R Under development (unstable) (2024-03-19 r86153 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 Cplasma Calvppmv
[1,] 0.00 0.0000 0.0000 0.00000 0.0000 0.00000 0.0000   0.000 0.00000  0.0e+00
[2,] 0.05 0.8585 0.1894 0.01611 0.3684 0.04362 0.1126   1.387 0.02138  4.5e-08
[3,] 0.10 1.1860 0.2632 0.02532 0.5802 0.05639 0.2437   1.816 0.03360  5.8e-08
     Cendexhppmv Cmixexhppmv Cmuc  Atubules Ametabolized       AUC
[1,]    0.000000     0.01227    0 0.0000000        0.000 0.0000000
[2,]    0.003920     0.01501 1545 0.0007019        1.992 0.0006714
[3,]    0.006559     0.01686 2591 0.0017090        5.972 0.0020490
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 Cplasma Calvppmv
[1,] 0.00 0.0000 0.0000 0.00000 0.0000 0.00000 0.0000   0.000 0.00000  0.0e+00
[2,] 0.05 0.8585 0.1894 0.01611 0.3684 0.04362 0.1126   1.387 0.02138  4.5e-08
[3,] 0.10 1.1860 0.2632 0.02532 0.5802 0.05639 0.2437   1.816 0.03360  5.8e-08
     Cendexhppmv Cmixexhppmv Cmuc  Atubules Ametabolized       AUC
[1,]    0.000000     0.01227    0 0.0000000        0.000 0.0000000
[2,]    0.003920     0.01501 1545 0.0007019        1.992 0.0006714
[3,]    0.006559     0.01686 2591 0.0017090        5.972 0.0020490
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 Cplasma Calvppmv
[1,] 0.00 0.0000 0.0000 0.00000 0.0000 0.00000 0.0000   0.000 0.00000  0.0e+00
[2,] 0.05 0.8585 0.1894 0.01611 0.3684 0.04362 0.1126   1.387 0.02138  4.5e-08
[3,] 0.10 1.1860 0.2632 0.02532 0.5802 0.05639 0.2437   1.816 0.03360  5.8e-08
     Cendexhppmv Cmixexhppmv Cmuc  Atubules Ametabolized       AUC
[1,]    0.000000     0.01227    0 0.0000000        0.000 0.0000000
[2,]    0.003920     0.01501 1545 0.0007019        1.992 0.0006714
[3,]    0.006559     0.01686 2591 0.0017090        5.972 0.0020490
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.
> 
> parameterize_gas_pbtk(chem.name="styrene")
$BW
[1] 70

$Clint
[1] 56.4

$Clint.dist
[1] NA

$Clmetabolismc
[1] 9.568

$Fabsgut
[1] 0.8043

$Fhep.assay.correction
[1] 0.7622

$Funbound.plasma
[1] 0.08292

$Funbound.plasma.adjustment
[1] 0.4604

$Funbound.plasma.dist
[1] NA

$hematocrit
[1] 0.44

$Kblood2air
[1] 79.09

$Kgut2pu
[1] 44.76

$kgutabs
[1] 2.18

$Kkidney2pu
[1] 70.47

$Kliver2pu
[1] 88.32

$Klung2pu
[1] 8.209

$km
[1] 1

$Kmuc2air
[1] 97.16

$Krbc2pu
[1] 4.105

$Krest2pu
[1] 29.71

$kUrtc
[1] 11

$liver.density
[1] 1.05

$MA
[1] 155.2

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

$MW
[1] 104.2

$pKa_Accept
pKa_Accept 
        NA 

$pKa_Donor
pKa_Donor 
       NA 

$Pow
[1] 891.3

$Qalvc
[1] 18.59

$Qcardiacc
[1] 13.88

$Qgfrc
[1] 0.3099

$Qgutf
[1] 0.2054

$Qkidneyf
[1] 0.2214

$Qliverf
[1] 0.0535

$Qlungf
[1] 0.025

$Rblood2plasma
[1] 0.7098

$Vartc
[1] 0.03827

$Vgutc
[1] 0.0158

$Vkidneyc
[1] 0.00419

$Vliverc
[1] 0.02448

$Vlungc
[1] 0.007235

$vmax
[1] 0

$Vmucc
[1] 1e-04

$Vrestc
[1] 0.7765

$Vvenc
[1] 0.03827

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.
> 
> quit("no")
> proc.time()
   user  system elapsed 
   7.06    0.53    7.67