BMD: Calculating benchmark dose (BMD) and lower limit of benchmark...

In mixtox: Dose Response Curve Fitting and Mixture Toxicity Assessment

Calculating benchmark dose (BMD) and lower limit of benchmark dose (BMDL)

Description

Calculation of BMD and BMDL for both quantal and continuous dose responses. Six 2- or 3-paramter models ('Hill', 'Weibull', 'Logit', 'Weibull_three', 'Hill_three', 'Logit_three') were employed for quantal dose responses. Three 4-parameter models ('Weibull_four', 'Logit_four', 'Hill_four') were employed for continuous data.

Usage

BMD(object, bmr = 0.10, backg = 0, def = 'additional', eq = 'as.is', 
         sigLev = 0.05, ci = 'CI', sav = FALSE)

Arguments

object	object of class curveFit.
bmr	numeric vector of bench mark response levels for which to calculate benchmark doses (should be between 0 and 1)
backg	numeric value specifying the background level (defaults to 0)
def	character string specifiying the definition of the benchmark dose to use in the calculations. "excess" and "additional" are for binomial response whereas "relative" and "hybrid" (additive hybrid) are for continuous response.
eq	default list of equations.
sigLev	the significance level for Dunnett's test. The default is 0.05.
ci	types of confidence intervals (CI or PI).CI: non-simultaneous confidence intervals; PI: non-simultaneous prediction intervals.
sav	TRUE: save output to a default file; FALSE: output will not be saved; a custom file directory: save output to the custom file directory.

Details

Selecting the Benchmark Response Level (BMR) (https://www.epa.gov/bmds/ benchmark-dose-bmd-methods#bmr).BMR is usually set as 0.10.

Value

bmds	values of BMDL, BMD, and BMDU.

Note

three default equations (Hill, Weibull, and Logit) were used to calculate BMD for quantal dose response. Three default equations('Weibull_four', 'Logit_four', 'Hill_four') were used to calculate BMD for continuous dose response. BMD calculation is only availabale for monotonic dose reponses in this version.

References

Benchmark Dose Technical Guidance, Risk Assessment Forum, U.S. Environmental Protection Agency, Washington, DC 20460, EPA/100/R-12/001, June 2012
Kennyp (2002). Critical Issues in Benchmark Calculations from Continuous Data. Crit. Rev. Toxicol., 32, 133-153.

Examples

## example 1
# calcualte the BMD of heavy metal Ni(2+) on the MCF-7 cells 
x <- cytotox$Ni$x
rspn <- cytotox$Ni$y
obj <- curveFit(x, rspn, eq = 'Logit', param = c(12, 3), effv = c(0.05, 0.5), rtype = 'quantal')
BMD(obj, bmr = 0.10, backg = 0, def = 'additional', eq = 'default', sigLev = 0.05, ci = 'CI')

mixtox documentation built on June 20, 2022, 5:05 p.m.