Man pages for Burke-Lauenroth-Lab/SoilWat_R_Wrapper
Simulation Framework for SOILWAT2

add_delta_to_PPTAdditive Precipitation adjustment by a delta value
add_granular_dbWorkCreate new table 'need_outputs' for granular control of...
add_layer_to_soilSplit soil layer in two layers
add_status_dbWorkCreate a new table 'modification_status' with one row for...
adjustLayersDepthThe wrapper only handles 1-cm resolution of soil depths...
adjust.WindspeedHeightFunction to extrapolate windspeeds measured at a height...
align_with_target_gridAligns 'grid_from' with 'grid_to' for certain cells
align_with_target_resCalculate resolution of one coordinate system for points in...
applyDeltasAdd/multiply deltas to historic daily data to generate future...
applyPPTdelta_detailedAdd/multiply deltas to historic daily precipitation to...
applyPPTdelta_simpleAdd/multiply deltas to historic daily precipitation to...
assign_aggregation_soillayersDetermine which soil layers will be aggregated into two,...
biomassBiomass equations
calc_BareSoilEvapCoefsCalculate potential bare-soil evaporation coefficients
calc_cell_ISRICWISECalculate weighted mean soil variables from one of the...
calc_Days_withLoweredPPTDistribute precipitation among days without too extreme...
calcDeltasCalculate Deltas, used for downscaling functionality
calc_drylandindicesCalculates temperate dryland criteria
calc_DurationFavorableCondsFunction to calculate for each day of the year, duration in...
calc_RequestedSoilLayersAdd soil layers (by interpolation) if not already present and...
calc.ScenarioWeatherExtract climate scenario data and downscale to daily weather...
calc_SeedlingMortalityFunction to calculate mortality under conditions and checks...
calc_SiteClimateCalculate climate variables from daily weather
calc_timeSlicesCalculate historical and future simulation time slices
calc_TimeToGerminateFunction to estimate time to germinate for each day of a...
check_aggregated_outputRun checks on the values of the output database table...
check_cltoolCheck availability and version of a command-line tool
check_dbWeather_versionCheck that version of 'dbWeather' suffices
check_intracker_designCheck whether input tracker design is up-to-date
check_monotonic_increaseCheck that values in matrix-like object are (strictly)...
check_outputDB_completenessCheck whether 'dbOutput' contains a complete set of...
check_rSFSW2_project_input_dataAttempt to check input data of a 'rSFSW2' project for...
check_soilcoCheck that soil moisture extraction coefficients meet...
check_SuitableGrowthThisYearFunction to calculate favorable conditions for seedling...
check_weatherDBChecks data in a weather database
circularFunctions for circular descriptive statistics
clean_SFSW2_clusterClean memory and workspace of parallel cluster workers
clean_workerRemove almost all objects from a worker's global environment
climscen_determine_sourcesDetermine climate scenario data sources
climscen_metadataMeta data for climate scenarios
compare_test_outputCompare test project output database with reference database
compare_two_dbOutputCompare one output database with another output database
compile_overall_timerWrite timing information to the timing file
controlExtremePPTeventsCheck for and handle days with too extreme precipitation...
convert_precipitationConverts units of precipitation data
convert_temperatureConverts units of temperature data
create_dbWorkCreate a SQLite-database 'dbWork' to manage runs of a...
crs_unitsExtracts the sQuoteunits argument from a CRS object
dbConnect2Connect to SQLite-database
dbExecute2Execute a SQL statement on a database connection with...
dbOut_check_valuesCheck that cells of dbOutput agree with corresponding cells...
dbOutput_ListDesignTablesList the design tables of 'dbOutput'
dbOutput_ListInternalTablesList the SQLite internal tables of 'dbOutput'
dbOutput_ListOutputTablesList the available output tables of 'dbOutput'
dbOutput_subsetMake a copy of 'dbOutput' with a subset of tables and/or...
dbOutput_Tables_have_SoilLayersChecks whether output tables of 'dbOutput' store output of...
dbOutput_update_OverallAggregationTableAdd fields to an existing 'dbOutput'
dbOut_update_valuesUpdate values of dbOutput based on a new database
dbVacuumRollackPerform a vacuum operation if there is a rollback journal...
