calc_total_clearance

This function calculates the total clearance rate for a one compartment model
for plasma
where clearance is entirely due to metablism by the liver and glomerular
filtration in the kidneys, identical to clearance of three compartment
steady state model.

Parameter

1compartment

Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predictions for chemicals
where in vivo data do exist. The models are systems of ordinary
differential equations that are developed in MCSim and solved
using compiled (C-based) code for speed. A Monte Carlo sampler is
included for simulating human biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and propagating parameter uncertainty
(Wambaugh et al., 2019 <doi:10.1093/toxsci/kfz205>).
Empirically calibrated methods are included for predicting
tissue:plasma partition coefficients and volume of distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for using IVIVE to
convert concentrations from high-throughput screening experiments
(for example, Tox21, ToxCast) to real-world exposures via reverse
dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).

John Wambaugh

httk

High-Throughput Toxicokinetics

Sarah Davidson-Fritz

Robert Pearce

Caroline Ring

Greg Honda

Mark Sfeir

Matt Linakis

Dustin Kapraun

Nathan Pollesch

Miyuki Breen

Shannon Bell

Xiaoqing Chang

Todor Antonijevic

Jimena Davis

Elaina Kenyon

Katie Paul Friedman

Celia Schacht

Meredith Scherer

James Sluka

Noelle Sinski

Nisha Sipes

Barbara Wetmore

Lily Whipple

Woodrow Setzer

calc_total_clearance function

<dl><dt>chem.cas</dt>
<dd>Either the chemical name, CAS number, or the parameters must
be specified.</dd>
<dt>chem.name</dt>
<dd>Either the chemical name, CAS number, or the parameters
must be specified.</dd>
<dt>dtxsid</dt>
<dd>EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard)
the chemical must be identified by either CAS, name, or DTXSIDs</dd>
<dt>parameters</dt>
<dd>Chemical parameters from parameterize_steadystate
function, overrides chem.name and chem.cas.</dd>
<dt>model</dt>
<dd>The model used to calculate total clearance (defaults to "3compartmentss")</dd>
<dt>species</dt>
<dd>Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or
default "Human").</dd>
<dt>suppress.messages</dt>
<dd>Whether or not the output message is suppressed.</dd>
<dt>default.to.human</dt>
<dd>Substitutes missing animal values with human values
if true.</dd>
<dt>class.exclude</dt>
<dd>Exclude chemical classes identified as outside of 
domain of applicability by relevant modelinfo_[MODEL] file (default TRUE).</dd>
<dt>restrictive.clearance</dt>
<dd>Protein binding is not taken into account (set
to 1) in liver clearance if FALSE.</dd>
<dt>...</dt>
<dd>Additional parameters passed to parameterize_steadystate if
parameters is NULL.</dd></dl>

Arguments

Author

Calculate the total plasma clearance. — calc_total_clearance

<dl>

<dt>chem.cas</dt>
<dd>Either the chemical name, CAS number, or the parameters must
be specified.</dd>


<dt>chem.name</dt>
<dd>Either the chemical name, CAS number, or the parameters
must be specified.</dd>


<dt>dtxsid</dt>
<dd>EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard)
the chemical must be identified by either CAS, name, or DTXSIDs</dd>


<dt>parameters</dt>
<dd>Chemical parameters from parameterize_steadystate
function, overrides chem.name and chem.cas.</dd>


<dt>model</dt>
<dd>The model used to calculate total clearance (defaults to "3compartmentss")</dd>


<dt>species</dt>
<dd>Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or
default "Human").</dd>


<dt>suppress.messages</dt>
<dd>Whether or not the output message is suppressed.</dd>


<dt>default.to.human</dt>
<dd>Substitutes missing animal values with human values
if true.</dd>


<dt>class.exclude</dt>
<dd>Exclude chemical classes identified as outside of 
domain of applicability by relevant modelinfo_[MODEL] file (default TRUE).</dd>


<dt>restrictive.clearance</dt>
<dd>Protein binding is not taken into account (set
to 1) in liver clearance if FALSE.</dd>


<dt>...</dt>
<dd>Additional parameters passed to parameterize_steadystate if
parameters is NULL.</dd>

</dl>

Calculate the total plasma clearance.

calc_total_clearance: Calculate the total plasma clearance.

Description

Usage

Value

Arguments

Author

Examples