R Under development (unstable) (2023-12-07 r85661 ucrt) -- "Unsuffered Consequences"
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> # 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] 1.259
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] 1.259
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] 1.259
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] 23.13
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] 7.348
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     Crest
[1,] 0.00000000    263.90  0.00  0.0000 0.00000 0.000000 0.0000000 0.000e+00
[2,] 0.00100000    250.40 11.60  0.3535 0.00219 0.006982 0.0003398 5.172e-06
[3,] 0.01041667    153.00 62.08 20.4900 0.24610 2.023000 0.2145000 5.680e-02
[4,] 0.02083333     88.72 63.01 42.3500 0.58480 5.095000 0.5606000 3.564e-01
[5,] 0.03125000     51.45 51.12 50.8900 0.77210 6.850000 0.7620000 8.430e-01
[6,] 0.04166667     29.83 39.15 49.9000 0.82150 7.345000 0.8209000 1.381e+00
       Ckidney  Cplasma  Atubules Ametabolized       AUC
[1,] 0.000e+00 0.000000 0.000e+00     0.000000 0.000e+00
[2,] 3.918e-04 0.002755 3.700e-07     0.001339 7.780e-07
[3,] 2.699e+00 0.309600 4.154e-03     0.951800 1.198e-03
[4,] 1.065e+01 0.735700 2.683e-02     4.729000 6.760e-03
[5,] 1.690e+01 0.971300 6.559e-02    10.270000 1.583e-02
[6,] 1.960e+01 1.033000 1.116e-01    16.200000 2.639e-02
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     Crest
[1,] 0.00000000    263.90  0.00  0.0000 0.00000 0.000000 0.0000000 0.000e+00
[2,] 0.00100000    250.40 11.60  0.3535 0.00219 0.006982 0.0003398 5.172e-06
[3,] 0.01041667    153.00 62.08 20.4900 0.24610 2.023000 0.2145000 5.680e-02
[4,] 0.02083333     88.72 63.01 42.3500 0.58480 5.095000 0.5606000 3.564e-01
[5,] 0.03125000     51.45 51.12 50.8900 0.77210 6.850000 0.7620000 8.430e-01
[6,] 0.04166667     29.83 39.15 49.9000 0.82150 7.345000 0.8209000 1.381e+00
       Ckidney  Cplasma  Atubules Ametabolized       AUC
[1,] 0.000e+00 0.000000 0.000e+00     0.000000 0.000e+00
[2,] 3.918e-04 0.002755 3.700e-07     0.001339 7.780e-07
[3,] 2.699e+00 0.309600 4.154e-03     0.951800 1.198e-03
[4,] 1.065e+01 0.735700 2.683e-02     4.729000 6.760e-03
[5,] 1.690e+01 0.971300 6.559e-02    10.270000 1.583e-02
[6,] 1.960e+01 1.033000 1.116e-01    16.200000 2.639e-02
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     Crest
[1,] 0.00000000    263.90  0.00  0.0000 0.00000 0.000000 0.0000000 0.000e+00
[2,] 0.00100000    250.40 11.60  0.3535 0.00219 0.006982 0.0003398 5.172e-06
[3,] 0.01041667    153.00 62.08 20.4900 0.24610 2.023000 0.2145000 5.680e-02
[4,] 0.02083333     88.72 63.01 42.3500 0.58480 5.095000 0.5606000 3.564e-01
[5,] 0.03125000     51.45 51.12 50.8900 0.77210 6.850000 0.7620000 8.430e-01
[6,] 0.04166667     29.83 39.15 49.9000 0.82150 7.345000 0.8209000 1.381e+00
       Ckidney  Cplasma  Atubules Ametabolized       AUC
[1,] 0.000e+00 0.000000 0.000e+00     0.000000 0.000e+00
[2,] 3.918e-04 0.002755 3.700e-07     0.001339 7.780e-07
[3,] 2.699e+00 0.309600 4.154e-03     0.951800 1.198e-03
[4,] 1.065e+01 0.735700 2.683e-02     4.729000 6.760e-03
[5,] 1.690e+01 0.971300 6.559e-02    10.270000 1.583e-02
[6,] 1.960e+01 1.033000 1.116e-01    16.200000 2.639e-02
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 :  2.18 
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 
   5.01    0.35    5.37