Man pages for Burke-Lauenroth-Lab/SoilWat_R_Wrapper
Simulation Framework for SOILWAT2
| add_delta_to_PPT | Additive Precipitation adjustment by a delta value |
| add_granular_dbWork | Create new table 'need_outputs' for granular control of... |
| add_status_dbWork | Create a new table 'modification_status' with one row for... |
| adjustLayersDepth | The wrapper only handles 1-cm resolution of soil depths... |
| adjust.WindspeedHeight | Function to extrapolate windspeeds measured at a height... |
| align_with_target_grid | Aligns 'grid_from' with 'grid_to' for certain cells |
| align_with_target_res | Calculate resolution of one coordinate system for points in... |
| applyDeltas | Add/multiply deltas to historic daily data to generate future... |
| applyPPTdelta_detailed | Add/multiply deltas to historic daily precipitation to... |
| applyPPTdelta_simple | Add/multiply deltas to historic daily precipitation to... |
| assign_aggregation_soillayers | Determine which soil layers will be aggregated into two,... |
| calc_BareSoilEvapCoefs | Calculate potential bare-soil evaporation coefficients |
| calc_cell_ISRICWISE | Calculate weighted mean soil variables from one of the... |
| calc_DailyScenarioWeather | Extract daily climate scenario data |
| calc_Days_withLoweredPPT | Distribute precipitation among days without too extreme... |
| calcDeltas | Calculate Deltas, used for downscaling functionality |
| calc_drylandindices | Calculates temperate dryland criteria |
| calc_MonthlyScenarioWeather | Extract monthly climate scenario data and downscale to daily... |
| calc_RequestedSoilLayers | Add soil layers (by interpolation) if not already present and... |
| calc_timeSlices | Calculate historical and future simulation time slices |
| check_aggregated_output | Run checks on the values of the output database table... |
| check_cltool | Check availability and version of a command-line tool |
| check_dbWeather_version | Check that version of 'dbWeather' suffices |
| check_intracker_design | Check whether input tracker design is up-to-date |
| check_outputDB_completeness | Check whether 'dbOutput' contains a complete set of... |
| check_rSFSW2_project_input_data | Attempt to check input data of a 'rSFSW2' project for... |
| check_rSW2_version | Check version of a 'rSOILWAT2' input or output object... |
| check_soilco | Check that soil moisture extraction coefficients meet... |
| check_weatherDB | Checks data in a weather database |
| clean_SFSW2_cluster | Clean memory and workspace of parallel cluster workers |
| clean_worker | Remove almost all objects from a worker's global environment |
| climscen_determine_sources | Determine climate scenario data sources |
| climscen_metadata | Meta data for climate scenarios |
| compare_test_output | Compare test project output database with reference database |
| compare_two_dbOutput | Compare one output database with another output database |
| compile_overall_timer | Write timing information to the timing file |
| controlExtremePPTevents | Check for and handle days with too extreme precipitation... |
| create_dbWork | Create a SQLite-database 'dbWork' to manage runs of a... |
| crs_units | Extracts the sQuoteunits argument from a CRS object |
| dbConnect2 | Connect to SQLite-database |
| dbExecute2 | Execute a SQL statement on a database connection with... |
| dbOut_check_values | Check that cells of dbOutput agree with corresponding cells... |
| dbOutput_add_calculated_field | Add new field(s) to a table in dbOutput that is/are based on... |
| dbOutput_ListDesignTables | List the design tables of 'dbOutput' |
| dbOutput_ListInternalTables | List the SQLite internal tables of 'dbOutput' |
| dbOutput_ListOutputTables | List the available output tables of 'dbOutput' |
| dbOutput_subset | Make a copy of 'dbOutput' with a subset of tables and/or... |
| dbOutput_Tables_have_SoilLayers | Checks whether output tables of 'dbOutput' store output of... |
| dbOutput_update_OverallAggregationTable | Add fields to an existing 'dbOutput' |
