R Under development (unstable) (2024-12-19 r87451 ucrt) -- "Unsuffered Consequences"
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> # R CMD BATCH --no-timing --no-restore --no-save fetal_pbtk_testing.R fetal_pbtk_testing.Rout
>
> # Get rid of anything in the workspace:
> rm(list=ls())
>
> library(httk)
>
> head(solve_fetal_pbtk(chem.name = 'bisphenol a', daily.dose = 1,
+ doses.per.day = 3))
None of the monitored components undergo unit conversions (i.e. conversion factor of 1).
AUC is area under the maternal plasma concentration curve in uM*days units.
fAUC is area under the fetal plasma concentration curve in uM*days units.
The model outputs are provided in the following units:
umol: Agutlumen, Atubules, Ametabolized, Aplacenta
uM: Cgut, Cliver, Cven, Clung, Cart, Cadipose, Crest, Ckidney, Cplasma, Cplacenta, Cfliver, Cfven, Cfart, Cfgut, Cflung, Cfrest, Cfthyroid, Cfkidney, Cfbrain, Cfplasma
unitless: Rblood2plasma, Rfblood2plasma
uM*days: AUC, fAUC
L/d: Qcardiac, Qthyroid
time Agutlumen Cgut Cliver Cven Clung Cart Cadipose
[1,] 90.99990 0.000 0.00000 0.0000000 0.000e+00 0.000000 0.0e+00 0.0000
[2,] 91.00000 0.000 0.00000 0.0000000 0.000e+00 0.000000 0.0e+00 0.0000
[3,] 91.00010 57.410 0.04509 0.0005921 4.540e-06 0.000001 1.0e-07 0.0000
[4,] 91.33323 2.954 2.09200 2.9590000 5.400e-01 1.133000 5.4e-01 0.8699
[5,] 91.33333 2.951 2.09200 2.9590000 5.401e-01 1.133000 5.4e-01 0.8699
[6,] 91.33343 60.360 2.13700 2.9600000 5.401e-01 1.133000 5.4e-01 0.8700
Crest Ckidney Cplasma Atubules Ametabolized Rblood2plasma AUC
[1,] 0.0000 0.0e+00 0.000e+00 0.0000 0.0000 3.390 0.00000
[2,] 0.0000 0.0e+00 0.000e+00 0.0000 0.0000 3.390 0.00000
[3,] 0.0000 1.0e-08 1.340e-06 0.0000 0.0000 3.390 0.00000
[4,] 0.7718 3.1e+00 1.593e-01 0.2141 0.1961 3.389 0.04107
[5,] 0.7718 3.1e+00 1.593e-01 0.2142 0.1962 3.389 0.04108
[6,] 0.7719 3.1e+00 1.594e-01 0.2143 0.1963 3.389 0.04110
fAUC Aplacenta Cplacenta Cfliver Cfven Cfart Cfgut Cflung Cfrest
[1,] 0.00000 0.00000 0.0000 0.000 0.0000 0.0000 0.00 0.000 0.0000
[2,] 0.00000 0.00000 0.0000 0.000 0.0000 0.0000 0.00 0.000 0.0000
[3,] 0.00000 0.00000 0.0000 0.000 0.0000 0.0000 0.00 0.000 0.0000
[4,] 0.03146 0.06167 0.5733 2.667 0.4737 0.4737 1.91 1.098 0.7407
[5,] 0.03148 0.06168 0.5733 2.667 0.4737 0.4737 1.91 1.098 0.7407
[6,] 0.03149 0.06168 0.5734 2.667 0.4737 0.4737 1.91 1.098 0.7407
Cfthyroid Cfkidney Cfbrain Cfplasma Rfblood2plasma Qcardiac Qthyroid
[1,] 0.000 0.000 0.0000 0.0000 3.788 8656 118.6
[2,] 0.000 0.000 0.0000 0.0000 3.788 8656 118.6
[3,] 0.000 0.000 0.0000 0.0000 3.788 8656 118.6
[4,] 1.044 2.871 0.8332 0.1249 3.792 8661 118.6
[5,] 1.044 2.871 0.8332 0.1249 3.792 8661 118.6
[6,] 1.045 2.871 0.8332 0.1249 3.792 8661 118.6
> head(solve_fetal_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 maternal plasma concentration curve in uM*days units.
fAUC is area under the fetal plasma concentration curve in uM*days units.
