get_wetmore_oral_equiv

This function is included for backward compatibility. It calls
<code>get_lit_oral_equiv</code> which
converts a chemical plasma concetration to an oral equivalent
dose using the values from the Wetmore et al. (2012) and (2013) publications
and other literature.

Monte-Carlo

Literature

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

get_wetmore_oral_equiv function

<dl><dt>conc</dt>
<dd>Bioactive in vitro concentration in units of specified
input.units, default of uM.</dd>
<dt>chem.name</dt>
<dd>Either the chemical name or the CAS number must be
specified.</dd>
<dt>chem.cas</dt>
<dd>Either the CAS number or the chemical name must be
specified.</dd>
<dt>suppress.messages</dt>
<dd>Suppress output messages.</dd>
<dt>which.quantile</dt>
<dd>Which quantile from the SimCYP Monte Carlo simulation
is requested. Can be a vector. Papers include 0.05, 0.5, and 0.95 for
humans and 0.5 for rats.</dd>
<dt>species</dt>
<dd>Species desired (either "Rat" or default "Human").</dd>
<dt>input.units</dt>
<dd>Units of given concentration, default of uM but can also
be mg/L.</dd>
<dt>output.units</dt>
<dd>Units of dose, default of 'mg' for mg/kg BW/ day or
'mol' for mol/ kg BW/ day.</dd>
<dt>clearance.assay.conc</dt>
<dd>Concentration of chemical used in measureing
intrinsic clearance data, 1 or 10 uM.</dd>
<dt>...</dt>
<dd>Additional parameters passed to get_lit_css.</dd></dl>

Arguments

Author

Get Literature Oral Equivalent Dose (deprecated). — get_wetmore_oral_equiv

<dl>

<dt>conc</dt>
<dd>Bioactive in vitro concentration in units of specified
input.units, default of uM.</dd>


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


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


<dt>suppress.messages</dt>
<dd>Suppress output messages.</dd>


<dt>which.quantile</dt>
<dd>Which quantile from the SimCYP Monte Carlo simulation
is requested. Can be a vector. Papers include 0.05, 0.5, and 0.95 for
humans and 0.5 for rats.</dd>


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


<dt>input.units</dt>
<dd>Units of given concentration, default of uM but can also
be mg/L.</dd>


<dt>output.units</dt>
<dd>Units of dose, default of 'mg' for mg/kg BW/ day or
'mol' for mol/ kg BW/ day.</dd>


<dt>clearance.assay.conc</dt>
<dd>Concentration of chemical used in measureing
intrinsic clearance data, 1 or 10 uM.</dd>


<dt>...</dt>
<dd>Additional parameters passed to get_lit_css.</dd>

</dl>

Get Literature Oral Equivalent Dose (deprecated).

get_wetmore_oral_equiv: Get Literature Oral Equivalent Dose (deprecated).

Description

Usage

Value

Arguments

Author

References

Examples