bmdbounds: BMD Bounds

In tcplfit2: A Concentration-Response Modeling Utility

BMD Bounds

Description

Uses maximum likelihood method to tune the upper and lower bounds on the BMD (BMDU, BMDL)

Usage

bmdbounds(
  fit_method,
  bmr,
  pars,
  conc,
  resp,
  onesidedp = 0.05,
  bmd = NULL,
  which.bound = "lower",
  poly2.biphasic = TRUE,
  x_v
)

Arguments

fit_method	Fit method: "exp2", "exp3", "exp4", "exp5", "hill", "gnls", "poly1", "poly2", or "pow".
bmr	Benchmark response.
pars	Named vector of model parameters: a,b,tp,ga,p,la,q,er output by httrfit, and in that order.
conc	Vector of concentrations (NOT in log units).
resp	Vector of responses corresponding to given concentrations.
onesidedp	The one-sided p-value. Default of .05 corresponds to 5 percentile BMDL, 95 percentile BMDU, and 90 percent CI.
bmd	Can optionally input the bmd when already known to avoid unnecessary calculation.
which.bound	Returns BMDU if which.bound = "upper"; returns BMDL if which.bound = "lower".
poly2.biphasic	If poly2.biphasic = TRUE, constraints are set to allow for the polynomial 2 model fit to be bi-phasic (i.e. non-monotonic).
x_v	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.

Details

Takes in concentration response fit details and outputs a bmdu or bmdl, as desired. If bmd is not finite, returns NA. If the objective function doesn't change sign or the root finding otherwise fails, it returns NA. These failures are not uncommon since some curves just don't reach the desired confidence level.

Value

Returns either the BMDU or BMDL.

Examples

conc = c(.03, .1, .3, 1, 3, 10, 30, 100)
resp = c(.1,-.1,0,1.1,1.9,2,2.1,1.9)
pars = c(tp = 1.973356, ga = 0.9401224, p = 3.589397, er =  -2.698579)
bmdbounds(fit_method = "hill", bmr = .5, pars, conc, resp)
bmdbounds(fit_method = "hill", bmr = .5, pars, conc, resp, which.bound = "upper")

tcplfit2 documentation built on Sept. 24, 2024, 1:07 a.m.