dbWork_agg_timingCalculate mean and standard deviation of stored execution...
dbWork_check_designCheck that 'dbWork' has an up-to-date structure of tables and...
dbWork_check_granularCheck granular run status
dbWork_checkpointInitiate a checkpoint operation on a SQLite-database 'dbWork'...
dbWork_check_runCheck run status
dbWork_check_statusCheck modification status of 'dbWork' against 'dbOut' and...
dbWork_cleanDo maintenance work on a SQLite-database 'dbWork' if it...
dbWork_NtodoNumbers of runs of a 'rSFSW2' simulation project which are...
dbWork_redoSet runs information that need to be redone / simulated...
dbWork_report_completionEstimate percentage of completed runs
dbWork_timingExtract stored execution times of completed runs of a...
dbWork_todosExtract identification numbers of runs of a 'rSFSW2'...
dbWork_update_granularUpdate granular run information of a 'rSFSW2' simulation...
dbWork_update_IncludeYNUpdate 'include_YN'
dbWork_update_jobUpdate run information of a 'rSFSW2' simulation project
dbWork_update_statusUpdate modification status of a 'rSFSW2' simulation project
delete_test_outputDelete output of a test project
determine_simulation_sizeCalculate the size of the simulation experiment: number of...
dir_safe_createCreate the elements of paths
do_compareRecursive comparisons which also works for nested lists
do_compare_ncCompare two netCDF files
do_OneSiteThe main simulation function which does all the heavy lifting
do_prior_TableLookupsLook-up input values from spreadsheet tables
doQmapQUANTApply a quantile mapping
downscaleDownscale and temporal disaggregation
downscale.deltaDownscale with the 'delta approach'
downscale.deltahybridDownscale with the 'delta-hybrid approach' old version (prior...
downscale.deltahybrid3modDownscale with the new version of the sQuotedelta-hybrid...
downscale.periodsTime periods for downscaling functions
downscale.rawDownscale with the 'direct approach'
dw_determine_sourcesDetermine sources of daily weather
enable_debug_dumpExpression for dumping of objects from an evaluation stack
erfError function
estimate_PotNatVeg_biomassAdjust mean monthly biomass values of grass and shrub...
estimate_PotNatVeg_compositionCalculate the composition of a potential natural vegetation...
exit_SFSW2_clusterClean up and terminate a parallel cluster used for a 'rSFSW2'...
export_objects_to_workersExport objects to workers
extract_blocksExtract values from 'raster::Raster' objects that are covered...
ExtractClimateChangeScenariosExtract climate scenarios
extract_climate_NCEPCFSRExtract gridded mean monthly data from NCEP/CFSR for sites...
ExtractClimateWizardExtract climate scenarios from downloaded <URL:...
extract_daily_weather_from_livnehExtract Gridded Weather Data from a Livneh Database
ExtractData_ElevationExtract elevation data
ExtractData_MeanMonthlyClimateExtract mean monthly climate data: cloud cover, relative...
ExtractData_SoilsExtract soil characteristics
ExtractDayMetExtract gridded daily weather from "DayMet" for North...
extract_from_external_raster_oldFunction to extract data for raster cells
ExtractGriddedDailyWeatherFromMaurer2002_NorthAmericaExtract gridded daily weather from Maurer et al. 2002...
ExtractGriddedDailyWeatherFromNRCan_10km_CanadaExtract gridded daily weather from NR Canada for Canadian...
extract_rSFSW2Extract raster data for point or cell locations
extract_SFSW2_cells_from_rasterExtract the weighted mean (and sample quantiles) for raster...
extract_SFSW2_cells_from_shpExtract spatial polygon data for polygons or rectangles.
extract_SFSW2_points_from_shpExtract spatial polygon data for point locations
extract_soil_CONUSSOIL'CONUS-SOIL' is a rasterized and controlled 'STATSGO'...
extract_soil_ISRICWISEExtract soil data from one of the 'ISRIC-WISE' datasets
find_sites_with_bad_weatherDetermine which site_ids in the weather database do not have...
