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

addDataSetServer side function for the UI used to add external...
addDataSetUIUI for adding external observation datasets to projects
calc_ces1cCalculate ces1c fraction
calc_ces1mCalculate ces1m fraction
calc_ces2cCalculate ces2c fraction
calc_ces2mCalculate ces2m fraction
calc_cyp1a2Calculate cyp1a2 fraction
calc_cyp2b6Calculate cyp2b6 fraction
calc_cyp2c19Calculate cyp2c19 fraction
calc_cyp2c9Calculate cyp2c9 fraction
calc_cyp3a4Calculate cyp3a4 fraction
calcMPCPPGLCalcuate MPPGL and CPPGL based on age
calculateInhVolCsscalculate steady state concentration of inhaled volatile...
calculateOralNonvolCsscalculate steady state concentration of orally adminitered...
calculateOralVolCsscalculate steady state concentration of orally administered...
calculatePartitionCoefficientsCalculate Partition Coefficient
calculateRecombClearanceCalculate scaled in-vivo clearance if in-vitro clearance is...
calculateScaledS9ClearanceCalculate scaled in-vivo clearance if in-vitro clearance is...
calculateScaledSCClearanceCalculate scaled in-vivo clearance if in-vitro clearance is...
calculateScaledWholeHepClearanceCalculate sclaed in-vivo clearance if in-vitro clearance is...
chemicalServer side function for the UI used to edit local chemical...
chemicalInputUI for modufying the user chemical database
clearProjectDbClear Project Db
createUserDbCreates a new userDb based on the empty database in the...
doIVIVErun IVIVE gadget and save files as needed.
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...
getChemDataFromDbGet the chemical data from the project Db This function is...
getDbConnGets the connection to the pDb to run all the queries against
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...
getLifecourseTissuePerfusionGet perfusion for tissues provided on the basis of age and...
getLifecourseTissueVolumesGet volumes for tissues provided on the basis of age and...
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 This function is...
HT_IVIVEUIModule for editing high throughput reverse dosimetry...
importHTTKDataUIUI for importing data from HTTK
importParameterSetServer for import parameter module
importParameterSetUIUI for importing parameter sets
interactivePBPKLaunch PBPK interface valid values for names are "rapidPBPK"
interp2Small utility function for linear interpolation Used...
listProjectsList all the project currently in the PLETHEM
loadProjectLoad the project with the given name
mainDbSelectRuns all select queries to the main database.
mainDbUpdateRuns all update queries to the main database.
newEditVariabilityServer side function for variability
newProjectStart a new PLETHEM project.
perform_HTIVIVEMain function to run HT-Reverse Dosimetry from command line
performIVIVEserver side function for performing IVIVE for a chemical
performIVIVEUIShiny module that is called when perform IVIVE button is...
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
qsarModelDefaultCalculate Partition Coefficient using the default QSAR model
reshapePlotDatareshape plotted data to create wide form
runFDPBPKRun the PBPK models in forward dosimetry mode
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 clerance 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. 18, 2018, 10:38 p.m.