The model outputs are provided in the following units:
umol: Agutlumen, Atubules, Ametabolized, Aplacenta
uM: Cgut, Cliver, Cven, Clung, Cart, Cadipose, Crest, Ckidney, Cplasma, Cplacenta, Cfliver, Cfven, Cfart, Cfgut, Cflung, Cfrest, Cfthyroid, Cfkidney, Cfbrain, Cfplasma
unitless: Rblood2plasma, Rfblood2plasma
uM*days: AUC, fAUC
L/d: Qcardiac, Qthyroid
time Agutlumen Cgut Cliver Cven Clung Cart Cadipose
[1,] 91.0000 1.724e+02 0.0000 0.000000 0.000e+00 0.000000 0.0000000 0.000
[2,] 91.0001 1.722e+02 0.1353 0.001776 1.362e-05 0.000003 0.0000003 0.000
[3,] 92.0000 2.336e-02 6.1920 8.954000 1.655e+00 3.475000 1.6550000 2.748
[4,] 93.0000 3.170e-06 6.0160 8.701000 1.608e+00 3.376000 1.6080000 2.670
[5,] 94.0000 0.000e+00 5.8460 8.454000 1.562e+00 3.281000 1.5620000 2.595
[6,] 95.0000 0.000e+00 5.6800 8.215000 1.517e+00 3.188000 1.5170000 2.521
Crest Ckidney Cplasma Atubules Ametabolized Rblood2plasma AUC
[1,] 0.000 0.000e+00 0.000e+00 0.000 0.000e+00 3.390 0.0000
[2,] 0.000 4.000e-08 4.020e-06 0.000 1.000e-08 3.390 0.0000
[3,] 2.390 9.509e+00 4.885e-01 2.349 2.012e+00 3.388 0.4499
[4,] 2.323 9.240e+00 4.747e-01 4.869 4.107e+00 3.387 0.9315
[5,] 2.257 8.978e+00 4.613e-01 7.321 6.143e+00 3.386 1.4000
[6,] 2.193 8.724e+00 4.482e-01 9.709 8.121e+00 3.385 1.8540
fAUC Aplacenta Cplacenta Cfliver Cfven Cfart Cfgut Cflung Cfrest
[1,] 0.0000 0.0000 0.000e+00 0.000 0.000 0.000 0.000 0.000 0.000
[2,] 0.0000 0.0000 1.000e-08 0.000 0.000 0.000 0.000 0.000 0.000
[3,] 0.3511 0.1919 1.759e+00 8.202 1.459 1.459 5.874 3.376 2.278
[4,] 0.7296 0.1905 1.709e+00 7.971 1.423 1.423 5.708 3.281 2.214
[5,] 1.0970 0.1891 1.661e+00 7.745 1.387 1.387 5.546 3.188 2.151
[6,] 1.4550 0.1875 1.613e+00 7.525 1.351 1.351 5.389 3.097 2.090
Cfthyroid Cfkidney Cfbrain Cfplasma Rfblood2plasma Qcardiac Qthyroid
[1,] 0.000 0.000 0.000 0.0000 3.788 8656 118.6
[2,] 0.000 0.000 0.000 0.0000 3.788 8656 118.6
[3,] 3.211 8.828 2.564 0.3840 3.800 8673 118.7
[4,] 3.120 8.579 2.491 0.3731 3.812 8690 118.8
[5,] 3.032 8.335 2.420 0.3626 3.824 8707 118.9
[6,] 2.946 8.099 2.352 0.3523 3.836 8724 119.0
> head(solve_fetal_pbtk(parameters=parameterize_fetal_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 maternal plasma concentration curve in uM*days units.
fAUC is area under the fetal plasma concentration curve in uM*days units.
