Man pages for ScitoVation/plethem
Population Life Course Exposure to Health Effects Modeling

addChemsToHTTKFunction that adds chemical to httk package chem list.
addDataSetServer side function for the UI used to add external...
addDataSetUIUI for adding external observation datasets to projects
calc_cyp2b6Calculate cyp2b6 fraction
calcMPCPPGLCalcuate MPPGL and CPPGL based on age
calculatePartitionCoefficientsCalculate Partition Coefficient
clearProjectDbClear Project Db
createEmptyUserDbCreates a new userDb based on the empty database in the...
doIVIVErun IVIVE gadget and save files as needed.
editUserDbGadget for creating/editing the a user database
externDbSelectRuns all select queries an arbitrary database
getAllCypDataget data for human cyp fraction by age
getAllParamValuesForModelGets all the parameter values for the model. This function...
getAllSetChoicesget all set names for a given paramter set
getAllVariabilityValuesForModelGets all the variability values for the model. This data...
getDbConnGets the connection to the Db to run all the queries against
getFileFolderPathShow dialogs to select files or folders
getLifecourseBodyHeightGet average body height using the life course equation
getLifecourseBodyHeightMaleCalculate body height of average human male using the...
getLifecourseBodyWeightGet average body weight using the life course equation
getLifecourseBodyWeightFemaleCalculate body weight in kg of average human female using the...
getLifecourseBodyWeightMaleCalculate body weight in kg of average human male using the...
getLifecourseCardiacOutputGet the cardiac output based on the life course equations
getLifecourseGlomerularFiltrationRateGet the Glomerular Filteration Rate for a given age and...
getLifecourseLungDeadSpaceGet the Lung Dead Space for a given age and gender
getLifecourseTidalVolumeGet the tidal volume for a given age and gender
getLifecourseTissuePerfusionGet perfusion for tissues provided on the basis of age and...
getLifecourseTissueVolumesGet volumes for tissues provided on the basis of age and...
getLifecourseUrineProductionRateGet the urine production rate for a given age and gender
getLifecourseVentilationRateGet the ventilation rate for a given age and gender
getMetabDataGets the metabolism data. Should not be used by directly by...
getNextIDGet the next Id for the table entry
getObservationSetChoicesGet all observation sets
getParameterSetGet the values for parameters in a given set
getProjectChemicalListget the list of chemicals currently in the project database
getVariabilitySetChoicesGet all variability sets
HT_IVIVEserver function of high throughput dosimetry
HT_IVIVEUIModule for editing high throughput reverse dosimetry...
httkCalcOralEqDoseFunction that runs the httk oral equivalent dose gadget.
httkParameterPBTKCall httk function for parameterizing PBPK models
importAllExposureDataServer function for all (Batch Exposure, TRA, SEEM, and...
importAllExposureDataUIUI for importing all (Batch Exposure, TRA, SEEM, and SHEDS)...
importBatchExposureServer function for batch data module
importBatchExposureUIUI function for importing generic exposure data
importHTTKDataServer function for importing HTTK data
importHTTKDataUIUI for importing data from HTTK
importParameterSetServer for import parameter module
importParameterSetUIUI for importing parameter sets
importSEEMDataServer function for seem data module
importSEEMDataUIUI for importing SEEM data.
importShedsDataServer function for importing SHEDS data
importShedsDataUIUI function for importing SHEDS data
interactiveHTLaunch HT-IVIVE interface
iviveGadgetCommand line function for running the IVIVE gadget
loadProjectLoad the project from the project file located at the given...
loadTRArun TRA gadget and save files as needed.
mainDbSelectRuns all select queries to the main database.
mainDbUpdateRuns all update queries to the main database.
newEditVariabilityServer function for defining variability and uncertainty...
newEditVariabilityUIUI function for defining variability and uncertainty datasets
newProjectStart a new PLETHEM project.
newProjectGadgetCommand line function launching the new project gadget
parseTRAFileParse uploaded file for Consumer TRA
performIVIVEserver side function for performing IVIVE for a chemical
performIVIVEUIShiny module that is called when perform IVIVE button is...
performPlethemNCAFunctions for performing NCA and returning the data
preprocessUIDatapreprocess value list from UI
projectDbSelectRuns all select queries to the project database.
projectDbUpdateRuns all update queries to the project database.
projectReadTableRead all the contents of a table
projectWriteTableWrite the dataframe to the table
qsarModeloneCalculate Partition Coefficient using the default QSAR model
qsarModeltwoCalculate Partition Coefficient using the default QSAR model
readBatchChemicalFileRead and parse the chemical batch file
readOperaPredictionsRead and parse the predictions from OPERA
reshapePlotDatareshape plotted data to create wide form
runFDPBPKRun the PBPK models in forward dosimetry mode
runHTIVIVERun HT-IVIVE
runPlthemHTIVIVEHigh Throughput reverse dosimetry calculation using UI
saveAsParameterSetserver side function for saving a new physiological, chemical...
saveAsParameterSetUIUI for saving a new physiological, chemical or exposure set...
saveProjectSave the current project to a location
saveRestoreParameterSetServer for the restore/save dialog
saveRestoreParameterSetUIUI for the restore/save dialog
scale_cellular_enzymaticScale clearance by age when both cellular and enzymatic...
scale_enzymaticScale clearance by age for when enzymatic clearance is known...
setUserDbSets the path to the existing Db
updateUIInputsUpdate Inputs for PLETHEM UI
userDbSelectRuns all select queries to the user database.
userDbUpdateRuns all update queries to the user database.
ScitoVation/plethem documentation built on Aug. 23, 2019, 2:13 p.m.