toplikelihood: Top Likelihood

In USEPA/CompTox-ToxCast-tcplFit2: A Concentration-Response Modeling Utility

Top Likelihood

Description

Probability of top (maximal change in response from baseline) being outside the cutoff band.

Usage

toplikelihood(
  fname,
  cutoff,
  conc,
  resp,
  ps,
  top,
  mll,
  errfun = "dt4",
  poly2.biphasic = TRUE,
  verbose = FALSE
)

Arguments

fname	Model function name (equal to model name except hill which uses "hillfn")
cutoff	Desired cutoff.
conc	Vector of concentrations.
resp	Vector of responses.
ps	Vector of parameters, must be in order: a, tp, b, ga, p, la, q, er
top	Model predicted top, maximal predicted change in response from baseline.
mll	Winning model maximum log-likelihood.
errfun	Which error distribution to assume for each point, defaults to "dt4". "dt4" is the original 4 degrees of freedom t-distribution. Another supported distribution is "dnorm", the normal distribution.
poly2.biphasic	Which fitting method to use for poly2. If poly2.biphasic = TRUE, allows for biphasic polynomial 2 model fits (i.e. both monotonic and non-monotonic). (Defaults to TRUE.)
verbose	If verbose = TRUE, will print status of empirical calculations. (Defaults to FALSE.)

Details

Should only be called by hitcontinner. Uses profile likelihood, similar to bmdbounds. Here, the y-scale type parameter is substituted in such a way that the top equals the cutoff. Then the log-likelihood is compared to the maximum log-likelihood using pchisq function to retrieve probability.

Value

Probability of top being outside the cutoff band.

Examples

fname = "hillfn"
conc = c(.03,.1,.3,1,3,10,30,100)
resp = c(0,.1,0,.2,.6,.9,1.1,1)
ps = c(1.033239, 2.453014, 1.592714, er = -3.295307)
top = 1.023239
mll = 12.71495
toplikelihood(fname, cutoff = .8, conc, resp, ps, top, mll)
toplikelihood(fname, cutoff = 1, conc, resp, ps, top, mll)
toplikelihood(fname, cutoff = 1.2, conc, resp, ps, top, mll)

USEPA/CompTox-ToxCast-tcplFit2 documentation built on June 9, 2025, 9:59 p.m.