bmdobj

The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the tcpl R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). tcplfit2 can be used independently to support analysis for diverse chemical screening efforts.

Jason Brown

tcplfit2

A Concentration-Response Modeling Utility

Thomas Sheffield

Richard S Judson

Sarah E. Davidson

Zhihui Zhao

Madison Feshuk

Katie Paul Friedman

bmdobj function

<dl><dt>bmd</dt>
<dd>Benchmark dose.</dd>
<dt>fname</dt>
<dd>Function name: "exp2", "exp3", "exp4", "exp5", "hillfn", "gnls",
"poly1", "poly2", or "pow".</dd>
<dt>bmr</dt>
<dd>Benchmark response.</dd>
<dt>conc</dt>
<dd>Vector of concentrations NOT in log units.</dd>
<dt>resp</dt>
<dd>Vector of corresponding responses.</dd>
<dt>ps</dt>
<dd>Named list of parameters.</dd>
<dt>mll</dt>
<dd>Maximum log-likelihood of winning model.</dd>
<dt>onesp</dt>
<dd>One-sided p-value.</dd>
<dt>partype</dt>
<dd>Number for parameter type. Type 1 is y-scaling: a or tp.
Type 2 is x-scaling: b or ga, when available, a otherwise. Type 3 is
power scaling: p when available, then b or ga, then a if no others.
Since bmd is linked to the x-scale, type 2 should always be used. Other
types can also be vulnerable to underflow/overflow.</dd>
<dt>poly2.biphasic</dt>
<dd>If poly2.biphasic = TRUE, constraints are set to allow
for the polynomial 2 model fit to be bi-phasic (i.e. non-monotonic).</dd>
<dt>x_v</dt>
<dd>The vertex of the quadratic/parabolic fit.
Only in use when estimating the BMDL and BMDU values for the "poly2" model
when poly2.biphasic = TRUE. No default is set.</dd></dl>

Arguments

BMD Objective Function — bmdobj

<dl>

<dt>bmd</dt>
<dd>Benchmark dose.</dd>


<dt>fname</dt>
<dd>Function name: "exp2", "exp3", "exp4", "exp5", "hillfn", "gnls",
"poly1", "poly2", or "pow".</dd>


<dt>bmr</dt>
<dd>Benchmark response.</dd>


<dt>conc</dt>
<dd>Vector of concentrations NOT in log units.</dd>


<dt>resp</dt>
<dd>Vector of corresponding responses.</dd>


<dt>ps</dt>
<dd>Named list of parameters.</dd>


<dt>mll</dt>
<dd>Maximum log-likelihood of winning model.</dd>


<dt>onesp</dt>
<dd>One-sided p-value.</dd>


<dt>partype</dt>
<dd>Number for parameter type. Type 1 is y-scaling: a or tp.
Type 2 is x-scaling: b or ga, when available, a otherwise. Type 3 is
power scaling: p when available, then b or ga, then a if no others.
Since bmd is linked to the x-scale, type 2 should always be used. Other
types can also be vulnerable to underflow/overflow.</dd>


<dt>poly2.biphasic</dt>
<dd>If poly2.biphasic = TRUE, constraints are set to allow
for the polynomial 2 model fit to be bi-phasic (i.e. non-monotonic).</dd>


<dt>x_v</dt>
<dd>The vertex of the quadratic/parabolic fit.
Only in use when estimating the BMDL and BMDU values for the "poly2" model
when poly2.biphasic = TRUE. No default is set.</dd>

</dl>

BMD Objective Function

bmdobj: BMD Objective Function

Description

Usage

Value

Arguments