R Under development (unstable) (2023-12-07 r85661 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] 1.584
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] 1.584
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] 9.243
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")))
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    234.90      0.00000     0.000000 0.000e+00
[2,] 0.00100000    222.90      0.02699     0.002541 1.361e-05
[3,] 0.01041667    136.20      0.22200     0.235500 1.262e-03
[4,] 0.02083333     78.98      0.34970     0.802600 4.300e-03
[5,] 0.03125000     45.80      0.42280     1.560000 8.360e-03
[6,] 0.04166667     26.56      0.46420     2.426000 1.300e-02
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] 2.325
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] 2.325
> 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] 2.324
> 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] 2.325
> 
> parameterize_1comp(chem.name="Aminopterin")
Human volume of distribution returned in units of L/kg BW.
$BW
[1] 70

$Caco2.Pab
[1] 1.6

$Caco2.Pab.dist
[1] NA

$Clint
[1] 0

$Clint.dist
[1] NA

$Fabsgut
[1] 0.8719

$Fhep.assay.correction
[1] 0.9482

$Funbound.plasma
[1] 0.7498

$Funbound.plasma.dist
[1] NA

$Funbound.plasma.adjustment
[1] 0.9998

$hepatic.bioavailability
[1] 1

$hematocrit
[1] 0.44

$kelim
[1] 0.1346

$kgutabs
[1] 2.18

$liver.density
[1] 1.05

$million.cells.per.gliver
[1] 110

$MA
[1] 7.082

$MW
[1] 440.4

$Rblood2plasma
[1] 0.8046

$plasma.vol
[1] 0.04286

$Pow
[1] 0.03467

$pKa_Donor
pKa_Donor 
   "2.81" 

$pKa_Accept
pKa_Accept 
    "8.09" 

$Vdist
[1] 0.5966

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 apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
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 apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
5: In calc_rblood2plasma(chem.cas = chem.cas, species = species, adjusted.Funbound.plasma = adjusted.Funbound.plasma,  :
  Rblood2plasma has been recalculated.
6: In available_rblood2plasma(chem.cas = chem.cas, chem.name = chem.name,  :
  Human Rblood2plasma calculated with calc_rblood2plasma.
> 
> quit("no")
> proc.time()
   user  system elapsed 
   5.50    0.35    5.84