Man pages for Burke-Lauenroth-Lab/rSOILWAT2
An Ecohydrological Ecosystem-Scale Water Balance Simulation Model
| activate_swOUT_OutKey-set | Activate/deactivate an output slot (swOUT_OutKey) |
| adj_phenology_by_temp | Adjust a phenological pattern to a different temperature... |
| adjust_TranspirationRegions | Adjust transpiration regions for roots and soil layers |
| biomass | Biomass equations |
| calc_dailyInputFlags | Determine used weather variables based on values |
| calc_SiteClimate | Calculate climate variables from daily weather |
| check_content | Check availability of content in registered weather database |
| check_ptf_availability | Check availability of 'PTFs' |
| check_swrcp | Check Soil Water Retention Curve parameters |
| check_SWRC_vs_PTF | Check whether 'PTF' and 'SWRC' are compatible and implemented |
| check_TranspirationRegions | Check transpiration regions |
| check_updatedDB | Run database integrity checks on a weather database |
| check_version | Check that version of an input or output object is up-to-date |
| compare_weather | Compare two weather datasets: produces comparison plots for... |
| dbW_addFromFolders | Read 'SOILWAT2'-style weather data from disk and store in... |
| dbW_addScenarios | Adds new Scenarios to a registered weather database |
| dbW_addSite | Add a new site description to a weather database |
| dbW_addSites | Adds new sites to a registered weather database |
| dbW_addWeatherData | Adds daily weather data to a registered weather database |
| dbW_blob_to_weatherData | Conversion: (Compressed) raw vector (e.g., SQL-retrieved... |
| dbW_check_version | Check that version of registered weather database is... |
| dbW_check_weatherData | Check that weather data is well-formed |
| dbW_compression | Query compression type of registered weather database |
| dbW_convert_to_GregorianYears | Transfer existing weather data to a different (Gregorian)... |
| dbW_createDatabase | Create a weather database |
| dbW_dataframe_to_weatherData | Conversion: data.frame to object of class 'swWeatherData' |
| dbW_delete_duplicated_weatherData | Remove duplicated weather data records |
| dbW_deleteSite | Delete a site and all associated weather data from a... |
| dbW_deleteSiteData | Delete a weather data record from a registered weather... |
| dbW_disconnectConnection | Disconnects a SQLite weather database from the package |
| dbW_estimate_WGen_coefs | Estimate coefficients of the 'SOILWAT2' weather generator |
| dbW_fixWeather | Fix weather data |
| dbW_generateWeather | Generate daily weather data using SOILWAT2's weather... |
| dbW_getIDs | Locate keys for weather database tables in the registered... |
| dbW_getScenarioId | Extract table keys to connect scenario(s) with weather data... |
| dbW_getScenariosTable | Read entire table of Scenarios from the registered weather... |
| dbW_getSiteId | Extract table keys to connect sites with weather data in the... |
| dbW_getSiteTable | Read entire table of sites from the registered weather... |
| dbW_getWeatherData | Extracts daily weather data from a registered weather... |
| dbW_imputeWeather | Impute missing weather values |
| dbW_IsValid | Check whether registered weather database connection is valid |
