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Type 'q()' to quit R. > # 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 0.000e+00 [2,] 0.05 0.9644 0.8895 0.02384 0.4072 0.05132 0.1226 1.597 0.03164 1.298e-06 [3,] 0.10 1.5220 1.7390 0.04374 0.7268 0.07478 0.2932 2.376 0.05805 1.891e-06 Cendexhppmv Cmixexhppmv Cmuc Atubules Ametabolized AUC [1,] 0.0000 0.3000 0 0.0000000 0.00000 0.0000000 [2,] 0.0968 0.3678 1543 0.0007566 0.01178 0.0008709 [3,] 0.1612 0.4129 2584 0.0020170 0.05068 0.0031180 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 0.000e+00 [2,] 0.05 0.9644 0.8895 0.02384 0.4072 0.05132 0.1226 1.597 0.03164 1.298e-06 [3,] 0.10 1.5220 1.7390 0.04374 0.7268 0.07478 0.2932 2.376 0.05805 1.891e-06 Cendexhppmv Cmixexhppmv Cmuc Atubules Ametabolized AUC [1,] 0.0000 0.3000 0 0.0000000 0.00000 0.0000000 [2,] 0.0968 0.3678 1543 0.0007566 0.01178 0.0008709 [3,] 0.1612 0.4129 2584 0.0020170 0.05068 0.0031180 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 0.000e+00 [2,] 0.05 0.9644 0.8895 0.02384 0.4072 0.05132 0.1226 1.597 0.03164 1.298e-06 [3,] 0.10 1.5220 1.7390 0.04374 0.7268 0.07478 0.2932 2.376 0.05805 1.891e-06 Cendexhppmv Cmixexhppmv Cmuc Atubules Ametabolized AUC [1,] 0.0000 0.3000 0 0.0000000 0.00000 0.0000000 [2,] 0.0968 0.3678 1543 0.0007566 0.01178 0.0008709 [3,] 0.1612 0.4129 2584 0.0020170 0.05068 0.0031180 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 9.75 0.40 10.14