Population Life Course Exposure to Health Effects Modeling


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Documentation for package ‘plethem’ version 1.0.1

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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.