Nothing
# R CMD BATCH --no-timing --no-restore --no-save ivive_test.R ivive_test.Rout
# Get rid of anything in the workspace:
rm(list=ls())
library(httk)
# Reduce the number of samples used by Monte Carlo to decrease runtime for
# CRAN checks (never use predictions with only ten draws):
NSAMP <- 5
# From Honda et al. (2019) (currently only use mean conc's because steady-state
# calculation does not give max):
#
# Default HTTK function arguments correspond to "Honda3"
#
# in vivo Conc. Metabolic Clearance In Vivo Conc. In Vitro Conc.
#Honda1 Veinous (Plasma) Restrictive Free Free
#Honda2 Veinous Restrictive Free Nominal
#Honda3 Veinous Restrictive Total Nominal
#Honda4 Target Tissue Non-restrictive Total Nominal
#
# "Honda1" uses plasma concentration, restrictive clearance, and treats the
# unbound invivo concentration as bioactive. For IVIVE, any input nominal
# concentration in vitro should be converted to cfree.invitro using
# \code{\link{armitage_eval}}, otherwise performance will be the same as
# "Honda2".
#
# Use \code{\link{show_honda.ivive()}} to print summary of Honda et al. (2019)
# results.
# Default HTTK:
set.seed(12345)
Css0 <- calc_mc_css(chem.name="bisphenol a",
output.units="uM",
samples=NSAMP)
set.seed(12345)
# This should be the same as calc_mc_oral_equiv:
signif(3/Css0,4) ==
calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
samples=NSAMP)
# Honda1:
set.seed(12345)
Css1 <- calc_mc_css(chem.name="bisphenol a",
calc.analytic.css.arg.list=list(
restrictive.clearance = TRUE,
bioactive.free.invivo = TRUE),
output.units="uM",
samples=NSAMP)
temp <- armitage_eval(
casrn.vector = c("80-05-7"),
this.FBSf = 0.1,
this.well_number = 384,
nomconc = 3)
cfree <- temp$cfree.invitro
set.seed(12345)
# This should be the same as calc_mc_oral_equiv with IVIVE=="Honda1":
signif(cfree/Css1,4) ==
calc_mc_oral_equiv(cfree,chem.name="bisphenol a",
calc.analytic.css.arg.list=list(IVIVE="Honda1"),
samples=NSAMP)
# Should be different from default:
!(Css1 %in% c(Css0))
# Honda2:
set.seed(12345)
Css2 <- calc_mc_css(chem.name="bisphenol a",
calc.analytic.css.arg.list=list(
restrictive.clearance = TRUE,
bioactive.free.invivo = TRUE),
output.units="uM",
samples=NSAMP)
set.seed(12345)
# This should be the same as calc_mc_oral_equiv with IVIVE=="Honda2":
signif(3/Css2,4) ==
calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
calc.analytic.css.arg.list=list(IVIVE="Honda2"),
samples=NSAMP)
# Should be different from previous:
!(Css2 %in% c(Css0))
# Honda 3 (should be the same as degault HTTK):
set.seed(12345)
Css3 <- calc_mc_css(chem.name="bisphenol a",
calc.analytic.css.arg.list=list(
restrictive.clearance = TRUE,
bioactive.free.invivo = FALSE),
output.units="uM",
samples=NSAMP)
set.seed(12345)
# This should be the same as calc_mc_oral_equiv with IVIVE=="Honda3":
signif(3/Css3,4) ==
calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
calc.analytic.css.arg.list=list(IVIVE="Honda3"),
samples=NSAMP)
# Should be same as default:
Css0 == Css3
# Should be different from previous:
!(Css3 %in% c(Css1, Css2))
# Honda4:
set.seed(12345)
Css4 <- calc_mc_css(chem.name="bisphenol a",
calc.analytic.css.arg.list=list(
tissue="liver",
restrictive.clearance = FALSE,
bioactive.free.invivo = FALSE),
model="pbtk",
output.units="uM",
samples=NSAMP)
set.seed(12345)
# This should be the same as calc_mc_oral_equiv with IVIVE=="Honda4":
signif(3/Css4,4) ==
calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
calc.analytic.css.arg.list=list(IVIVE="Honda4"),
samples=NSAMP,
model="pbtk")
# Should be different from previous:
!(Css4 %in% c(Css0, Css1, Css2, Css3))
# Quit without saving or displaying messages:
quit("no")
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