| dbW_setConnection | Registers/connects a SQLite weather database with the package |
| dbW_substituteWeather | Replace missing values with values from another weather data... |
| dbW_temporal_summaries | Summarize daily weather to weekly, monthly, or yearly values |
| dbW_updateSites | Updates existing sites or adds new sites to a registered... |
| dbW_upgrade | Weather database upgrade functions |
| dbW_version | Query version number of registered weather database |
| dbW_weatherData_round | Round weather data |
| dbW_weatherData_to_blob | Conversion: R object to (compressed) SQL-blob-ready character... |
| dbW_weatherData_to_dataframe | Convert an object of class 'swWeatherData' to a data.frame |
| dbW_weather_to_SOILWATfiles | Conversion: object of class 'swWeatherData' or data.frame to... |
| estimate_PotNatVeg_biomass | Adjust mean monthly biomass values of grass and shrub... |
| estimate_PotNatVeg_composition | Calculate the composition (land cover) representing a... |
| estimate_PotNatVeg_roots | Calculate rooting profile for a soil profile from lookup... |
| format_timestamp | Format time stamp of an input or output object |
| get_derived_output | Calculate derived variables from output |
| get_evaporation | Calculate evaporation from output |
| get_Markov | 'get_Markov' |
| get_soilmoisture | Extract or calculate soil moisture |
| get_soiltemp | Extract soil temperature |
| get_swCarbon | 'get_swCarbon' |
| get_swCloud | 'get_swCloud' |
| get_swEstab | 'get_swEstab' |
| get_swFiles | 'get_swFiles' |
| get_swMarkov | 'get_swMarkov' |
| get_swOUT | 'get_swOUT' |
| get_swProd | 'get_swProd' |
| get_swSite | 'get_swSite' |
| get_swSoils | 'get_swSoils' |
| get_swSWC | 'get_swSWC' |
| get_swWeather | 'get_swWeather' |
| get_swWeatherData | 'get_swWeatherData' |
| get_swYears | 'get_swYears' |
| get_timestamp | Retrieve time stamp of an object |
| get_transpiration | Calculate transpiration from output |
| get_version | Retrieve version of 'rSOILWAT2' that was used to create... |
| getWeatherData_folders | Reads daily weather data from files |
| get_WeatherHistory | 'get_WeatherHistory' |
| get_years_from_weatherData | Extract years from a weatherData object |
| get_years_from_weatherDF | Extract years to weather data.frame |
| has_soilTemp_failed | Check if soil temperature simulation failed |
| is_missing_weather | Check which weather values are missing |
| list_matched_swrcs_ptfs | Matching pairs of implemented 'SWRCs' and 'PTFs' |
| lookup_annual_CO2a | Look-up yearly atmospheric CO2 concentration values |
| nrow_output | Number of time steps in output |
| pedotransfer | Deprecated pedotransfer functions to convert between soil... |
| prepare_TranspirationRegions | Prepare transpiration regions |
| print_mkv_files | Print Markov weather generator files as required by SOILWAT2 |
| ptf_estimate | Estimate 'SWRC' parameters from soil texture with a... |
| ptf_names | List Pedotransfer Functions 'PTFs' |
| ptf_neuroFX2021_for_FXW | Estimate 'FXW' 'SWRC' parameters using 'neuroFX2021' |
| ptf_Rosetta_for_vanGenuchten1980 | Estimate van Genuchten 1980 'SWRC' parameters using 'Rosetta'... |
| ptfs_implemented_by_rSW2 | List 'PTFs' implemented by 'rSOILWAT2' |
| ptfs_implemented_by_SW2 | List 'PTFs' implemented by 'SOILWAT2' |
