This function provides the necessary parameters to run
predict_partitioning_schmitt, excluding the data in table
tissue.data. The model is based on the Schmitt (2008) method
for predicting tissue:plasma partition coefficients as modified by Pearce
et al. (2017). The modifications include approaches adapted from Peyret
et al. (2010).
parameterize_schmitt(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
parameters = NULL,
species = "Human",
default.to.human = FALSE,
force.human.fup = FALSE,
adjusted.Funbound.plasma = TRUE,
suppress.messages = FALSE,
class.exclude = TRUE,
minimum.Funbound.plasma = 1e-04
)Unbound fraction in plasma, adjusted for lipid binding according to Pearce et al. (2017)
measured unbound fraction in plasma (0.005 if below limit of detection)
octanol:water partition coefficient (not log transformed)
compound H dissociation equilibrium constant(s)
compound H association equilibrium constant(s)
phospholipid:water distribution coefficient, membrane affinity
protein fraction in plasma
pH of the plasma
Chemical Abstract Services Registry Number (CAS-RN) -- if parameters is not specified then the chemical must be identified by either CAS, name, or DTXISD
Chemical name (spaces and capitalization ignored) -- if parameters is not specified then the chemical must be identified by either CAS, name, or DTXISD
EPA's DSSTox Structure ID (https://comptox.epa.gov/dashboard) -- if parameters is not specified then the chemical must be identified by either CAS, name, or DTXSIDs
Chemcial and physiological description parameters needed to run the Schmitt et al. (2008) model
Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").
Substitutes missing fraction of unbound plasma with human values if true.
Returns human fraction of unbound plasma in calculation for rats if true. When species is specified as rabbit, dog, or mouse, the human unbound fraction is substituted.
Uses Pearce et al. (2017) lipid binding adjustment for Funbound.plasma (which impacts partition coefficients) when set to TRUE (Default).
Whether or not the output message is suppressed.
Exclude chemical classes identified as outside of domain of applicability by relevant modelinfo_[MODEL] file (default TRUE).
Monte Carlo draws less than this value are set equal to this value (default is 0.0001 -- half the lowest measured Fup in our dataset).
Robert Pearce and John Wambaugh
pearce2017httkhttk
schmitt2008generalhttk
schmitt2008corrigendumhttk
pearce2017evaluationhttk
peyret2010unifiedhttk
predict_partitioning_schmitt
tissue.data
calc_ma
apply_fup_adjustment
parameterize_schmitt(chem.name='bisphenola')
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