| dbOut_read_variables_from_scenario | Reads variables/fields from the header view or from tables... |
| dbOut_update_values | Update values of dbOutput based on a new database |
| dbVacuumRollack | Perform a vacuum operation if there is a rollback journal... |
| dbWork_agg_timing | Calculate mean and standard deviation of stored execution... |
| dbWork_check_design | Check that 'dbWork' has an up-to-date structure of tables and... |
| dbWork_check_granular | Check granular run status |
| dbWork_checkpoint | Initiate a checkpoint operation on a SQLite-database 'dbWork'... |
| dbWork_check_run | Check run status |
| dbWork_check_status | Check modification status of 'dbWork' against 'dbOut' and... |
| dbWork_clean | Do maintenance work on a SQLite-database 'dbWork' if it... |
| dbWork_Ntodo | Numbers of runs of a 'rSFSW2' simulation project which are... |
| dbWork_redo | Set runs information that need to be redone / simulated... |
| dbWork_report_completion | Estimate percentage of completed runs |
| dbWork_timing | Extract stored execution times of completed runs of a... |
| dbWork_todos | Extract identification numbers of runs of a 'rSFSW2'... |
| dbWork_update_granular | Update granular run information of a 'rSFSW2' simulation... |
| dbWork_update_IncludeYN | Update 'include_YN' |
| dbWork_update_job | Update run information of a 'rSFSW2' simulation project |
| dbWork_update_status | Update modification status of a 'rSFSW2' simulation project |
| delete_test_output | Delete output of a test project |
| determine_simulation_size | Calculate the size of the simulation experiment: number of... |
| dir_safe_create | Create the elements of paths |
| do_compare_nc | Compare two netCDF files |
| do_OneSite | The main simulation function which does all the heavy lifting |
| do_prior_TableLookups | Look-up input values from spreadsheet tables |
| doQmapQUANT | Apply a quantile mapping |
| downscale | Downscale and temporal disaggregation |
| downscale.delta | Downscale with the 'delta approach' |
| downscale.deltahybrid | Downscale with the 'delta-hybrid approach' old version (prior... |
| downscale.deltahybrid3mod | Downscale with the new version of the sQuotedelta-hybrid... |
| downscale.periods | Time periods for downscaling functions |
| downscale.raw | Downscale with the 'direct approach' |
| dw_determine_sources | Determine sources of daily weather |
| enable_debug_dump | Expression for dumping of objects from an evaluation stack |
| exit_SFSW2_cluster | Clean up and terminate a parallel cluster used for a 'rSFSW2'... |
| export_objects_to_workers | Export objects to workers |
| extract_blocks | Extract values from 'raster::Raster' objects that are covered... |
| ExtractClimateChangeScenarios | Extract climate scenarios |
| extract_climate_NCEPCFSR | Extract gridded mean monthly data from NCEP/CFSR for sites... |
| ExtractClimateWizard | Extract climate scenarios from downloaded <URL:... |
| extract_daily_weather_from_gridMET | Extract daily gridded weather data from the gridMET dataset |
| extract_daily_weather_from_livneh | Extract Gridded Weather Data from a Livneh Database |
| ExtractData_Elevation | Extract elevation data |
| ExtractData_MeanMonthlyClimate | Extract mean monthly climate data: cloud cover, relative... |
| ExtractData_Soils | Extract soil characteristics |
| ExtractDayMet | Extract gridded daily weather from "DayMet" for North... |
| extract_from_external_raster_old | Function to extract data for raster cells |
| ExtractGriddedDailyWeatherFromMaurer2002_NorthAmerica | Extract gridded daily weather from Maurer et al. 2002... |
| ExtractGriddedDailyWeatherFromNRCan_10km_Canada | Extract gridded daily weather from NR Canada for Canadian... |
| extract_rSFSW2 | Extract raster data for point or cell locations |
| extract_SFSW2_cells_from_raster | Extract the weighted mean (and sample quantiles) for raster... |
| extract_SFSW2_cells_from_shp | Extract spatial polygon data for polygons or rectangles. |
| extract_SFSW2_points_from_shp | Extract spatial polygon data for point locations |
| extract_soil_CONUSSOIL | 'CONUS-SOIL' is a rasterized and controlled 'STATSGO'... |