| rSOILWAT2 | Package 'rSOILWAT2': summary information |
| rSOILWAT2-defunct | Defunct functions in package 'rSOILWAT2' |
| rSW2_SWRC_PTF_estimate_parameters | Estimate parameters of selected soil water retention curve... |
| rSW2_timestamp | Create 'rSOILWAT2' time stamp |
| rSW2_version | Create 'rSOILWAT2' version representation |
| set_Markov | 'set_Markov' |
| set_Markov-set | 'set_Markov<-' |
| set_missing_weather | Deal with missing weather values: convert to NAs |
| set_requested_flags | Assign requested values to (scalar) input flags |
| set_swCarbon | 'set_swCarbon' |
| set_swCarbon-set | 'set_swCarbon<-' |
| set_swCloud | 'set_swCloud' |
| set_swCloud-set | 'set_swCloud<-' |
| set_swEstab-set | 'set_swEstab<-' |
| set_swFiles | 'set_swFiles' |
| set_swFiles-set | 'set_swFiles<-' |
| set_swMarkov | 'set_swMarkov' |
| set_swMarkov-set | 'set_swMarkov<-' |
| set_swOUT | 'set_swOUT' |
| set_swOUT-set | 'set_swOUT<-' |
| set_swProd | 'set_swProd' |
| set_swProd-set | 'set_swProd<-' |
| set_swSite | 'set_swSite' |
| set_swSite-set | 'set_swSite<-' |
| set_swSoils | 'set_swSoils' |
| set_swSoils-set | 'set_swSoils<-' |
| set_swSWC | 'set_swSWC' |
| set_swSWC-set | 'set_swSWC<-' |
| set_swWeather | 'set_swWeather' |
| set_swWeatherData | 'set_swWeatherData' |
| set_swWeatherData-set | 'set_swWeatherData<-' |
| set_swWeather-set | 'set_swWeather<-' |
| set_swYears | 'set_swYears' |
| set_swYears-set | 'set_swYears<-' |
| set_WeatherHistory | 'set_WeatherHistory' |
| set_WeatherHistory-set | 'set_WeatherHistory<-' |
| sw2_tr_CO2a | Lookup table of yearly atmospheric CO2 concentrations |
| sw2_trco_table | Lookup table of rooting profiles |
| sw2_tr_VegBiom | Default vegetation biomass table |
| swCarbon-class | Class '"swCarbon"' |
| swCarbon_CO2ppm | 'swCarbon_CO2ppm' |
| swCarbon_CO2ppm-set | 'swCarbon_CO2ppm<-' |
| swCarbon_DeltaYear | 'swCarbon_DeltaYear' |
| swCarbon_DeltaYear-set | 'swCarbon_DeltaYear<-' |
| swCarbon_Scenario | 'swCarbon_Scenario' |
| swCarbon_Scenario-set | 'swCarbon_Scenario<-' |
| swCarbon_Use_Bio | 'swCarbon_Use_Bio' |
| swCarbon_Use_Bio-set | 'swCarbon_Use_Bio<-' |
| swCarbon_Use_WUE | 'swCarbon_Use_WUE' |
| swCarbon_Use_WUE-set | 'swCarbon_Use_WUE<-' |
| sw_Cheatgrass_ClimVar | Calculate climate variables required to estimate percent... |
| swCloud-class | Class '"swCloud"' |
| swCloud_Humidity | 'swCloud_Humidity' |
| swCloud_Humidity-set | 'swCloud_Humidity<-' |
| swCloud_RainEvents | 'swCloud_RainEvents' |
| swCloud_RainEvents-set | 'swCloud_RainEvents<-' |
| swCloud_SkyCover | 'swCloud_SkyCover' |
| swCloud_SkyCover-set | 'swCloud_SkyCover<-' |
| swCloud_SnowDensity | 'swCloud_SnowDensity' |
| swCloud_SnowDensity-set | 'swCloud_SnowDensity<-' |
| swCloud_WindSpeed | 'swCloud_WindSpeed' |
| swCloud_WindSpeed-set | 'swCloud_WindSpeed<-' |
| sw_dailyC4_TempVar | Calculate variables required to estimate percent C4 species... |
| swEstab-class | Class '"swEstab"' |
| swEstabSpecies-class | Class '"swEstabSpecies"' |
| swEstab_useEstab | 'swEstab_useEstab' |
| swEstab_useEstab-set | 'swEstab_useEstab<-' |
| sw_exampleData | Input data object for a site |
| sw_exec | Execute a 'rSOILWAT2' simulation run |
| swFiles_Carbon | 'swFiles_Carbon' |
| swFiles_Carbon-set | 'swFiles_Carbon<-' |
| swFiles-class | Class '"swFiles"' |
