augment.table

This internal function is used by <code>add_chemtable</code> to add a single 
new parameter to the table of chemical parameters. It should not be typically
used from the command line.

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

Kimberly Truong

Colin Thomson

Meredith Scherer

Annabel Meade

Celia Schacht

Leonie Lautz

Todor Antonijevic

Miyuki Breen

Shannon Bell

Xiaoqing Chang

Jimena Davis

Elaina Kenyon

Gilberto Padilla Mercado

Katie Paul Friedman

Nathan Pollesch

Noelle Sinski

Nisha Sipes

James Sluka

Caroline Stevens

Barbara Wetmore

Lily Whipple

Woodrow Setzer

augment.table function

<dl><dt>this.table</dt>
<dd>Object of class data.frame containing one row per chemical.</dd>
<dt>this.CAS</dt>
<dd>The Chemical Abstracts Service registry number (CAS-RN)
correponding to the parameter value</dd>
<dt>compound.name</dt>
<dd>A name associated with the chemical (defaults to NULL)</dd>
<dt>this.property</dt>
<dd>The property being added/modified.</dd>
<dt>value</dt>
<dd>The value being assigned to this.property.</dd>
<dt>species</dt>
<dd>This is the species for the data in the new table. This may
be omitted if a column in data.list gives the species value for each
chemical or if the data are not species-specific (e.g., MW).</dd>
<dt>reference</dt>
<dd>This is the reference for the data in the new table. This
may be omitted if a column in data.list gives the reference value for each
chemical.</dd>
<dt>overwrite</dt>
<dd>If overwrite=TRUE then data in current.table will be
replaced by any data in new.table that is for the same chemical and
property. If overwrite=FALSE (DEFAULT) then new data for the same chemical
and property are ignored. Funbound.plasma values of 0 (below limit of
detection) are overwritten either way.</dd>
<dt>sig.fig</dt>
<dd>Sets the number of significant figures stored (defaults to 4)</dd>
<dt>clint.pvalue.overwrite</dt>
<dd>If TRUE then the Cl_int p-value is set to NA 
when the Cl_int value is changed unless a new p-value is provided. (defaults
to TRUE)</dd>
<dt>allow.na</dt>
<dd>If TRUE (default is FALSE) then NA values are written to the
table, otherwise they are ignored.</dd>
<dt>suppress.messages</dt>
<dd>Whether or not the output messages are suppressed.</dd></dl>

Arguments

Author

Add a parameter value to the chem.physical_and_invitro.data table — augment.table

<dl>

<dt>this.table</dt>
<dd>Object of class data.frame containing one row per chemical.</dd>


<dt>this.CAS</dt>
<dd>The Chemical Abstracts Service registry number (CAS-RN)
correponding to the parameter value</dd>


<dt>compound.name</dt>
<dd>A name associated with the chemical (defaults to NULL)</dd>


<dt>this.property</dt>
<dd>The property being added/modified.</dd>


<dt>value</dt>
<dd>The value being assigned to this.property.</dd>


<dt>species</dt>
<dd>This is the species for the data in the new table. This may
be omitted if a column in data.list gives the species value for each
chemical or if the data are not species-specific (e.g., MW).</dd>


<dt>reference</dt>
<dd>This is the reference for the data in the new table. This
may be omitted if a column in data.list gives the reference value for each
chemical.</dd>


<dt>overwrite</dt>
<dd>If overwrite=TRUE then data in current.table will be
replaced by any data in new.table that is for the same chemical and
property. If overwrite=FALSE (DEFAULT) then new data for the same chemical
and property are ignored. Funbound.plasma values of 0 (below limit of
detection) are overwritten either way.</dd>


<dt>sig.fig</dt>
<dd>Sets the number of significant figures stored (defaults to 4)</dd>


<dt>clint.pvalue.overwrite</dt>
<dd>If TRUE then the Cl_int p-value is set to NA 
when the Cl_int value is changed unless a new p-value is provided. (defaults
to TRUE)</dd>


<dt>allow.na</dt>
<dd>If TRUE (default is FALSE) then NA values are written to the
table, otherwise they are ignored.</dd>


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

</dl>

Add a parameter value to the chem.physical_and_invitro.data table

augment.table: Add a parameter value to the chem.physical_and_invitro.data table

Description

Usage

Value

Arguments

Author