| extract_soil_ISRICWISE | Extract soil data from one of the 'ISRIC-WISE' datasets |
| find_gridMET_files | List gridMET data files available on disk |
| find_sites_with_bad_weather | Determine which site_ids in the weather database do not have... |
| fix_PPTdata_length | Adds/removes elements of data |
| gather_objects_for_export | Export R objects to MPI or socket workers |
| generate_OverallAggregation_fields | Generate field names (and their numbers) for overall... |
| generate_RNG_streams | Implementation RngStreams for N tasks according to Pierre... |
| get_BareSoilEvapCoefs | Calculate bare-soil evaporation coefficients based on soil... |
| get_DailyGCMdata_netCDF | Extract all daily GCM projection values for precipitation,... |
| get_fieldnames | Access data from a database |
| get_fnames_dbTempOut | Locate file names of temporary output database files |
| get_fnames_temporaryOutput | Locate file names of temporary output text files |
| get_GCMdata_NEX | Download downscaled GCM projections from NEX |
| get_MonthlyGCMdata_netCDF | Extract monthly GCM projection from a netCDF file |
| get_nc_time_axis | read time values |
| get_Pid_from_temptxt | Extract P_id from content of temporary output files |
| get.SeveralOverallVariables | Get data of variables in the overall aggregation table for... |
| get.SeveralOverallVariables_Ensemble | Get data of variables in the overall aggregation table for... |
| get.SeveralOverallVariables_Scenario | Get data of variables in the overall aggregation table for... |
| get.SeveralOverallVariables_Scenario_old | Get data of variables in the overall aggregation table for... |
| get_simulation_time | Determine maximal span of simulation years across all... |
| get_SoilLayerID_from_temptxt | Extract soil layer ID from content of temporary output files |
| get.Table | Get data-part for an entire table for one of the 'climCat'... |
| get.Table_Ensemble | Get header and data for an entire table for one of the... |
| get_tablename_from_temptxt | Extract names of 'dbOutput' tables from content of temporary... |
| get.Table_Scenario | Get header and data for an entire table for one of the... |
| global_args_do_OneSite | List of objects to export which are required by 'do_OneSite'... |
| GriddedDailyWeatherFromNCEPCFSR_Global | Extract gridded daily weather from NCEP/CFSR for sites... |
| gridMET_download_and_check | Prepare script to download all or missing files of the... |
| gridMET_metadata | Description of the gridMET dataset |
| has_NAs_pooled_at_depth | NAs present but only in deepest soil layers |
| indices | Index functions |
| init_intracker | Initialize a new input status tracker object |
| init_rSFSW2_project | Initialize a 'rSFSW2' project (setup description file) |
| init_SFSW2_cluster | Initialize a parallel cluster |
| init_timer | Initialize a timing file for a simulation job |
| isdone_intracker | Query whether an input tracker is completed |
| is_project_script_file_recent | Compare elements and 1-st level structure of project script... |
| ISRICWISE_extract_SUIDs | A wrapper for 'reaggregate_raster' designed to work with the... |
| list.dbTables | List tables and variables of a database |
| list.dbVariables | List variables of a database |
| list.dbVariablesOfAllTables | List tables and variables of a database |
| load_preprocessed_inputs | Load pre-processed simulation project inputs |
| load_project_description | Load a project description script |
| local_weatherDirName | Get name of weather file from database 'dbOutput' |
| make_dbOutput | Create 'dbOutput' if requested and/or not already present |
| make_dbW | Create and populate a 'rSOILWAT2' daily weather SQLite... |
| make_test_output_reference | Copy output database of a test project to reference folder |
| merge_2soils | Merge two soil input datafiles |
| missing_Pids_outputDB | Identify P_id for which output is not completely available in... |
| move_dbTempOut_to_dbOut | Moves simulation output that was written to temporary... |