| swFiles_Cloud | 'swFiles_Cloud' |
| swFiles_Cloud-set | 'swFiles_Cloud<-' |
| swFiles_Estab | 'swFiles_Estab' |
| swFiles_Estab-set | 'swFiles_Estab<-' |
| swFiles_filesIn | 'swFiles_filesIn' |
| swFiles_filesIn-set | 'swFiles_filesIn<-' |
| swFiles_LogFile | 'swFiles_LogFile' |
| swFiles_LogFile-set | 'swFiles_LogFile<-' |
| swFiles_MarkovCov | 'swFiles_MarkovCov' |
| swFiles_MarkovCov-set | 'swFiles_MarkovCov<-' |
| swFiles_MarkovProbs | 'swFiles_MarkovProbs' |
| swFiles_MarkovProbs-set | 'swFiles_MarkovProbs<-' |
| swFiles_Output | 'swFiles_Output' |
| swFiles_OutputPrefix | 'swFiles_OutputPrefix' |
| swFiles_OutputPrefix-set | 'swFiles_OutputPrefix<-' |
| swFiles_Output-set | 'swFiles_Output<-' |
| swFiles_Prod | 'swFiles_Prod' |
| swFiles_Prod-set | 'swFiles_Prod<-' |
| swFiles_ProjDir | 'swFiles_ProjDir' |
| swFiles_ProjDir-set | 'swFiles_ProjDir<-' |
| swFiles_SiteParams | 'swFiles_SiteParams' |
| swFiles_SiteParams-set | 'swFiles_SiteParams<-' |
| swFiles_Soils | 'swFiles_Soils' |
| swFiles_Soils-set | 'swFiles_Soils<-' |
| swFiles_SWCsetup | 'swFiles_SWCsetup' |
| swFiles_SWCsetup-set | 'swFiles_SWCsetup<-' |
| swFiles_SWRCp | 'swFiles_SWRCp' |
| swFiles_SWRCp-set | 'swFiles_SWRCp<-' |
| swFiles_WeatherPrefix | 'swFiles_WeatherPrefix' |
| swFiles_WeatherPrefix-set | 'swFiles_WeatherPrefix<-' |
| swFiles_WeatherSetup | 'swFiles_WeatherSetup' |
| swFiles_WeatherSetup-set | 'swFiles_WeatherSetup<-' |
| swFiles_Years | 'swFiles_Years' |
| swFiles_Years-set | 'swFiles_Years<-' |
| sw_inputData | Default input object for 'rSOILWAT2'. Use this as a template... |
| swInputData-class | Class '"swInputData"' |
| sw_inputDataFromFiles | Read simulation input data from files on disk |
| swLog-class | Class '"swLog"' |
| swLog_setLine-set | 'swLog_setLine<-' |
| swMarkov-class | Class '"swMarkov"' |
| swMarkov_Conv | 'swMarkov_Conv' |
| swMarkov_Conv-set | 'swMarkov_Conv<-' |
| swMarkov_Prob | 'swMarkov_Prob' |
| swMarkov_Prob-set | 'swMarkov_Prob<-' |
| sw_meteo_obtain | Extract meteorological data from external source and format... |
| swMonthlyScalingParams-class | Class '"swMonthlyScalingParams"' |
| swOUT-class | Class 'swOUT' |
| sw_out_flags | Slot names of swOutput |
| swOUT_key-class | Class '"swOUT_key"' |
| swOUT_OutputSeparator | 'swOUT_OutputSeparator' |
| swOUT_OutputSeparator-set | 'swOUT_OutputSeparator<-' |
| swOutput-class | Class '"swOutput"' |
| sw_outputData | Return output data |
| swOutput_getKEY | 'swOutput_getKEY' |
| swOutput_KEY-class | Class '"swOutput_KEY"' |
| swOutput_KEY_Columns | 'swOutput_KEY_Columns' |
| swOutput_KEY_Columns-set | 'swOutput_KEY_Columns<-' |
| swOutput_KEY_Period | 'swOutput_KEY_Period' |
| swOutput_KEY_Period-set | 'swOutput_KEY_Period<-' |
| swOutput_KEY_TimeStep | 'swOutput_KEY_TimeStep' |
| swOutput_KEY_TimeStep-set | 'swOutput_KEY_TimeStep<-' |
| swOutput_setKEY-set | 'swOutput_setKEY<-' |
| swOUT_TimeStep | 'swOUT_TimeStep' |
| swOUT_TimeStep-set | 'swOUT_TimeStep<-' |
| swOUT_TimeStepsForEveryKey | 'swOUT_TimeStepsForEveryKey' |
| swOUT_TimeStepsForEveryKey-set | 'swOUT_TimeStepsForEveryKey<-' |
| swProd_Albedo | 'swProd_Albedo' |
| swProd_Albedo-set | 'swProd_Albedo<-' |
| swProd_CanopyHeight | 'swProd_CanopyHeight' |
| swProd_CanopyHeight-set | 'swProd_CanopyHeight<-' |
