ISRICWISE.Rd man/calc_drylandindices.Rd man/calc_timeSlices.Rd man/check_SuitableGrowthThisYear.Rd man/check_aggregated_output.Rd man/check_cltool.Rd man/check_dbWeather_version.Rd man/check_intracker_design.Rd man/check_monotonic_increase.Rd man/check_outputDB_completeness.Rd man/check_rSFSW2_project_input_data.Rd man/check_soilco.Rd man/check_weatherDB.Rd man/circular.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/convert_precipitation.Rd man/convert_temperature.Rd man/create_dbWork.Rd man/crs_units.Rd man/dbConnect2.Rd man/dbExecute2.Rd man/dbOut_check_values.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_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.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/erf.Rd man/estimate_PotNatVeg_biomass.Rd man/estimate_PotNatVeg_composition.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_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_sites_with_bad_weather.Rd man/fix_PPTdata_length.Rd man/fun_kLargest.Rd man/gather_objects_for_export.Rd man/generate_OverallAggregation_fields.Rd man/generate_RNG_streams.Rd man/germination_wait_times.Rd man/get.SeveralOverallVariables.Rd man/get.SeveralOverallVariables_Ensemble.Rd man/get.SeveralOverallVariables_Scenario.Rd man/get.Table.Rd man/get.Table_Ensemble.Rd man/get.Table_Scenario.Rd man/get_BareSoilEvapCoefs.Rd man/get_GCMdata_NEX.Rd man/get_GCMdata_netCDF.Rd man/get_KilledBySoilLayers.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_modifiedHardegree2006NLR.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/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/intersect2.Rd man/is.natural.Rd man/is_project_script_file_recent.Rd man/isdone_intracker.Rd man/kill_seedling.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/pedotransfer.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/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/seq_month_ofeach_day.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_simulation_time.Rd man/setup_spatial_simulation.Rd man/simTiming_ForEachUsedTimeUnit.Rd man/simulate_SOILWAT2_experiment.Rd man/stretch_values.Rd man/swOutput_access.Rd man/sw_dailyC4_TempVar.Rd man/synchronicity.Rd man/test_sigmaGamma.Rd man/test_sigmaNormal.Rd man/todo_intracker.Rd man/try.ScenarioWeather.Rd man/tryToGet_ClimDB.Rd man/try_cell_ISRICWISE.Rd man/update_actions.Rd man/update_biomass.Rd man/update_intracker.Rd man/update_requested_years.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/GISSM_germination_wait_times.cpp
src/GISSM_get_KilledBySoilLayers.cpp
src/GISSM_setFALSE_SeedlingSurvival_1stSeason.cpp
src/RcppExports.cpp
src/init.c
src/ncepcfsr_convert.c
tests/test_data/0_ReferenceOutput/dbOutput_TestPrj4_v2.7.4.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_v09.csv
tests/test_data/TestPrj4/1_Input/SWRuns_InputData_SoilLayers_v9.csv
tests/test_data/TestPrj4/1_Input/SWRuns_InputData_TreatmentDesign_v17.csv
tests/test_data/TestPrj4/1_Input/SWRuns_InputMaster_Test_v11.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_v14.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/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/cloud.in
tests/test_data/TestPrj4/1_Input/treatments/tr_prodin/prod.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/simTime2_year1980.rds
tests/test_data/swp_values.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/test_data/weatherList_year1980.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_GISSM_germination_wait_times.R tests/testthat/test_GISSM_get_KilledBySoilLayers.R tests/testthat/test_GISSM_setFALSE_SeedlingSurvival_1stSeason.R tests/testthat/test_IO_SWSFinputfiles.R tests/testthat/test_Mathematical_Functions.R tests/testthat/test_OutputDatabase.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_climate_functions.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_match.R tests/testthat/test_netCDF_functions.R tests/testthat/test_pedotransferfunctions.R tests/testthat/test_projects.R tests/testthat/test_rSFSW2_CodeStylePractices.R tests/testthat/test_rSFSW2_Spelling.R tests/testthat/test_soil_functions.R tests/testthat/test_soillayers.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/SoilMoistureRegimes_SoilTemperatureRegimes.Rmd vignettes/rSFSW2_FAQs.Rmd
Burke-Lauenroth-Lab/rSFSW2 documentation built on March 17, 2019, 4:53 p.m.