R Under development (unstable) (2024-09-04 r87094 ucrt) -- "Unsuffered Consequences"
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> # R CMD BATCH --no-timing --no-restore --no-save solve_gas_test.R solve_gas_test.Rout
> 
> # Get rid of anything in the workspace:
> rm(list=ls()) 
> 
> library(httk)
> 
> # The following arguments were added: method = "lsode",mf = 10.
> # Rationale: Following is required for the same results on various OS's due to
> #   precision differences.
> head(solve_gas_pbtk(chem.name="pyrene",times=c(0,0.1,0.05),
+                     method = "lsode",mf = 10))
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 = 0.754.
The model outputs are provided in the following units:
	uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cmuc
	ppmv: Calvppmv, Cendexhppmv, Cmixexhppmv
	umol: Atubules, Ametabolized
	uM*days: AUC

      time     Cgut   Cliver     Cven    Clung     Cart    Crest  Ckidney
[1,] 0e+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[2,] 1e-04 0.000456 0.000077 0.000001 0.000122 0.005813 0.000022 0.001848
[3,] 5e-02 0.964400 0.889500 0.023840 0.407200 0.051320 0.122600 1.597000
[4,] 1e-01 1.522000 1.739000 0.043740 0.726800 0.074780 0.293200 2.376000
      Cplasma Calvppmv Cendexhppmv Cmixexhppmv     Cmuc Atubules Ametabolized
[1,] 0.000000    0e+00    0.000000      0.3000    0.000 0.000000      0.00000
[2,] 0.000002    0e+00    0.000254      0.3002    3.731 0.000000      0.00000
[3,] 0.031640    1e-06    0.096800      0.3678 1543.000 0.000757      0.01178
[4,] 0.058050    2e-06    0.161200      0.4129 2584.000 0.002017      0.05068
          AUC
[1,] 0.000000
[2,] 0.000000
[3,] 0.000871
[4,] 0.003118
Warning messages:
1: 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.
2: In parameterize_gas_pbtk(chem.cas = "129-00-0", chem.name = "pyrene",  :
  Funbound.plasma adjusted for in vitro partitioning (Pearce, 2017). Set adjusted.Funbound.plasma to FALSE to use original value.
3: In parameterize_gas_pbtk(chem.cas = "129-00-0", chem.name = "pyrene",  :
  Cannot calculate saturable metabolism with Vmax = 0. Defaulting to first-order metabolic clearance.
4: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> head(solve_gas_pbtk(chem.cas="129-00-0",times=c(0,0.1,0.05),
+                     method = "lsode",mf = 10))
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 = 0.754.
The model outputs are provided in the following units:
	uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cmuc
	ppmv: Calvppmv, Cendexhppmv, Cmixexhppmv
	umol: Atubules, Ametabolized
	uM*days: AUC

      time     Cgut   Cliver     Cven    Clung     Cart    Crest  Ckidney
[1,] 0e+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[2,] 1e-04 0.000456 0.000077 0.000001 0.000122 0.005813 0.000022 0.001848
[3,] 5e-02 0.964400 0.889500 0.023840 0.407200 0.051320 0.122600 1.597000
[4,] 1e-01 1.522000 1.739000 0.043740 0.726800 0.074780 0.293200 2.376000
      Cplasma Calvppmv Cendexhppmv Cmixexhppmv     Cmuc Atubules Ametabolized
[1,] 0.000000    0e+00    0.000000      0.3000    0.000 0.000000      0.00000
[2,] 0.000002    0e+00    0.000254      0.3002    3.731 0.000000      0.00000
[3,] 0.031640    1e-06    0.096800      0.3678 1543.000 0.000757      0.01178
[4,] 0.058050    2e-06    0.161200      0.4129 2584.000 0.002017      0.05068
          AUC
[1,] 0.000000
[2,] 0.000000
[3,] 0.000871
[4,] 0.003118
Warning messages:
1: 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.
2: In parameterize_gas_pbtk(chem.cas = "129-00-0", chem.name = "Pyrene",  :
  Funbound.plasma adjusted for in vitro partitioning (Pearce, 2017). Set adjusted.Funbound.plasma to FALSE to use original value.
3: In parameterize_gas_pbtk(chem.cas = "129-00-0", chem.name = "Pyrene",  :
  Cannot calculate saturable metabolism with Vmax = 0. Defaulting to first-order metabolic clearance.
4: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> head(solve_gas_pbtk(
+   parameters=parameterize_gas_pbtk(chem.cas="129-00-0"),
+   times=c(0,0.1,0.05),
+   method = "lsode",mf = 10))
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 = 0.754.
The model outputs are provided in the following units:
	uM: Cgut, Cliver, Cven, Clung, Cart, Crest, Ckidney, Cplasma, Cmuc
	ppmv: Calvppmv, Cendexhppmv, Cmixexhppmv
	umol: Atubules, Ametabolized
	uM*days: AUC