The model outputs are provided in the following units:
umol: Agutlumen, Atubules, Ametabolized, Aplacenta
uM: Cgut, Cliver, Cven, Clung, Cart, Cadipose, Crest, Ckidney, Cplasma, Cplacenta, Cfliver, Cfven, Cfart, Cfgut, Cflung, Cfrest, Cfthyroid, Cfkidney, Cfbrain, Cfplasma
unitless: Rblood2plasma, Rfblood2plasma
uM*days: AUC, fAUC
L/d: Qcardiac, Qthyroid
time Agutlumen Cgut Cliver Cven Clung Cart Cadipose
[1,] 91.0000 1.724e+02 0.0000 0.000000 0.000e+00 0.000000 0.0000000 0.000
[2,] 91.0001 1.722e+02 0.1353 0.001776 1.362e-05 0.000003 0.0000003 0.000
[3,] 92.0000 2.336e-02 6.1920 8.954000 1.655e+00 3.475000 1.6550000 2.748
[4,] 93.0000 3.170e-06 6.0160 8.701000 1.608e+00 3.376000 1.6080000 2.670
[5,] 94.0000 0.000e+00 5.8460 8.454000 1.562e+00 3.281000 1.5620000 2.595
[6,] 95.0000 0.000e+00 5.6800 8.215000 1.517e+00 3.188000 1.5170000 2.521
Crest Ckidney Cplasma Atubules Ametabolized Rblood2plasma AUC
[1,] 0.000 0.000e+00 0.000e+00 0.000 0.000e+00 3.390 0.0000
[2,] 0.000 4.000e-08 4.020e-06 0.000 1.000e-08 3.390 0.0000
[3,] 2.390 9.509e+00 4.885e-01 2.349 2.012e+00 3.388 0.4499
[4,] 2.323 9.240e+00 4.747e-01 4.869 4.107e+00 3.387 0.9315
[5,] 2.257 8.978e+00 4.613e-01 7.321 6.143e+00 3.386 1.4000
[6,] 2.193 8.724e+00 4.482e-01 9.709 8.121e+00 3.385 1.8540
fAUC Aplacenta Cplacenta Cfliver Cfven Cfart Cfgut Cflung Cfrest
[1,] 0.0000 0.0000 0.000e+00 0.000 0.000 0.000 0.000 0.000 0.000
[2,] 0.0000 0.0000 1.000e-08 0.000 0.000 0.000 0.000 0.000 0.000
[3,] 0.3511 0.1919 1.759e+00 8.202 1.459 1.459 5.874 3.376 2.278
[4,] 0.7296 0.1905 1.709e+00 7.971 1.423 1.423 5.708 3.281 2.214
[5,] 1.0970 0.1891 1.661e+00 7.745 1.387 1.387 5.546 3.188 2.151
[6,] 1.4550 0.1875 1.613e+00 7.525 1.351 1.351 5.389 3.097 2.090
Cfthyroid Cfkidney Cfbrain Cfplasma Rfblood2plasma Qcardiac Qthyroid
[1,] 0.000 0.000 0.000 0.0000 3.788 8656 118.6
[2,] 0.000 0.000 0.000 0.0000 3.788 8656 118.6
[3,] 3.211 8.828 2.564 0.3840 3.800 8673 118.7
[4,] 3.120 8.579 2.491 0.3731 3.812 8690 118.8
[5,] 3.032 8.335 2.420 0.3626 3.824 8707 118.9
[6,] 2.946 8.099 2.352 0.3523 3.836 8724 119.0
Warning messages:
1: In solve_model(chem.name = chem.name, chem.cas = chem.cas, dtxsid = dtxsid, :
Rblood2plasma not recalculated.
Set recalc.blood2plasma to TRUE if desired.
2: 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_fetal_pbtk(chem.name='bisphenol a')[sort(names(parameterize_fetal_pbtk(chem.name='bisphenol a')))]
> # 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=""))
adipose_density: 0.95
amnf_density: 1.01
arterial_blood_fraction: 0.16
brain_density: 1.04
BW: 61.1
BW_cubic_theta1: -0.010614
BW_cubic_theta2: 0.029161
BW_cubic_theta3: -0.00050203
Clint: 29.51
Clint.dist: 19.9,10.2,29.8,0
Clmetabolismc: 0.1219
Fabsgut: 0.6441
fblood_weight_ratio: 80
fBW_gompertz_theta0: 0.0018282
fBW_gompertz_theta1: 1.1735
fBW_gompertz_theta2: 0.077577
ffmx_density: 1.1
fhematocrit_cubic_theta1: 4.5061
fhematocrit_cubic_theta2: -0.18487
fhematocrit_cubic_theta3: 0.0026766
Fhep.assay.correction: 0.6744
Fraction_unbound_plasma_fetus: 0.03111
Funbound.plasma: 0.02434
Funbound.plasma.adjustment: 0.6321
Funbound.plasma.dist: 0.0385,0.0334,0.0456
gut_density: 1.04