| move_output_to_dbOutput | Move temporary output data to output databases |
| move_temporary_to_outputDB | Moves simulation output that was written to temporary text... |
| mpi_last | Properly end "mpi" workers before quitting R (e.g., at a... |
| mpi_work | 'Rmpi' work function for calling 'do_OneSite' |
| obtain_CMIP5_MACAv2metdata_USA | Check and prepare local copy of CMIP5_MACAv2metdata dataset |
| populate_rSFSW2_project_with_data | Populate 'rSFSW2' project with input data |
| pragmas | Set some useful 'PRAGMA' |
| prepare_climatedata_netCDFs | Process downloaded netCDF files to concatenate if needed... |
| PrepareClimateScenarios | Extracts climate change scenarios and downscales monthly to... |
| prepare_ExtractData_Soils | Preparations for the extraction of external soil datasets |
| process_inputs | Load and prepare inputs for a 'rSFSW2' simulation project |
| quickprepare_dbOutput_dbWork | Prepare output database without running proper steps of... |
| rbind_2cols_nonoverlapping | 'rbind' two objects, but make sure that there is no... |
| read_SOILWAT2_DefaultInputs | Prepare default inputs from 'rSOILWAT2' |
| read_time_netCDF | Read and interpret time dimension of a netCDF file with CF 1... |
| reaggregate_raster | Extract all raster cell values that occur within each... |
| reaggregate_shapefile | Re-aggregation of spatial polygon data by spatial... |
| reconstitute_inputfile | Re-combine elements to create a 'rSFSW2-inputfile' |
| recreate_dbWork | Re-create or update 'dbWork' based on 'dbOutput' |
| remove_from_onexit_expression | Remove one of possibly several expressions recorded by... |
| res_to_polygons | Convert resolution/rectangles into 'sp::SpatialPolygons' |
| rSFSW2 | 'rSFSW2': Framework for 'rSOILWAT2' simulations: creating... |
| run_simulation_experiment | Run a 'rSFSW2' simulation experiment |
| run_test_projects | Run test projects |
| save_to_rds_with_backup | Serialization Interface for Single Objects with backup |
| select_suitable_CFs | Subset a list of netCDF CF file names to specific models,... |
| set_full_RNG | Specify all aspects of the R random number generator |
| set_glovar | Setting values of package-level global variables on workers |
| set_options_warn_error | Setting global 'warn' and 'error' options |
| set_RNG_stream | Set the seed of a random number generator (stream) |
| setup_dbWork | Setup or connect to SQLite-database 'dbWork' to manage runs... |
| setup_RNG | Organizing previous state and streams of random number... |
| setup_rSFSW2_project_infrastructure | Setup infrastructure (skeleton) for a new 'rSFSW2' simulation... |
| setup_SFSW2_cluster | Set-up a parallel cluster to be used for a 'rSFSW2'... |
| setup_spatial_simulation | Set-up information for a spatially aware simulation project |
| setup_time_simulation_project | Describe the time of a simulation project |
| SFSW2_read_csv | Read a comma-separated value (csv) file |
| SFSW2_read_inputfile | Read the data from a 'rSFSW2-inputfile' |
| simulate_SOILWAT2_experiment | Carry out a 'rSFSW2' simulation experiment |
| swOutput_access | 'rSOILWAT2' data access functions |
| synchronicity | Synchronicity with backing store locks |
| todo_intracker | Query whether an input tracker is not yet completed |
| trewartha_climate | Main climate classification according to Trewartha |
| try_cell_ISRICWISE | Wrapping 'calc_cell_ISRICWISE' in 'try' to handle errors... |
| try_MonthlyScenarioWeather | Make daily weather for a scenario |
| tryToGet_ClimDB | Organizes the calls (in parallel) which obtain specified... |
| update_actions | Update actions for simulation project |
| update_intracker | Update input tracker status |
| update_runIDs_sites_by_dbW | Lookup IDs of sites as found in a weather database |
| update_todos | Update todos for simulation project |
| upgrade_datafile | Upgrade a 'data input file' |
| vp0 | Saturation vapor pressure |
| vpd | Vapor pressure deficit |
| weighted.agg | The 'weighted mean' (and sample quantiles) of re-aggregation... |
| whereNearest | Index of the closest value in the matrix to the passed in... |
