R Under development (unstable) (2024-08-23 r87049 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # R CMD BATCH --no-timing --no-restore --no-save pbtk_test.R pbtk_test.Rout
> 
> # Get rid of anything in the workspace:
> rm(list=ls()) 
> 
> library(httk)
> 
> calc_analytic_css(chem.name="bisphenol a",model="pbtk")
Plasma concentration returned in uM units.
[1] 0.9417
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> calc_analytic_css(chem.cas="80-05-7",model="pbtk")
Plasma concentration returned in uM units.
[1] 0.9417
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> calc_analytic_css(parameters=parameterize_pbtk(chem.cas="80-05-7"),model="pbtk")
Plasma concentration returned in uM units.
[1] 0.9417
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> calc_analytic_css(chem.name="bisphenol a",model="pbtk",tissue="liver")
Plasma concentration for liver returned in uM units.
[1] 20.58
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> calc_analytic_css(chem.name="bisphenol a",model="pbtk",tissue="brain")
Plasma concentration for brain returned in uM units.
[1] 5.496
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> 
> head(solve_pbtk(chem.name="bisphenol a"))
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, Atubules, Ametabolized
	uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma
	uM*days: AUC

           time Agutlumen    Cgut    Cliver      Cven     Clung      Cart
[1,] 0.00000000     197.5  0.0000 0.000e+00 0.000e+00 0.000e+00 0.000e+00
[2,] 0.00010000     197.3  0.1582 4.792e-04 5.620e-07 3.220e-07 2.000e-09
[3,] 0.01041667     180.0 10.1400 3.070e+00 3.649e-02 2.976e-01 3.140e-02
[4,] 0.02083333     164.0 13.6300 7.610e+00 1.027e-01 8.865e-01 9.700e-02
[5,] 0.03125000     149.5 14.7600 1.113e+01 1.622e-01 1.425e+00 1.576e-01
[6,] 0.04166667     136.3 14.9800 1.339e+01 2.072e-01 1.834e+00 2.038e-01
        Crest Ckidney   Cplasma  Atubules Ametabolized       AUC
[1,] 0.000000  0.0000 0.000e+00 0.0000000    0.000e+00 0.0000000
[2,] 0.000000  0.0000 7.060e-07 0.0000000    5.000e-09 0.0000000
[3,] 0.008015  0.3847 4.590e-02 0.0005859    3.316e-03 0.0001704
[4,] 0.056450  1.7590 1.292e-01 0.0042390    1.856e-02 0.0010780
[5,] 0.150100  3.2970 2.041e-01 0.0116100    4.541e-02 0.0028280
[6,] 0.276300  4.5580 2.606e-01 0.0220600    8.041e-02 0.0052650
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> head(solve_pbtk(chem.cas="80-05-7"))
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, Atubules, Ametabolized
	uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma
	uM*days: AUC

           time Agutlumen    Cgut    Cliver      Cven     Clung      Cart
[1,] 0.00000000     197.5  0.0000 0.000e+00 0.000e+00 0.000e+00 0.000e+00
[2,] 0.00010000     197.3  0.1582 4.792e-04 5.620e-07 3.220e-07 2.000e-09
[3,] 0.01041667     180.0 10.1400 3.070e+00 3.649e-02 2.976e-01 3.140e-02
[4,] 0.02083333     164.0 13.6300 7.610e+00 1.027e-01 8.865e-01 9.700e-02
[5,] 0.03125000     149.5 14.7600 1.113e+01 1.622e-01 1.425e+00 1.576e-01
[6,] 0.04166667     136.3 14.9800 1.339e+01 2.072e-01 1.834e+00 2.038e-01
        Crest Ckidney   Cplasma  Atubules Ametabolized       AUC
[1,] 0.000000  0.0000 0.000e+00 0.0000000    0.000e+00 0.0000000
[2,] 0.000000  0.0000 7.060e-07 0.0000000    5.000e-09 0.0000000
[3,] 0.008015  0.3847 4.590e-02 0.0005859    3.316e-03 0.0001704
[4,] 0.056450  1.7590 1.292e-01 0.0042390    1.856e-02 0.0010780
[5,] 0.150100  3.2970 2.041e-01 0.0116100    4.541e-02 0.0028280
[6,] 0.276300  4.5580 2.606e-01 0.0220600    8.041e-02 0.0052650
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> head(solve_pbtk(parameters=parameterize_pbtk(chem.cas="80-05-7")))
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, Atubules, Ametabolized
	uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma
	uM*days: AUC

           time Agutlumen    Cgut    Cliver      Cven     Clung      Cart
[1,] 0.00000000     197.5  0.0000 0.000e+00 0.000e+00 0.000e+00 0.000e+00
[2,] 0.00010000     197.3  0.1582 4.792e-04 5.620e-07 3.220e-07 2.000e-09
[3,] 0.01041667     180.0 10.1400 3.070e+00 3.649e-02 2.976e-01 3.140e-02
[4,] 0.02083333     164.0 13.6300 7.610e+00 1.027e-01 8.865e-01 9.700e-02
[5,] 0.03125000     149.5 14.7600 1.113e+01 1.622e-01 1.425e+00 1.576e-01
[6,] 0.04166667     136.3 14.9800 1.339e+01 2.072e-01 1.834e+00 2.038e-01
        Crest Ckidney   Cplasma  Atubules Ametabolized       AUC
[1,] 0.000000  0.0000 0.000e+00 0.0000000    0.000e+00 0.0000000
[2,] 0.000000  0.0000 7.060e-07 0.0000000    5.000e-09 0.0000000
[3,] 0.008015  0.3847 4.590e-02 0.0005859    3.316e-03 0.0001704
[4,] 0.056450  1.7590 1.292e-01 0.0042390    1.856e-02 0.0010780
[5,] 0.150100  3.2970 2.041e-01 0.0116100    4.541e-02 0.0028280
[6,] 0.276300  4.5580 2.606e-01 0.0220600    8.041e-02 0.0052650
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 get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
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 available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
7: In solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid,  :
  Rblood2plasma not recalculated. 
Set recalc.blood2plasma to TRUE if desired.
8: In solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid,  :
  Clearance not recalculated. 
Set recalc.clearance to TRUE if desired.
> 
> p <- parameterize_pbtk(chem.name="Aminopterin")[sort(names(parameterize_pbtk(chem.name="Aminopterin")))]
There were 16 warnings (use warnings() to see them)
> for (this.param in sort(tolower(names(p)))) cat(paste(this.param,": ",p[[this.param]],"\n"))
bw :   
caco2.pab :   
caco2.pab.dist :   
clint :   
clint.dist :   
clmetabolismc :   
fabsgut :   
fhep.assay.correction :   
funbound.plasma :   
funbound.plasma.adjustment :   
funbound.plasma.dist :   
hematocrit :  0.44 
kgut2pu :   
kgutabs :  0.3711 
kkidney2pu :   
kliver2pu :   
klung2pu :   
krbc2pu :   
krest2pu :   
liver.density :  1.05 
ma :   
million.cells.per.gliver :  110 
mw :   
pka_accept :   
pka_donor :   
pow :   
qcardiacc :   
qgfrc :   
qgutf :   
qkidneyf :   
qliverf :   
rblood2plasma :   
vartc :   
vgutc :   
vkidneyc :   
vliverc :   
vlungc :   
vrestc :   
vvenc :   
> 
> quit("no")
> proc.time()
   user  system elapsed 
  12.51    0.45   12.90