      time     Cgut   Cliver     Cven    Clung     Cart    Crest  Ckidney
[1,] 0e+00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[2,] 1e-04 0.000456 0.000077 0.000001 0.000122 0.005813 0.000022 0.001848
[3,] 5e-02 0.964400 0.889500 0.023840 0.407200 0.051320 0.122600 1.597000
[4,] 1e-01 1.522000 1.739000 0.043740 0.726800 0.074780 0.293200 2.376000
      Cplasma Calvppmv Cendexhppmv Cmixexhppmv     Cmuc Atubules Ametabolized
[1,] 0.000000    0e+00    0.000000      0.3000    0.000 0.000000      0.00000
[2,] 0.000002    0e+00    0.000254      0.3002    3.731 0.000000      0.00000
[3,] 0.031640    1e-06    0.096800      0.3678 1543.000 0.000757      0.01178
[4,] 0.058050    2e-06    0.161200      0.4129 2584.000 0.002017      0.05068
          AUC
[1,] 0.000000
[2,] 0.000000
[3,] 0.000871
[4,] 0.003118
Warning messages:
1: 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.
2: In parameterize_gas_pbtk(chem.cas = "129-00-0") :
  Funbound.plasma adjusted for in vitro partitioning (Pearce, 2017). Set adjusted.Funbound.plasma to FALSE to use original value.
3: In parameterize_gas_pbtk(chem.cas = "129-00-0") :
  Cannot calculate saturable metabolism with Vmax = 0. Defaulting to first-order metabolic clearance.
4: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
5: In solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid,  :
  Rblood2plasma not recalculated. 
Set recalc.blood2plasma to TRUE if desired.
6: 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_gas_pbtk(chem.name="styrene")[sort(names(parameterize_gas_pbtk(chem.name="styrene")))]
Warning messages:
1: 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.
2: In parameterize_gas_pbtk(chem.name = "styrene") :
  Funbound.plasma adjusted for in vitro partitioning (Pearce, 2017). Set adjusted.Funbound.plasma to FALSE to use original value.
3: In parameterize_gas_pbtk(chem.name = "styrene") :
  Cannot calculate saturable metabolism with Vmax = 0. Defaulting to first-order metabolic clearance.
4: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
5: 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.
6: In parameterize_gas_pbtk(chem.name = "styrene") :
  Funbound.plasma adjusted for in vitro partitioning (Pearce, 2017). Set adjusted.Funbound.plasma to FALSE to use original value.
7: In parameterize_gas_pbtk(chem.name = "styrene") :
  Cannot calculate saturable metabolism with Vmax = 0. Defaulting to first-order metabolic clearance.
8: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> # Try to standardize order of variable names
> for (this.param in names(p)[order(toupper(names(p)))]) cat(paste(this.param,": ",p[[this.param]],"\r\n",sep=""))
BW: 70
Clint: 56.4
Clint.dist: NA
Clmetabolismc: 0.7934
Fabsgut: 0.6297
Fhep.assay.correction: 0.7622
Funbound.plasma: 0.08292
Funbound.plasma.adjustment: 0.4604
Funbound.plasma.dist: NA
hematocrit: 0.44
Kblood2air: 79.28
Kgut2pu: 44.76
kgutabs: 0.3711
Kkidney2pu: 70.47
Kliver2pu: 88.32
Klung2pu: 8.209
km: 1
Kmuc2air: 97.38
Krbc2pu: 4.105
Krest2pu: 29.71
kUrtc: 11
liver.density: 1.05
MA: 155.2
million.cells.per.gliver: 110
MW: 104.2
pKa_Accept: NA
pKa_Donor: NA
Pow: 891.3
Qalvc: 18.59
Qcardiacc: 13.88
Qgfrc: 0.3099
Qgutf: 0.2054
Qkidneyf: 0.2214
Qliverf: 0.0535
Qlungf: 0.025
Rblood2plasma: 0.7098
Vartc: 0.03827
Vgutc: 0.0158
Vkidneyc: 0.00419
Vliverc: 0.02448
Vlungc: 0.007235
vmax: 0
Vmucc: 1e-04
Vrestc: 0.7765
Vvenc: 0.03827
> 
> quit("no")
> proc.time()
   user  system elapsed 
   7.40    0.39    7.78