fix_PPTdata_lengthAdds/removes elements of data
fun_kLargestFind the 'k'-largest/smallest values (and apply a function to...
gather_objects_for_exportExport R objects to MPI/socket workers
generate_OverallAggregation_fieldsGenerate field names (and their numbers) for overall...
generate_RNG_streamsImplementation RngStreams for N tasks according to Pierre...
germination_wait_timesDetermine wait times until germination based on information...
get_BareSoilEvapCoefsCalculate bare-soil evaporation coefficients based on soil...
get_fieldnamesAccess data from a database
get_fnames_dbTempOutLocate file names of temporary output database files
get_fnames_temporaryOutputLocate file names of temporary output text files
get_GCMdata_netCDFExtract GCM projection from a netCDF file
get_GCMdata_NEXDownload downscaled GCM projections from NEX
get_KilledBySoilLayersDetermine if all conditions across rooted soil layers are...
get_modifiedHardegree2006NLRBased on the NLR model (equation 5) in Hardegree (2006) and...
get_nc_time_axisread time values
get_Pid_from_temptxtExtract P_id from content of temporary output files
get.SeveralOverallVariablesGet data of variables in the overall aggregation table for...
get.SeveralOverallVariables_EnsembleGet data of variables in the overall aggregation table for...
get.SeveralOverallVariables_ScenarioGet data of variables in the overall aggregation table for...
get_simulation_timeDetermine maximal span of simulation years across all...
get_SoilLayerID_from_temptxtExtract soil layer ID from content of temporary output files
get.TableGet data-part for an entire table for one of the 'climCat'...
get.Table_EnsembleGet header and data for an entire table for one of the...
get_tablename_from_temptxtExtract names of 'dbOutput' tables from content of temporary...
get.Table_ScenarioGet header and data for an entire table for one of the...
global_args_do_OneSiteList of objects to export which are required by 'do_OneSite'...
GriddedDailyWeatherFromNCEPCFSR_GlobalExtract gridded daily weather from NCEP/CFSR for sites...
has_NAs_pooled_at_depthNAs present but only in deepest soil layers
indicesIndex functions
init_intrackerInitialize a new input status tracker object
init_rSFSW2_projectInitialize a 'rSFSW2' project (setup description file)
init_SFSW2_clusterInitialize a parallel cluster
init_timerInitialize a timing file for a simulation job
intersect2The intersection on any number of vectors
isdone_intrackerQuery whether an input tracker is completed
is.naturalTest whether input represents a natural number
is_project_script_file_recentCompare elements and 1-st level structure of project script...
ISRICWISE_extract_SUIDsA wrapper for 'reaggregate_raster' designed to work with the...
kill_seedlingDetermine seedling survival in the first season ('ss1s')
list.dbTablesList tables and variables of a database
list.dbVariablesList variables of a database
list.dbVariablesOfAllTablesList tables and variables of a database
load_preprocessed_inputsLoad pre-processed simulation project inputs
load_project_descriptionLoad a project description script
local_weatherDirNameGet name of weather file from database 'dbOutput'
make_dbOutputCreate 'dbOutput' if requested and/or not already present
make_dbWCreate and populate a 'rSOILWAT2' daily weather SQLite...
make_test_output_referenceCopy output database of a test project to reference folder
merge_2soilsMerge two soil input datafiles
missing_Pids_outputDBIdentify P_id for which output is not completely available in...
move_dbTempOut_to_dbOutMoves simulation output that was written to temporary...
move_output_to_dbOutputMove temporary output data to output databases
move_temporary_to_outputDBMoves simulation output that was written to temporary text...
mpi_lastProperly end "mpi" workers before quitting R (e.g., at a...
mpi_work'Rmpi' work function for calling 'do_OneSite'
pedotransferPedotransfer functions to convert between soil moisture...
populate_rSFSW2_project_with_dataPopulate 'rSFSW2' project with input data
pragmasSet some useful 'PRAGMA'
prepare_climatedata_netCDFsProcess downloaded netCDF files to concatenate if needed...
