tests/3comp_test.R

In httk: High-Throughput Toxicokinetics

#R CMD BATCH --no-timing --no-restore --no-save 3comp_test.R 3comp_test.Rout
library(httk)

calc_analytic_css(chem.name="bisphenol a",model="3compartment")
calc_analytic_css(chem.cas="80-05-7",model="3compartment")
calc_analytic_css(parameters=parameterize_3comp(chem.cas="80-05-7"),model="3compartment")
calc_analytic_css(chem.name="bisphenol a",model="3compartment",tissue="liver")
calc_analytic_css(chem.name="bisphenol a",model="3compartment",tissue="brain")

head(solve_3comp(chem.name="bisphenol a"))
head(solve_3comp(chem.cas="80-05-7"))
head(solve_3comp(parameters=parameterize_3comp(chem.cas="80-05-7")))

#Test that the input daily.dose and doses.per.day are all that goes through, 
#excluding any default dosing. We want any specified dosing to take the place
#of the default, not add to it.

#first get BW param for 3 comp model:
BW = parameterize_3comp(chem.name = 'bisphenol a')[['BW']]
#and get MW of bisphenol a for checking units
MW = get_physchem_param(param = "MW",chem.name = "bisphenol a")
#record intended default dosing in solve_model when no other dosing specified:
default_initial_dose_target_unscaled = 1 #mg/kg BW
initial_default_dose_target = default_initial_dose_target_unscaled*
  BW/(MW*10^-3) #factor of 10^-3 to convert 
#from g/mol to mg/umol, yielding a dose target in umol
head(initial_default_dose_target)

out_default_dosing = solve_3comp(chem.name = "bisphenol a")
#The following two initial dose metrics should be the same, and the same as
#the initial_default_dose_target in turn.
initial_default_dose = sum(out_default_dosing[1,])
head(initial_default_dose)
initial_default_dose_intestine = out_default_dosing[1,"Aintestine"]
head(initial_default_dose_intestine)

out_nondefault_dosing = solve_3comp(chem.name = "bisphenol a", 
                                    daily.dose =3,doses.per.day = 5)
#so, the dose target of what should appear at time zero in the intestine is:
initial_nondefault_dose_target = 3/5*BW/(MW*10^-3)
head(initial_nondefault_dose_target)

#the following two dose metrics should also be the same:
initial_nondefault_dose = sum(out_nondefault_dosing[2,]) #Use second row because
#it looks like eventdata only gets registered in the output after time zero.
head(initial_nondefault_dose)
initial_nondefault_dose_intestine = out_nondefault_dosing[2,"Aintestine"]
head(initial_nondefault_dose_intestine)

#parameterize_3comp(chem.name="Aminopterin")[sort(names(parameterize_3comp(chem.name="Aminopterin")))]

script.args <- commandArgs(TRUE)
if (length(script.args) > 0) 
{
  if (any(script.args=="mctest"))
  {
    set.seed(12345)
    calc_mc_css(chem.name="bisphenol a",model="3compartment")
    set.seed(12345)
    calc_mc_css(chem.cas="80-05-7",model="3compartment")
    set.seed(12345)
    calc_mc_css(parameters=parameterize_3comp(chem.cas="80-05-7"),model="3compartment")
  }                                            
  if (any(script.args=="wetmoretest"))
  {
    wetmore.chems <- subset(chem.physical_and_invitro.data,
      regexpr("Wetmore",Human.Clint.Reference)!=-1 &
      regexpr("Wetmore",Human.Funbound.plasma.Reference)!=-1)
    Css.table <- data.frame()
    for (this.cas in sort(get_lit_cheminfo()))
      if (this.cas %in% get_cheminfo(model="pbtk") &
        this.cas %in% wetmore.chems$CAS)
      {
        Css.table[this.cas,"Css.lit"] <- get_lit_css(chem.cas=this.cas,
          output.units="uM",
          which.quantile=0.5)
        Css.table[this.cas,"Css.calc"] <- calc_analytic_css(chem.cas=this.cas,
          model="3compartment")
      }                                                                          
    cat(lm(log(Css.lit)~log(Css.calc),data=Css.table)$coefficients)
      
    #library(ggplot2)
    #test.fig <- ggplot(Css.table,aes(x=Css.calc,y=Css.lit)) +
    #         geom_point(size=3)+
    #   scale_y_log10()+
    #   scale_x_log10()+
    #  ylab(expression(paste(C[aa]," Literature (uM)"))) +
    #  xlab(expression(paste(C[aa]," 3compartment model (uM)"))) +
    #  geom_abline(intercept = 0, slope = 1,linetype="dashed", colour="Blue") 
    #
    #dev.new()
    #print(test.fig)
  }
}



quit("no")