R Under development (unstable) (2024-08-23 r87049 ucrt) -- "Unsuffered Consequences"
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> # R CMD BATCH --no-timing --no-restore --no-save 1comp_test.R 1comp_test.Rout
> 
> # Get rid of anything in the workspace:
> rm(list=ls()) 
> 
> library(httk)
> 
> #calc_analytic_css(chem.name="bisphenol a",model="1compartment")
> calc_analytic_css(chem.cas="80-05-7",model="1compartment")
Human volume of distribution returned in units of L/kg BW.
Plasma concentration returned in uM units.
[1] 1.185
Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
3: In available_rblood2plasma(chem.cas = chem.cas, chem.name = chem.name,  :
  Human in vivo measured Rblood2plasma used.
> calc_analytic_css(chem.cas="80-05-7",parameters=parameterize_1comp(chem.cas="80-05-7"),model="1compartment")
Human volume of distribution returned in units of L/kg BW.
Plasma concentration returned in uM units.
[1] 1.185
Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
3: In available_rblood2plasma(chem.cas = chem.cas, chem.name = chem.name,  :
  Human in vivo measured Rblood2plasma used.
> #calc_analytic_css(chem.cas="80-05-7",model="1compartment",tissue="liver")
> calc_analytic_css(chem.cas="80-05-7",model="1compartment",tissue="brain")
Human volume of distribution returned in units of L/kg BW.
Plasma concentration for brain returned in uM units.
[1] 6.917
Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
3: In available_rblood2plasma(chem.cas = chem.cas, chem.name = chem.name,  :
  Human in vivo measured Rblood2plasma used.
> 
> ##head(solve_1comp(chem.name="bisphenol a"))
> #head(solve_1comp(chem.cas="80-05-7"))
> head(solve_1comp(parameters=parameterize_1comp(chem.cas="80-05-7"),days=1))
Human volume of distribution returned in units of L/kg BW.
None of the monitored components undergo unit conversions  (i.e. conversion factor of 1).

AUC is area under the plasma concentration curve in uM*days units with Rblood2plasma = 0.795.
The model outputs are provided in the following units:
	umol: Agutlumen, Ametabolized
	uM: Ccompartment
	uM*days: AUC

           time Agutlumen Ccompartment Ametabolized       AUC
[1,] 0.00000000    175.80     0.000000    0.000e+00 0.000e+00
[2,] 0.00010000    174.90     0.002068    1.931e-05 1.030e-07
[3,] 0.01041667    101.90     0.166100    1.762e-01 9.442e-04
[4,] 0.02083333     59.11     0.261700    6.006e-01 3.218e-03
[5,] 0.03125000     34.27     0.316400    1.168e+00 6.256e-03
[6,] 0.04166667     19.87     0.347400    1.816e+00 9.729e-03
Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
3: In available_rblood2plasma(chem.cas = chem.cas, chem.name = chem.name,  :
  Human in vivo measured Rblood2plasma used.
4: In solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid,  :
  Rblood2plasma not recalculated. 
Set recalc.blood2plasma to TRUE if desired.
5: In solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid,  :
  Clearance not recalculated. 
Set recalc.clearance to TRUE if desired.
> 
> calc_vdist(chem.name="triclosan")
Human volume of distribution returned in units of L/kg BW.
[1] 2.327
Warning messages:
1: In calc_ma(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Membrane affintity (MA) predicted with method of Yun and Edginton (2013), see calc_ma.
2: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
3: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
> calc_vdist(chem.cas="80-05-7")
Human volume of distribution returned in units of L/kg BW.
[1] 6.337
Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
> params <- parameterize_schmitt(chem.name="triclosan")
Warning messages:
1: In calc_ma(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Membrane affintity (MA) predicted with method of Yun and Edginton (2013), see calc_ma.
2: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
3: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
> params <- c(params, predict_partitioning_schmitt(parameters = params))
> calc_vdist(parameters=params)
Volume of distribution returned in units of L/kg BW.
[1] 2.327
> params <- parameterize_3comp(chem.name="triclosan")
Warning messages:
1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Clint is provided as a distribution.
2: In apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
  Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
3: In calc_ma(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Membrane affintity (MA) predicted with method of Yun and Edginton (2013), see calc_ma.
4: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
5: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
6: In available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
7: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> calc_vdist(parameters=params)
Volume of distribution returned in units of L/kg BW.
[1] 2.327
> params <- parameterize_pbtk(chem.name="triclosan")
Warning messages:
1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Clint is provided as a distribution.
2: In apply_clint_adjustment(Clint.point, Fu_hep = Fu_hep, suppress.messages = suppress.messages) :
  Clint adjusted for in vitro partitioning (Kilford, 2008), see calc_hep_fu.
3: In calc_ma(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Membrane affintity (MA) predicted with method of Yun and Edginton (2013), see calc_ma.
4: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
5: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
6: In available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
7: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> calc_vdist(parameters=params)
Volume of distribution returned in units of L/kg BW.
[1] 2.327
> 
> p <- parameterize_1comp(chem.name="Aminopterin")[sort(names(parameterize_1comp(chem.name="Aminopterin")))]
Human volume of distribution returned in units of L/kg BW.
Human volume of distribution returned in units of L/kg BW.
There were 12 warnings (use warnings() to see them)
> for (this.param in order(sort(tolower(names(p))))) cat(paste(names(p)[this.param],": ",p[[this.param]],"\n"))
BW :  70 
Caco2.Pab :  1.6 
Caco2.Pab.dist :  NA 
Clint :  0 
Clint.dist :  NA 
Fabsgut :  0.6448 
Fhep.assay.correction :  0.9561 
Funbound.plasma :  0.747 
Funbound.plasma.adjustment :  0.996 
Funbound.plasma.dist :  NA 
MA :  19 
MW :  440.4 
Pow :  0.8903 
Rblood2plasma :  0.8419 
Vdist :  0.7338 
hematocrit :  0.44 
hepatic.bioavailability :  1 
kelim :  0.1091 
kgutabs :  2.18 
liver.density :  1.05 
million.cells.per.gliver :  110 
pKa_Accept :  8.09 
pKa_Donor :  2.81 
plasma.vol :  0.04286 
> 
> quit("no")
> proc.time()
   user  system elapsed 
  20.06    0.37   20.42