R Under development (unstable) (2024-08-23 r87049 ucrt) -- "Unsuffered Consequences"
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> # R CMD BATCH --no-timing --no-restore --no-save adddata_test.R adddata_test.Rout
> 
> # Get rid of anything in the workspace:
> rm(list=ls()) 
> 
> library(httk)
> 
> # Number of chemicals distributed with the package:
> num.chems <- length(get_cheminfo())
Warning messages:
1: In get_cheminfo() :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model 3compartmentss each chemical must have non-NA values for:Human.Clint, Human.Funbound.plasma, logP, MW
2: In get_cheminfo() :
  Excluding compounds without a 'fup' value (i.e. fup value = NA).
3: In get_cheminfo() :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
4: In get_cheminfo() :
  Excluding compounds that do not have a clint value or distribution of clint values.
5: In get_cheminfo() :
  Excluding volatile compounds defined as log.Henry >= -4.5.
6: In get_cheminfo() :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> 
> fake <- data.frame(Compound="Tester",
+                    CASRN="222-11-1",
+                    DTXSID="DTX111222",
+                    MW=200,
+                    logP=3.5,
+                    Fup=0.1,
+                    Clint=0.1,
+                    Clint.pValue=0.001,stringsAsFactors=FALSE)
> 
> chem.physical_and_invitro.data <- add_chemtable(
+   fake,
+   current.table=chem.physical_and_invitro.data,
+   data.list=list(
+     Compound="Compound",
+     CAS="CASRN",
+     DTXSID="DTXSID",
+     MW="MW",
+     logP="logP",
+     Funbound.plasma="Fup",
+     Clint="Clint",
+     Clint.pValue="Clint.pValue"),
+   species="Human",
+   reference="Fake")
> 
> calc_css(chem.name="Tester")
$avg
[1] 32.74

$frac
[1] 0.9916

$max
[1] 32.82

$the.day
[1] 125

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.
> 
> #load_sipes2017()
> 
> # We should have the ADMet Predicted chemicals from Sipes et al. (2017),
> # this one is a good test since the logP is nearly 10!
> #calc_css(chem.cas="26040-51-7")
> 
> #Let's see how many chemicals we have now with the Sipes (2017) data loaded)=:
> #length(get_cheminfo())
> 
> #Now let's reset
> reset_httk()
> 
> # We should be back to our original number:
> num.chems == length(get_cheminfo())
[1] TRUE
Warning messages:
1: In get_cheminfo() :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model 3compartmentss each chemical must have non-NA values for:Human.Clint, Human.Funbound.plasma, logP, MW
2: In get_cheminfo() :
  Excluding compounds without a 'fup' value (i.e. fup value = NA).
3: In get_cheminfo() :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
4: In get_cheminfo() :
  Excluding compounds that do not have a clint value or distribution of clint values.
5: In get_cheminfo() :
  Excluding volatile compounds defined as log.Henry >= -4.5.
6: In get_cheminfo() :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> 
> quit("no")
> proc.time()
   user  system elapsed 
   6.06    0.50    6.54