hematocrit_quadratic_theta0: 39.192
hematocrit_quadratic_theta1: -0.10562
hematocrit_quadratic_theta2: -0.00071045
Kadipose2pu: 230.8
Kfbrain2pu: 214.6
Kfgut2pu: 491.7
Kfkidney2pu: 739
Kfliver2pu: 686.6
Kflung2pu: 282.6
Kfplacenta2pu: 147.2
Kfrbc2pu: 301.9
Kfrest2pu: 190.7
Kfthyroid2pu: 268.8
Kgut2pu: 520.6
kgutabs: 0.3711
kidney_density: 1.05
Kkidney2pu: 800.3
Kliver2pu: 753.2
Klung2pu: 292.2
Kplacenta2pu: 147.9
Krbc2pu: 301.5
Krest2pu: 200.9
Kthyroid2pu: 268.9
liver_density: 1.05
lung_density: 1.05
MA: 28840
million.cells.per.gliver: 110
MW: 228.3
pH_Plasma_fet: 7.28
pH_Plasma_mat: 7.38
pKa_Accept: NA
pKa_Donor: 9.46
placenta_density: 1.02
Pow: 2089
pre_pregnant_BW: 61.1
Qadipose_percent_initial: 8.5
Qadipose_percent_terminal: 7.8
Qbrain_percent: 12
Qcardiac_cubic_theta0: 301.78
Qcardiac_cubic_theta1: 3.2512
Qcardiac_cubic_theta2: 0.15947
Qcardiac_cubic_theta3: -0.0047059
Qfbrain_percent: 14.3
Qfda_logistic_theta0: 1125.3
Qfda_logistic_theta1: 0.18031
Qfda_logistic_theta2: 35.939
Qfdv_gompertz_theta0: 1.892
Qfdv_gompertz_theta1: 0.098249
Qfdv_gompertz_theta2: 0.0064374
Qfgut_percent: 6.8
Qfkidney_percent: 5.4
Qfliver_percent: 6.5
Qflvtl_logistic_theta0: 506.3
Qflvtl_logistic_theta1: 0.21916
Qflvtl_logistic_theta2: 30.231
Qfnonplacental_percent: 75
Qfplacenta_logistic_theta0: 262.2
Qfplacenta_logistic_theta1: 0.22183
Qfplacenta_logistic_theta2: 28.784
Qfrvtl_logistic_theta0: 2466.5
Qfrvtl_logistic_theta1: 0.14837
Qfrvtl_logistic_theta2: 43.108
Qfthyroid_percent: 1.5
Qgfr_quadratic_theta0: 113.73
Qgfr_quadratic_theta1: 3.5784
Qgfr_quadratic_theta2: -0.067272
Qgut_percent: 16
Qgut_percent_initial: 17
Qgut_percent_terminal: 12.5
Qkidney_cubic_theta0: 53.248
Qkidney_cubic_theta1: 3.6447
Qkidney_cubic_theta2: -0.15357
Qkidney_cubic_theta3: 0.0016968
Qkidney_percent: 18
Qliver_percent_initial: 27
Qliver_percent_terminal: 20
Qplacenta_linear_theta1: 0.059176
Qthyroid_percent_initial: 1.5
Qthyroid_percent_terminal: 1.1
term: 40
thyroid_density: 1.05
Vamnf_logistic_theta0: 822.34
Vamnf_logistic_theta1: 0.26988
Vamnf_logistic_theta2: 20.15
venous_blood_fraction: 0.595
Vgutc: 0.019
Vkidneyc: 0.00458
Vliverc: 0.0233
Vlungc: 0.0158
Vplacenta_cubic_theta1: -1.7646
Vplacenta_cubic_theta2: 0.91775
Vplacenta_cubic_theta3: -0.011543
Vplasma_mod_logistic_theta0: 1.2406
Vplasma_mod_logistic_theta1: 0.31338
Vplasma_mod_logistic_theta2: 17.813
Vplasma_mod_logistic_theta3: 2.4958
Vthyroidc: 0.000283
Wadipose_linear_theta0: 17.067
Wadipose_linear_theta1: 0.14937
Wfbrain_gompertz_theta0: 0.01574
Wfbrain_gompertz_theta1: 0.70707
Wfbrain_gompertz_theta2: 0.064827
Wfgut_gompertz_theta0: 0.00081828
Wfgut_gompertz_theta1: 0.65028
Wfgut_gompertz_theta2: 0.047724
Wfkidney_gompertz_theta0: 6.3327e-05
Wfkidney_gompertz_theta1: 1.0409
Wfkidney_gompertz_theta2: 0.076435
Wfliver_gompertz_theta0: 0.0074774
Wfliver_gompertz_theta1: 0.65856
Wfliver_gompertz_theta2: 0.061662
Wflung_gompertz_theta0: 0.00030454
Wflung_gompertz_theta1: 1.0667
Wflung_gompertz_theta2: 0.084604
Wfthyroid_gompertz_theta0: 0.0038483
Wfthyroid_gompertz_theta1: 0.30799
Wfthyroid_gompertz_theta2: 0.0398
>
> quit("no")
> proc.time()
user system elapsed
9.09 0.28 9.35