# Population Life Course Exposure to Health Effects Modeling

## Documentation for package ‘plethem’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

addChemsToHTTK | Function that adds chemical to httk package chem list.
addDataSet | Server side function for the UI used to add external observation datasets to projects
addDataSetUI | UI for adding external observation datasets to projects
calcMPCPPGL | Calcuate MPPGL and CPPGL based on age
calculatePartitionCoefficients | Calculate Partition Coefficient
calc_cyp2b6 | Calculate cyp2b6 fraction
clearProjectDb | Clear Project Db
createEmptyUserDb | Creates a new userDb based on the empty database in the package
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 should not be used by the model
getAllSetChoices | get all set names for a given paramter set
getAllVariabilityValuesForModel | Gets all the variability values for the model. This data returned by the function is not meant to be understandable by the user
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 lifecourse equation
getLifecourseBodyWeight | Get average body weight using the life course equation
getLifecourseBodyWeightFemale | Calculate body weight in kg of average human female using the lifecourse equation
getLifecourseBodyWeightMale | Calculate body weight in kg of average human male using the lifecourse equation
getLifecourseCardiacOutput | Get the cardiac output based on the life course equations
getLifecourseGlomerularFiltrationRate | Get the Glomerular Filteration Rate for a given age and gender
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 gender
getLifecourseTissueVolumes | Get volumes for tissues provided on the basis of age and gender
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 the user
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
httkCalcOralEqDose | Function that runs the httk oral equivalent dose gadget.
httkParameterPBTK | Call httk function for parameterizing PBPK models
HT_IVIVE | server function of high throughput dosimetry
HT_IVIVEUI | Module for editing high throughput reverse dosimetry functions
importAllExposureData | Server function for all (Batch Exposure, TRA, SEEM, and SHEDS) data module
importAllExposureDataUI | UI for importing all (Batch Exposure, TRA, SEEM, and SHEDS) data module.
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 path
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 datasets
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 clicked on the chemical tab of a PBPK model
performPlethemNCA | Functions for performing NCA and returning the data
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 data
saveAsParameterSet | server side function for saving a new physiological, chemical or exposure set to the project database
saveAsParameterSetUI | UI for saving a new physiological, chemical or exposure set to the project database
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 clearance are known at reference age.
scale_enzymatic | Scale clearance by age for when enzymatic clearance is known at reference age.
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.