R Under development (unstable) (2024-09-04 r87094 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # R CMD BATCH --no-timing --no-restore --no-save cheminfo_test.R cheminfo_test.Rout
> 
> # Get rid of anything in the workspace:
> rm(list=ls()) 
> 
> library(httk)
> 
> # Check if the number of chemicals has changed:
> Css.list <- 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.
> pbpk.list <- get_cheminfo(model='pbtk')
Warning messages:
1: In get_cheminfo(model = "pbtk") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model pbtk each chemical must have non-NA values for:Human.Clint, Human.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "pbtk") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "pbtk") :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
4: In get_cheminfo(model = "pbtk") :
  Excluding compounds that do not have a clint value or distribution of clint values.
5: In get_cheminfo(model = "pbtk") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
6: In get_cheminfo(model = "pbtk") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> rat.list <- get_cheminfo(species="rat")
Warning messages:
1: In get_cheminfo(species = "rat") :
  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:Rat.Clint, Rat.Funbound.plasma, logP, MW
2: In get_cheminfo(species = "rat") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA).
3: In get_cheminfo(species = "rat") :
  Excluding compounds that do not have a clint value or distribution of clint values.
4: In get_cheminfo(species = "rat") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
5: In get_cheminfo(species = "rat") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(Css.list)
[1] 1021
> length(pbpk.list)
[1] 957
> length(rat.list)
[1] 187
>                                                  
> # check for duplicate entries (all of the following should be TRUE):
> # A unique CAS-RN for each row of chem.physical_and_invitro.data table:
> length(unique(chem.physical_and_invitro.data$CAS)) == 
+   dim(chem.physical_and_invitro.data)[1]
[1] TRUE
> # A unique compound name for each row of chem.physical_and_invitro.data table:
> length(unique(chem.physical_and_invitro.data$Compound)) == 
+   dim(chem.physical_and_invitro.data)[1]
[1] TRUE
> # A unique DTXSID for each row of chem.physical_and_invitro.data table:
> length(unique(subset(chem.physical_and_invitro.data,!is.na(DTXSID))$DTXSID)) == 
+   dim(subset(chem.physical_and_invitro.data,!is.na(DTXSID)))[1]
[1] TRUE
>   
> # Check if the requirements for diffrent models has changed:
> length(get_cheminfo())
[1] 1021
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.
> length(get_cheminfo(species="rat"))
[1] 187
Warning messages:
1: In get_cheminfo(species = "rat") :
  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:Rat.Clint, Rat.Funbound.plasma, logP, MW
2: In get_cheminfo(species = "rat") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA).
3: In get_cheminfo(species = "rat") :
  Excluding compounds that do not have a clint value or distribution of clint values.
4: In get_cheminfo(species = "rat") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
5: In get_cheminfo(species = "rat") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(model="pbtk"))
[1] 957
Warning messages:
1: In get_cheminfo(model = "pbtk") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model pbtk each chemical must have non-NA values for:Human.Clint, Human.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "pbtk") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "pbtk") :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
4: In get_cheminfo(model = "pbtk") :
  Excluding compounds that do not have a clint value or distribution of clint values.
5: In get_cheminfo(model = "pbtk") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
6: In get_cheminfo(model = "pbtk") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(model="pbtk",species="rat"))
[1] 160
Warning messages:
1: In get_cheminfo(model = "pbtk", species = "rat") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model pbtk each chemical must have non-NA values for:Rat.Clint, Rat.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "pbtk", species = "rat") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "pbtk", species = "rat") :
  Excluding compounds that do not have a clint value or distribution of clint values.
4: In get_cheminfo(model = "pbtk", species = "rat") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
5: In get_cheminfo(model = "pbtk", species = "rat") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(info="all"))
[1] 11
Warning messages:
1: In get_cheminfo(info = "all") :
  Clint values with a pvalue > 0.05 were set to 0.
2: In get_cheminfo(info = "all") :
  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
3: In get_cheminfo(info = "all") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA).