PrepareClimateScenariosExtracts climate change scenarios and downscales monthly to...
prepare_ExtractData_SoilsPreparations for the extraction of external soil datasets
process_inputsLoad and prepare inputs for a 'rSFSW2' simulation project
quickprepare_dbOutput_dbWorkPrepare output database without running proper steps of...
read_SOILWAT2_DefaultInputsPrepare default inputs from 'rSOILWAT2'
read_time_netCDFRead and interpret time dimension of a netCDF file with CF 1...
reaggregate_rasterExtract all raster cell values that occur within each...
reaggregate_shapefileRe-aggregation of spatial polygon data by spatial...
reconstitute_inputfileRe-combine elements to create a 'rSFSW2-inputfile'
recreate_dbWorkRe-create or update 'dbWork' based on 'dbOutput'
remove_from_onexit_expressionRemove one of possibly several expressions recorded by...
res_to_polygonsConvert resolution/rectangles into 'sp::SpatialPolygons'
rSFSW2'rSFSW2': Framework for 'rSOILWAT2' simulations: creating...
run_simulation_experimentRun a 'rSFSW2' simulation experiment
run_test_projectsRun test projects
save_to_rds_with_backupSerialization Interface for Single Objects with backup
SeedlingRootingDepthFunction to calculate rooting depth at given age Units: [age]...
seq_month_ofeach_dayThe sequence of month numbers for each day in the period from...
set_full_RNGSpecify all aspects of the R random number generator
set_glovarSetting values of package-level global variables on workers
set_options_warn_errorSetting global 'warn' and 'error' options
set_RNG_streamSet the seed of a random number generator (stream)
setup_dbWorkSetup or connect to SQLite-database 'dbWork' to manage runs...
setup_RNGOrganizing previous state and streams of random number...
setup_rSFSW2_project_infrastructureSetup infrastructure (skeleton) for a new 'rSFSW2' simulation...
setup_SFSW2_clusterSet-up a parallel cluster to be used for a 'rSFSW2'...
setup_simulation_timeDescribe the time of a simulation project
setup_spatial_simulationSet-up information for a spatially aware simulation project
SFSW2_read_csvRead a comma-separated value (csv) file
SFSW2_read_inputfileRead the data from a 'rSFSW2-inputfile'
simTiming_ForEachUsedTimeUnitCalculate indices along different time steps for simulation...
simulate_SOILWAT2_experimentCarry out a 'rSFSW2' simulation experiment
SMR_logicSoil moisture regime: Soil Survey Staff 2014 (Key to Soil...
SoilLayer_at_SoilDepthFunction to convert soil depth to soil layer
STMRCategories of soil temperature regimes and soil moisture...
stretch_valuesStretch values
STR_logicSoil temperature regime: based on Soil Survey Staff 2014 (Key...
sw_dailyC4_TempVarCalculate variables required to estimate percent C4 species...
swOutput_access'rSOILWAT2' data access functions
synchronicitySynchronicity with backing store locks
test_sigmaGammaCheck that data are within range of an approximated gamma...
test_sigmaNormalCheck that data are within range of normal distribution
todo_intrackerQuery whether an input tracker is not yet completed
TranspCoeffByVegTypeLookup transpiration coefficients
try_cell_ISRICWISEWrapping 'calc_cell_ISRICWISE' in 'try' to handle errors...
try.ScenarioWeatherMake daily weather for a scenario
tryToGet_ClimDBOrganizes the calls (in parallel) which obtain specified...
update_actionsUpdate actions for simulation project
update_biomassReplace selected biomass values of a rSOILWAT2::swProd object
update_intrackerUpdate input tracker status
update_requested_yearsCheck requested years
update_runIDs_sites_by_dbWLookup IDs of sites as found in a weather database
update_todosUpdate todos for simulation project
upgrade_datafileUpgrade a 'data input file'
vp0Saturation vapor pressure
vpdVapor pressure deficit
weighted.aggThe 'weighted mean' (and sample quantiles) of re-aggregation...
whereNearestIndex of the closest value in the matrix to the passed in...
Burke-Lauenroth-Lab/SoilWat_R_Wrapper documentation built on March 17, 2019, 4:50 p.m.