| swProd-class | Class '"swProd"' |
| swProd_CO2Coefficients | 'swProd_CO2Coefficients' |
| swProd_CO2Coefficients-set | 'swProd_CO2Coefficients<-' |
| swProd_Composition | 'swProd_Composition' |
| swProd_Composition-set | 'swProd_Composition<-' |
| swProd_CritSoilWaterPotential | 'swProd_CritSoilWaterPotential' |
| swProd_CritSoilWaterPotential-set | 'swProd_CritSoilWaterPotential<-' |
| swProd_Es_param_limit | 'swProd_Es_param_limit' |
| swProd_Es_param_limit-set | 'swProd_Es_param_limit<-' |
| swProd_EsTpartitioning_param | 'swProd_EsTpartitioning_param' |
| swProd_EsTpartitioning_param-set | 'swProd_EsTpartitioning_param<-' |
| swProd_HydrRedstro | 'swProd_HydrRedstro' |
| swProd_HydrRedstro-set | 'swProd_HydrRedstro<-' |
| swProd_HydrRedstro_use | 'swProd_HydrRedstro_use' |
| swProd_HydrRedstro_use-set | 'swProd_HydrRedstro_use<-' |
| swProd_LitterInterParam | 'swProd_LitterInterParam' |
| swProd_LitterInterParam-set | 'swProd_LitterInterParam<-' |
| swProd_MonProd_forb | 'swProd_MonProd_forb' |
| swProd_MonProd_forb-set | 'swProd_MonProd_forb<-' |
| swProd_MonProd_grass | 'swProd_MonProd_grass' |
| swProd_MonProd_grass-set | 'swProd_MonProd_grass<-' |
| swProd_MonProd_shrub | 'swProd_MonProd_shrub' |
| swProd_MonProd_shrub-set | 'swProd_MonProd_shrub<-' |
| swProd_MonProd_tree | 'swProd_MonProd_tree' |
| swProd_MonProd_tree-set | 'swProd_MonProd_tree<-' |
| swProd_MonProd_veg | 'swProd_MonProd_veg' |
| swProd_MonProd_veg-set | 'swProd_MonProd_veg<-' |
| swProd_Shade | 'swProd_Shade' |
| swProd_Shade-set | 'swProd_Shade<-' |
| swProd_VegInterParam | 'swProd_VegInterParam' |
| swProd_VegInterParam-set | 'swProd_VegInterParam<-' |
| swrc_conversion | Conversion between bulk soil water content and soil water... |
| swrc_names | List Soil Water Retention Curves 'SWRCs' |
| SWRCs | Functionality for Soil Water Retention Curves ('SWRC') |
| swReadLines | 'swReadLines' |
| swSite-class | Class '"swSite"' |
| swSite_DrainageCoefficient | 'swSite_DrainageCoefficient' |
| swSite_DrainageCoefficient-set | 'swSite_DrainageCoefficient<-' |
| swSite_EvapCoefficients | 'swSite_EvapCoefficients' |
| swSite_EvapCoefficients-set | 'swSite_EvapCoefficients<-' |
| swSite_hasSWRCp | Are 'SWRC' parameters provided in 'SWRCp'? |
| swSite_IntrinsicSiteParams | 'swSite_IntrinsicSiteParams' |
| swSite_IntrinsicSiteParams-set | 'swSite_IntrinsicSiteParams<-' |
| swSite_ModelCoefficients | 'swSite_ModelCoefficients' |
| swSite_ModelCoefficients-set | 'swSite_ModelCoefficients<-' |
| swSite_ModelFlags | 'swSite_ModelFlags' |
| swSite_ModelFlags-set | 'swSite_ModelFlags<-' |
| swSite_SnowSimulationParams | 'swSite_SnowSimulationParams' |
| swSite_SnowSimulationParams-set | 'swSite_SnowSimulationParams<-' |
| swSite_SoilDensityInputType | 'swSite_SoilTemperatureFlag' |
| swSite_SoilDensityInputType-set | 'swSite_SoilDensityInputType<-' |
| swSite_SoilTemperatureConsts | 'swSite_SoilTemperatureConsts' |
| swSite_SoilTemperatureConsts-set | 'swSite_SoilTemperatureConsts<-' |
| swSite_SoilTemperatureFlag | 'swSite_SoilTemperatureFlag' |
| swSite_SoilTemperatureFlag-set | 'swSite_SoilTemperatureFlag<-' |
| swSite_SWClimits | 'swSite_SWClimits' |
| swSite_SWClimits-set | 'swSite_SWClimits<-' |
| swSite_SWRCflags | Names of 'SWRC' and 'PTF' |