4: In get_cheminfo(info = "all") :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
5: In get_cheminfo(info = "all") :
  Excluding compounds that do not have a clint value or distribution of clint values.
6: In get_cheminfo(info = "all") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
7: In get_cheminfo(info = "all") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(model="schmitt"))
[1] 1706
Warning messages:
1: In get_cheminfo(model = "schmitt") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model schmitt each chemical must have non-NA values for:Human.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "schmitt") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "schmitt") :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
4: In get_cheminfo(model = "schmitt") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(model="schmitt",species="rat"))
[1] 298
Warning messages:
1: In get_cheminfo(model = "schmitt", species = "rat") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model schmitt each chemical must have non-NA values for:Rat.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "schmitt", species = "rat") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "schmitt", species = "rat") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(model="1compartment"))
[1] 1029
Warning messages:
1: In get_cheminfo(model = "1compartment") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model 1compartment each chemical must have non-NA values for:Human.Clint, Human.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "1compartment") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "1compartment") :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
4: In get_cheminfo(model = "1compartment") :
  Excluding compounds that do not have a clint value or distribution of clint values.
5: In get_cheminfo(model = "1compartment") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> length(get_cheminfo(model="1compartment",species="rat"))
[1] 195
Warning messages:
1: In get_cheminfo(model = "1compartment", species = "rat") :
  Excluding compounds that have one or more needed parameters missing in chem.physical_and_invitro.table.

For model 1compartment each chemical must have non-NA values for:Rat.Clint, Rat.Funbound.plasma, logP, MW
2: In get_cheminfo(model = "1compartment", species = "rat") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA) or a 'fup' value of 0.
3: In get_cheminfo(model = "1compartment", species = "rat") :
  Excluding compounds that do not have a clint value or distribution of clint values.
4: In get_cheminfo(model = "1compartment", species = "rat") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
>   
> # Check to see if the paramerer values have changed:
> print(subset(get_cheminfo(info="all"), CAS %in% c(
+   "80-05-7",
+   "335-67-1",
+   "1912-24-9",
+   "2921-88-2",	
+   "117-81-7")),
+   row.names=FALSE)
                      Compound       CAS        DTXSID  logP    MW pKa_Accept
                      Atrazine 1912-24-9 DTXSID9020112 2.611 215.7       3.79
                   Bisphenol-a   80-05-7 DTXSID7020182 3.320 228.3       <NA>
 Diethylhexyl phthalate (dehp)  117-81-7 DTXSID5020607 7.525 390.6       <NA>
                  Chlorpyrifos 2921-88-2 DTXSID4020458 4.959 350.6       2.03
 pKa_Donor      Human.Clint Human.Clint.pValue Human.Funbound.plasma
      <NA>                0            0.05366                0.1237
      9.46 19.9,10.2,29.8,0            0.00000  0.0385,0.0334,0.0456
      <NA>                0            0.19370                 0.005
      <NA>              2.6                 NA              0.007932
 Human.Rblood2plasma
                  NA
              0.7949
                  NA
              0.7333
Warning messages:
1: In get_cheminfo(info = "all") :
  Clint values with a pvalue > 0.05 were set to 0.
2: In get_cheminfo(info = "all") :
  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
3: In get_cheminfo(info = "all") :
  Excluding compounds without a 'fup' value (i.e. fup value = NA).
4: In get_cheminfo(info = "all") :
  Excluding compounds with uncertain 'fup' confidence/credible intervals.
5: In get_cheminfo(info = "all") :
  Excluding compounds that do not have a clint value or distribution of clint values.
6: In get_cheminfo(info = "all") :
  Excluding volatile compounds defined as log.Henry >= -4.5.
7: In get_cheminfo(info = "all") :
  Excluding compounds that are categorized in one or more of the following chemical classes: PFAS.
> 
> quit("no")
> proc.time()
   user  system elapsed 
   5.23    0.31    5.53