R Under development (unstable) (2024-12-19 r87451 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.
> signif(head(solve_gas_pbtk(chem.name="pyrene",times=c(0,0.1,0.05),
+                     method = "lsode",mf = 10)),2)
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
[1,] 0e+00 0.00000 0.0e+00 0.0e+00 0.00000 0.0000 0.0e+00  0.0000 0.0e+00
[2,] 1e-04 0.00046 7.7e-05 1.0e-06 0.00012 0.0058 2.2e-05  0.0018 2.0e-06
[3,] 5e-02 0.96000 8.9e-01 2.4e-02 0.41000 0.0510 1.2e-01  1.6000 3.2e-02
[4,] 1e-01 1.50000 1.7e+00 4.4e-02 0.73000 0.0750 2.9e-01  2.4000 5.8e-02
     Calvppmv Cendexhppmv Cmixexhppmv   Cmuc Atubules Ametabolized     AUC
[1,]    0e+00     0.00000        0.30    0.0  0.00000        0.000 0.00000
[2,]    0e+00     0.00025        0.30    3.7  0.00000        0.000 0.00000
[3,]    1e-06     0.09700        0.37 1500.0  0.00076        0.012 0.00087
[4,]    2e-06     0.16000        0.41 2600.0  0.00200        0.051 0.00310
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.
> signif(head(solve_gas_pbtk(chem.cas="129-00-0",times=c(0,0.1,0.05),
+                     method = "lsode",mf = 10)),2)
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
[1,] 0e+00 0.00000 0.0e+00 0.0e+00 0.00000 0.0000 0.0e+00  0.0000 0.0e+00
[2,] 1e-04 0.00046 7.7e-05 1.0e-06 0.00012 0.0058 2.2e-05  0.0018 2.0e-06
[3,] 5e-02 0.96000 8.9e-01 2.4e-02 0.41000 0.0510 1.2e-01  1.6000 3.2e-02
[4,] 1e-01 1.50000 1.7e+00 4.4e-02 0.73000 0.0750 2.9e-01  2.4000 5.8e-02
     Calvppmv Cendexhppmv Cmixexhppmv   Cmuc Atubules Ametabolized     AUC
[1,]    0e+00     0.00000        0.30    0.0  0.00000        0.000 0.00000
[2,]    0e+00     0.00025        0.30    3.7  0.00000        0.000 0.00000
[3,]    1e-06     0.09700        0.37 1500.0  0.00076        0.012 0.00087
[4,]    2e-06     0.16000        0.41 2600.0  0.00200        0.051 0.00310
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.
> signif(head(solve_gas_pbtk(
+   parameters=parameterize_gas_pbtk(chem.cas="129-00-0"),
+   times=c(0,0.1,0.05),
+   method = "lsode",mf = 10)),2)
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
[1,] 0e+00 0.00000 0.0e+00 0.0e+00 0.00000 0.0000 0.0e+00  0.0000 0.0e+00
[2,] 1e-04 0.00046 7.7e-05 1.0e-06 0.00012 0.0058 2.2e-05  0.0018 2.0e-06
[3,] 5e-02 0.96000 8.9e-01 2.4e-02 0.41000 0.0510 1.2e-01  1.6000 3.2e-02
[4,] 1e-01 1.50000 1.7e+00 4.4e-02 0.73000 0.0750 2.9e-01  2.4000 5.8e-02
     Calvppmv Cendexhppmv Cmixexhppmv   Cmuc Atubules Ametabolized     AUC
[1,]    0e+00     0.00000        0.30    0.0  0.00000        0.000 0.00000
[2,]    0e+00     0.00025        0.30    3.7  0.00000        0.000 0.00000
[3,]    1e-06     0.09700        0.37 1500.0  0.00076        0.012 0.00087
[4,]    2e-06     0.16000        0.41 2600.0  0.00200        0.051 0.00310
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
logHenry: -2.561
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 
   7.20    0.35    7.54