tests/ivive_test.R

In httk: High-Throughput Toxicokinetics

#R CMD BATCH --no-timing --no-restore --no-save ivive_test.R ivive_test.Rout
library(httk)

NSAMP <- 10

# 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)
Css <- calc_mc_css(chem.name="bisphenol a",
  output.units="uM",
  samples=NSAMP)
set.seed(12345)
calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
  samples=NSAMP)
params <- parameterize_steadystate(chem.name="bisphenol a")
# This should be the same as calc_mc_oral_equiv:
signif(3/Css,4)

## Honda1:
#set.seed(12345)
#Css <- calc_mc_css(chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(
#    restrictive.clearance=TRUE,
#    bioactive.free.invivo = T),
#  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)
#calc_mc_oral_equiv(cfree,chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(IVIVE="Honda1"),
#  samples=NSAMP)
## This should be the same as calc_mc_oral_equiv:
#signif(cfree/Css,4)
#
## Honda2:
#set.seed(12345)
#Css <- calc_mc_css(chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(
#    restrictive.clearance=TRUE,
#    bioactive.free.invivo = T),
#  output.units="uM",
#  samples=NSAMP)
#set.seed(12345)
#calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(IVIVE="Honda2"),
#  samples=NSAMP)
## This should be the same as calc_mc_oral_equiv:
#signif(3/Css,4)
#
## Honda 3 (should be the same as degault HTTK):
#set.seed(12345)
#Css <- calc_mc_css(chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(
#    restrictive.clearance=TRUE,
#    bioactive.free.invivo = F),
#  output.units="uM",
#  samples=NSAMP)
#set.seed(12345)
#calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(IVIVE="Honda3"),
#  samples=NSAMP)
## This should be the same as calc_mc_oral_equiv:
#signif(3/Css,4)
#
## Honda4:
#set.seed(12345)
#Css <- calc_mc_css(chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(
#    tissue="liver",
#    restrictive.clearance=FALSE,
#    bioactive.free.invivo = F),
#  output.units="uM",
#  samples=NSAMP)
#set.seed(12345)
#calc_mc_oral_equiv(3.0,chem.name="bisphenol a",
#  calc.analytic.css.arg.list=list(IVIVE="Honda4"),
#  samples=NSAMP)
## This should be the same as calc_mc_oral_equiv:
#signif(3/Css,4)


quit("no")