| swSite_TranspCoefficients | 'swSite_TranspCoefficients' |
| swSite_TranspCoefficients-set | 'swSite_TranspCoefficients<-' |
| swSite_TranspirationRegions | 'swSite_TranspirationRegions' |
| swSite_TranspirationRegions-set | 'swSite_TranspirationRegions<-' |
| swSoils-class | Class '"swSoils"' |
| swSoils_Layers | Interact with the soil layer data frame |
| swSoils_SWRCp | 'SWRC' parameters |
| swSWC-class | Class '"swSWC"' |
| swSWC_FirstYear | 'swSWC_FirstYear' |
| swSWC_FirstYear-set | 'swSWC_FirstYear<-' |
| swSWC_hist-class | Class '"swSWC_hist"' |
| swSWC_HistoricData | 'swSWC_HistoricData' |
| swSWC_HistoricData-set | 'swSWC_HistoricData<-' |
| swSWC_HistoricList | 'swSWC_HistoricList' |
| swSWC_HistoricList-set | 'swSWC_HistoricList<-' |
| swSWC_Method | 'swSWC_Method' |
| swSWC_Method-set | 'swSWC_Method<-' |
| swSWC_prefix | 'swSWC_prefix' |
| swSWC_prefix-set | 'swSWC_prefix<-' |
| swSWC_use | 'swSWC_use' |
| swSWC_use-set | 'swSWC_use<-' |
| sw_upgrade | Upgrade a 'rSOILWAT2'-classed object from an older package... |
| sw_verbosity | Turn on/off 'SOILWAT2' notes and warnings |
| swWeather-class | Class '"swWeather"' |
| sw_weather_data | 'rSOILWAT2' weather data functionality |
| sw_weather_database | Weather data base structure |
| swWeatherData-class | Class '"swWeatherData"' |
| swWeather_DaysRunningAverage | 'swWeather_DaysRunningAverage' |
| swWeather_DaysRunningAverage-set | 'swWeather_DaysRunningAverage<-' |
| swWeather_FirstYearHistorical | 'swWeather_FirstYearHistorical' |
| swWeather_FirstYearHistorical-set | 'swWeather_FirstYearHistorical<-' |
| swWeather_MonScalingParams | 'swWeather_MonScalingParams' |
| swWeather_MonScalingParams-set | 'swWeather_MonScalingParams<-' |
| swWeather_pct_SnowDrift | 'swWeather_pct_SnowDrift' |
| swWeather_pct_SnowDrift-set | 'swWeather_pct_SnowDrift<-' |
| swWeather_pct_SnowRunoff | 'swWeather_pct_SnowRunoff' |
| swWeather_pct_SnowRunoff-set | 'swWeather_pct_SnowRunoff<-' |
| swWeather_UseMarkov | 'swWeather_UseMarkov' |
| swWeather_UseMarkovOnly | 'swWeather_UseMarkovOnly' |
| swWeather_UseMarkovOnly-set | 'swWeather_UseMarkovOnly<-' |
| swWeather_UseMarkov-set | 'swWeather_UseMarkov<-' |
| swWeather_UseSnow | 'swWeather_UseSnow' |
| swWeather_UseSnow-set | 'swWeather_UseSnow<-' |
| swYears-class | Class '"swYears"' |
| swYears_EDOEY | 'swYears_EDOEY' |
| swYears_EDOEY-set | 'swYears_EDOEY<-' |
| swYears_EndYear | 'swYears_EndYear' |
| swYears_EndYear-set | 'swYears_EndYear<-' |
| swYears_FDOFY | 'swYears_FDOFY' |
| swYears_FDOFY-set | 'swYears_FDOFY<-' |
| swYears_isNorth | 'swYears_isNorth' |
| swYears_isNorth-set | 'swYears_isNorth<-' |
| swYears_StartYear | 'swYears_StartYear' |
| swYears_StartYear-set | 'swYears_StartYear<-' |
| time_columns | Output column indices with time information |
| TranspCoeffByVegType | Lookup transpiration coefficients |
| update_biomass | Replace selected biomass values of a rSOILWAT2::swProd object |
| weatherData | Daily weather data for a site |
| weather_dataAggFun | Functions to summarize currently implemented daily weather... |
| weather_dataColumns | List names of currently implemented daily weather variables |
| weatherGenerator_dataColumns | List daily weather variables incorporated in the weather... |
