httk (version 1.8)

get_cheminfo: Retrieve chemical information from HTTK package

Description

This function provides the information specified in "info=" (can be single entry or vector) for all chemicals for which a toxicokinetic model can be paramterized for a given species.

Usage

get_cheminfo(info="CAS",species="Human",exclude.fub.zero=NA,fub.lod.default=0.005,
             model='3compartmentss',default.to.human=F)

Arguments

info

A single character vector (or collection of character vectors) from "Compound", "CAS", "logP", "pKa_Donor"," pKa_Accept", "MW", "Clint", "Clint.pValue", "Funbound.plasma", "DSSTox_Substance_Id","Structure_Formula", or "Substance_Type". info="all" gives all information for the model and species.

species

Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").

exclude.fub.zero

Whether or not to exclude chemicals with a fraction of unbound plasma equal to zero or include them with a value of fub.lod.default. Defaults to TRUE for '3compartmentss' and FALSE for pk models and schmitt.

fub.lod.default

Default value used for fraction of unbound plasma for chemicals where measured value was below the limit of detection. Default value is 0.0005.

model

Model used in calculation, 'pbtk' for the multiple compartment model, '1compartment' for the one compartment model, '3compartment' for three compartment model, '3compartmentss' for the three compartment model without partition coefficients, or 'schmitt' for chemicals with logP and fraction unbound (used in predict_partitioning_schmitt).

default.to.human

Substitutes missing values with human values if true.

Value

info

Table/vector containing values specified in "info" for valid chemicals.

Details

When default.to.human is set to TRUE, and the species-specific data, Funbound.plasma and Clint, are missing from chem.physical_and_invitro.data, human values are given instead.

Examples

# NOT RUN {
# List all CAS numbers for which the 3compartmentss model can be run in humans: 
get_cheminfo()

get_cheminfo(info=c('compound','funbound.plasma','logP'),model='pbtk') 
# See all the data for humans:
get_cheminfo(info="all")

TPO.cas <- c("741-58-2", "333-41-5", "51707-55-2", "30560-19-1", "5598-13-0", 
"35575-96-3", "142459-58-3", "1634-78-2", "161326-34-7", "133-07-3", "533-74-4", 
"101-05-3", "330-54-1", "6153-64-6", "15299-99-7", "87-90-1", "42509-80-8", 
"10265-92-6", "122-14-5", "12427-38-2", "83-79-4", "55-38-9", "2310-17-0", 
"5234-68-4", "330-55-2", "3337-71-1", "6923-22-4", "23564-05-8", "101-02-0", 
"140-56-7", "120-71-8", "120-12-7", "123-31-9", "91-53-2", "131807-57-3", 
"68157-60-8", "5598-15-2", "115-32-2", "298-00-0", "60-51-5", "23031-36-9", 
"137-26-8", "96-45-7", "16672-87-0", "709-98-8", "149877-41-8", "145701-21-9", 
"7786-34-7", "54593-83-8", "23422-53-9", "56-38-2", "41198-08-7", "50-65-7", 
"28434-00-6", "56-72-4", "62-73-7", "6317-18-6", "96182-53-5", "87-86-5", 
"101-54-2", "121-69-7", "532-27-4", "91-59-8", "105-67-9", "90-04-0", 
"134-20-3", "599-64-4", "148-24-3", "2416-94-6", "121-79-9", "527-60-6", 
"99-97-8", "131-55-5", "105-87-3", "136-77-6", "1401-55-4", "1948-33-0", 
"121-00-6", "92-84-2", "140-66-9", "99-71-8", "150-13-0", "80-46-6", "120-95-6",
"128-39-2", "2687-25-4", "732-11-6", "5392-40-5", "80-05-7", "135158-54-2", 
"29232-93-7", "6734-80-1", "98-54-4", "97-53-0", "96-76-4", "118-71-8", 
"2451-62-9", "150-68-5", "732-26-3", "99-59-2", "59-30-3", "3811-73-2", 
"101-61-1", "4180-23-8", "101-80-4", "86-50-0", "2687-96-9", "108-46-3", 
"95-54-5", "101-77-9", "95-80-7", "420-04-2", "60-54-8", "375-95-1", "120-80-9",
"149-30-4", "135-19-3", "88-58-4", "84-16-2", "6381-77-7", "1478-61-1", 
"96-70-8", "128-04-1", "25956-17-6", "92-52-4", "1987-50-4", "563-12-2", 
"298-02-2", "79902-63-9", "27955-94-8")
httk.TPO.rat.table <- subset(get_cheminfo(info="all",species="rat"),
 CAS %in% TPO.cas)
 
httk.TPO.human.table <- subset(get_cheminfo(info="all",species="human"),
 CAS %in% TPO.cas)
# }