R Under development (unstable) (2024-03-18 r86148 ucrt) -- "Unsuffered Consequences"
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> # R CMD BATCH --no-timing --no-restore --no-save other_tests.R other_tests.Rout
> 
> # Get rid of anything in the workspace:
> rm(list=ls()) 
> 
> library(httk)
> 
> #calc_css(chem.name='nicotine')
> 
> calc_css(chem.name='nicotine', model="1compartment")
Human volume of distribution returned in units of L/kg BW.
$avg
[1] 0.5664

$frac
[1] 0.756

$max
[1] 1.376

$the.day
[1] 0

Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
3: In available_rblood2plasma(chem.cas = chem.cas, chem.name = chem.name,  :
  Human in vivo measured Rblood2plasma used.
> 
> calc_css(chem.name='nicotine', model="3compartment")
$avg
[1] 0.3386

$frac
[1] 0.4408

$max
[1] 1.113

$the.day
[1] 0

Warning messages:
1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Clint is provided as a distribution.
2: 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.
3: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
4: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
5: In available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma used.
6: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> 
> calc_css(chem.name="endrin")
$avg
[1] 986.4

$frac
[1] 0.9898

$max
[1] 986.7

$the.day
[1] 5673

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 calc_ma(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Membrane affintity (MA) predicted with method of Yun and Edginton (2013), see calc_ma.
3: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
4: In calc_ma(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Membrane affintity (MA) predicted with method of Yun and Edginton (2013), see calc_ma.
5: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
6: In calc_rblood2plasma(chem.cas = chem.cas, species = species, adjusted.Funbound.plasma = adjusted.Funbound.plasma,  :
  Rblood2plasma has been recalculated.
7: In available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human Rblood2plasma calculated with calc_rblood2plasma.
8: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
> 
> calc_tkstats(chem.name='nicotine',days=10)
Human plasma concentrations returned in uM units.
AUC is area under plasma concentration curve in uM * days units with Rblood2plasma = 0.8238 .
$AUC
[1] 6.002

$peak
[1] 3.938

$mean
[1] 0.6002

> 
> calc_tkstats(dtxsid="DTXSID0020442",days=1)
Plasma values returned in uM units.
AUC is area under plasma concentration curve in uM * days units with Rblood2plasma = 2.11 .
$AUC
[1] 9.227

$peak
[1] 10.32

$mean
[1] 9.227

> 
> calc_tkstats(dtxsid="DTXSID0020442",days=10)
Plasma values returned in uM units.
AUC is area under plasma concentration curve in uM * days units with Rblood2plasma = 2.11 .
$AUC
[1] 287.4

$peak
[1] 43.37

$mean
[1] 28.74

> 
> calc_tkstats(dtxsid="DTXSID0020442",days=100)
Plasma values returned in uM units.
AUC is area under plasma concentration curve in uM * days units with Rblood2plasma = 2.11 .
$AUC
[1] 4119

$peak
[1] 47.35

$mean
[1] 41.19

> 
> calc_analytic_css(
+   chem.name='Bisphenol-A',
+   tissue='liver',
+   species='rabbit',
+   parameterize.args = list(
+     default.to.human=TRUE,
+     adjusted.Funbound.plasma=TRUE,
+     regression=TRUE,
+     minimum.Funbound.plasma=1e-4),
+   daily.dose=2)
Plasma concentration for liver returned in uM units.
[1] 11.58
Warning messages:
1: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  rabbit coerced to Human for metabolic clearance data.
2: In get_clint(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Clint is provided as a distribution.
3: 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.
4: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  rabbit coerced to Human for protein binding data.
5: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
6: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
7: In predict_partitioning_schmitt(parameters = schmitt.params, species = species,  :
  Human fractional tissue volumes used in calculating partition coefficients.
8: In available_rblood2plasma(chem.cas = chem.cas, species = species,  :
  Human in vivo measured Rblood2plasma substituted.
9: In get_caco2(chem.cas = chem.cas, chem.name = chem.name, dtxsid = dtxsid,  :
  Default value of 1.6 used for Caco2 permeability.
10: In calc_fgut.oral(parameters = c(out, parameters), chem.cas = chem.cas,  :
  Human intestinal permeability and microvilli blood flow used to calculate fraction absorbed by gut
> 
> predict_partitioning_schmitt(chem.name='nicotine')
$Kadipose2pu
[1] 2.885

$Kbone2pu
[1] 0.9899

$Kbrain2pu
[1] 1.45

$Kgut2pu
[1] 2.535

$Kheart2pu
[1] 3.162

$Kkidney2pu
[1] 5.146

$Kliver2pu
[1] 6.172

$Klung2pu
[1] 1.502

$Kmuscle2pu
[1] 1.458

$Kskin2pu
[1] 1.869

$Kspleen2pu
[1] 1.662

$Krbc2pu
[1] 0.8019

$Krest2pu
[1] 2.15

Warning messages:
1: In get_fup(dtxsid = dtxsid, chem.name = chem.name, chem.cas = chem.cas,  :
  Fraction unbound is provided as a distribution.
2: In apply_fup_adjustment(fup.point, fup.correction = fup.adjustment,  :
  Fup adjusted for in vivo lipid partitioning (Pearce, 2017), see calc_fup_correction.
> 
> quit("no")
> proc.time()
   user  system elapsed 
  16.50    0.73   17.23