Man pages for ScitoVation/plethem
Population Life Course Exposure to Health Effects Modeling
| addChemsToHTTK | Function that adds chemical to httk package chem list. |
| addDataSet | Server side function for the UI used to add external... |
| addDataSetUI | UI for adding external observation datasets to projects |
| addParameters | Add user selected parameters to the PBPK reporting document.... |
| addPBPKequations | Add PBPK equations to the PBPK reporting document. Should not... |
| calc_cyp2b6 | Calculate cyp2b6 fraction |
| calcMPCPPGL | Calcuate MPPGL and CPPGL based on age |
| calculatePartitionCoefficients | Calculate Partition Coefficient |
| clearProjectDb | Clear Project Db |
| createEmptyUserDb | Creates a new userDb based on the empty database in the... |
| createHESIgraphs | Pipe to add concentration-timecourse data to the report... |
| createPBPKflowchart | Creates the PBPK model flowchart. Should not be used by... |
| externDbSelect | Runs all select queries an arbitrary database |
| getAllCypData | get data for human cyp fraction by age |
| getAllParamValuesForModel | Gets all the parameter values for the model. This function... |
| getAllSetChoices | get all set names for a given paramter set |
| getAllVariabilityValuesForModel | Gets all the variability values for the model. This data... |
| getDbConn | Gets the connection to the Db to run all the queries against |
| getFileFolderPath | Show dialogs to select files or folders |
| getLifecourseBodyHeight | Get average body height using the life course equation |
| getLifecourseBodyHeightMale | Calculate body height of average human male using the... |
| getLifecourseBodyWeight | Get average body weight using the life course equation |
| getLifecourseBodyWeightFemale | Calculate body weight in kg of average human female using the... |
| getLifecourseBodyWeightMale | Calculate body weight in kg of average human male using the... |
| getLifecourseCardiacOutput | Get the cardiac output based on the life course equations |
| getLifecourseGlomerularFiltrationRate | Get the Glomerular Filteration Rate for a given age and... |
| getLifecourseLungDeadSpace | Get the Lung Dead Space for a given age and gender |
| getLifecourseTidalVolume | Get the tidal volume for a given age and gender |
| getLifecourseTissuePerfusion | Get perfusion for tissues provided on the basis of age and... |
| getLifecourseTissueVolumes | Get volumes for tissues provided on the basis of age and... |
| getLifecourseUrineProductionRate | Get the urine production rate for a given age and gender |
| getLifecourseVentilationRate | Get the ventilation rate for a given age and gender |
| getMetabData | Gets the metabolism data. Should not be used by directly by... |
| getNextID | Get the next Id for the table entry |
| getObservationSetChoices | Get all observation sets |
| getParameterSet | Get the values for parameters in a given set |
| getProjectChemicalList | get the list of chemicals currently in the project database |
| getVariabilitySetChoices | Get all variability sets |
| HT_IVIVE | server function of high throughput dosimetry |
| HT_IVIVEUI | Module for editing high throughput reverse dosimetry... |
| httkCalcOralEqDose | Function that runs the httk oral equivalent dose gadget. |
| httkParameterPBTK | Call httk function for parameterizing PBPK models |
| importAllExposureData | Server function for all (Batch Exposure, TRA, SEEM, and... |
| importAllExposureDataUI | UI for importing all (Batch Exposure, TRA, SEEM, and SHEDS)... |
| importBatchExposure | Server function for batch data module |
| importBatchExposureUI | UI function for importing generic exposure data |
| importHTTKData | Server function for importing HTTK data |
| importHTTKDataUI | UI for importing data from HTTK |
| importParameterSet | Server for import parameter module |
| importParameterSetUI | UI for importing parameter sets |
| importSEEMData | Server function for seem data module |
| importSEEMDataUI | UI for importing SEEM data. |
| importShedsData | Server function for importing SHEDS data |
| importShedsDataUI | UI function for importing SHEDS data |
| interactiveHT | Launch HT-IVIVE interface |
| interactivePBPK | Launch the interactive PBPK workflow for the given model |
| interactiveReverseDosimetry | Launch Reverse Dosimetry Interface |
| loadProject | Load the project from the project file located at the given... |
| loadTRA | run TRA gadget and save files as needed. |
| mainDbSelect | Runs all select queries to the main database. |
| mainDbUpdate | Runs all update queries to the main database. |
| newEditVariability | Server function for defining variability and uncertainty... |
| newEditVariabilityUI | UI function for defining variability and uncertainty datasets |
| newProject | Start a new PLETHEM project. |
| newProjectGadget | Command line function launching the new project gadget |
| parseConsExpoFile | Parse uploaded file for consexpo |
| parseTRAFile | Parse uploaded file for Consumer TRA |
| performIVIVE | server side function for performing IVIVE for a chemical |
| performIVIVEUI | Shiny module that is called when perform IVIVE button is... |
| performPlethemNCA | Functions for performing NCA and returning the data |
| plethem-package | Population Life Course Exposure to Health Effects Modeling |
| preprocessUIData | preprocess value list from UI |
| projectDbSelect | Runs all select queries to the project database. |
| projectDbUpdate | Runs all update queries to the project database. |
| projectReadTable | Read all the contents of a table |
| projectWriteTable | Write the dataframe to the table |
| qsarModelone | Calculate Partition Coefficient using the default QSAR model |
| qsarModeltwo | Calculate Partition Coefficient using the default QSAR model |
| readBatchChemicalFile | Read and parse the chemical batch file |
| readOperaPredictions | Read and parse the predictions from OPERA |
| reshapePlotData | reshape plotted data to create wide form |
| runFDPBPK | Run the PBPK models in forward dosimetry mode |
| runHTIVIVE | Run HT-IVIVE |
| runPlthemHTIVIVE | High Throughput reverse dosimetry calculation using UI |
| runReverseDosimetry | Estimate exposure from montecarlo results and biomonitoring... |
| saveAsParameterSet | server side function for saving a new physiological, chemical... |
| saveAsParameterSetUI | UI for saving a new physiological, chemical or exposure set... |
| saveProject | Save the current project to a location |
| saveRestoreParameterSet | Server for the restore/save dialog |
| saveRestoreParameterSetUI | UI for the restore/save dialog |
| scale_cellular_enzymatic | Scale clearance by age when both cellular and enzymatic... |
| scale_enzymatic | Scale clearance by age for when enzymatic clearance is known... |
| setUserDb | Sets the path to the existing Db |
| updateUIInputs | Update Inputs for PLETHEM UI |
| userDbSelect | Runs all select queries to the user database. |
| userDbUpdate | Runs all update queries to the user database. |
