calc_vdist

This function predicts partition coefficients for all tissues using
<code>predict_partitioning_schmitt</code>, then lumps them
into a single compartment.

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_vdist function

<dl><dt>chem.cas</dt>
<dd>Either the CAS number or the chemical name must be specified
when Funbound.plasma is not given in parameter list.</dd>
<dt>chem.name</dt>
<dd>Either the chemical name or the CAS number must be
specified when Funbound.plasma is not given in parameter list.</dd>
<dt>dtxsid</dt>
<dd>EPA's DSSTox Structure ID (<a href="https://comptox.epa.gov/dashboard">https://comptox.epa.gov/dashboard</a>)
the chemical must be identified by either CAS, name, or DTXSIDs</dd>
<dt>parameters</dt>
<dd>Parameters from parameterize_3comp, parameterize_pbtk or
predict_partitioning_schmitt.</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>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>adjusted.Funbound.plasma</dt>
<dd>Uses adjusted Funbound.plasma when set to
TRUE along with parition coefficients calculated with this value.</dd>
<dt>regression</dt>
<dd>Whether or not to use the regressions in calculating
partition coefficients.</dd>
<dt>minimum.Funbound.plasma</dt>
<dd>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).</dd></dl>

Arguments

Author

Calculate the volume of distribution for a one compartment model. — calc_vdist

<dl>

<dt>chem.cas</dt>
<dd>Either the CAS number or the chemical name must be specified
when Funbound.plasma is not given in parameter list.</dd>


<dt>chem.name</dt>
<dd>Either the chemical name or the CAS number must be
specified when Funbound.plasma is not given in parameter list.</dd>


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


<dt>parameters</dt>
<dd>Parameters from parameterize_3comp, parameterize_pbtk or
predict_partitioning_schmitt.</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>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>adjusted.Funbound.plasma</dt>
<dd>Uses adjusted Funbound.plasma when set to
TRUE along with parition coefficients calculated with this value.</dd>


<dt>regression</dt>
<dd>Whether or not to use the regressions in calculating
partition coefficients.</dd>


<dt>minimum.Funbound.plasma</dt>
<dd>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).</dd>

</dl>

Calculate the volume of distribution for a one compartment model.

calc_vdist: Calculate the volume of distribution for a one compartment model.

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples