add_chemtable: Add a table of chemical information for use in making httk...

In wwiecek/httkgui: High-Throughput Toxicokinetics: Analtica Laser prototype

Description

This function adds chemical-specific information to the table chem.physical_and_invitro.data. This table is queried by the model parameterization functions when attempting to parameterize a model, so adding sufficient data to this table allows additional chemicals to be modeled.

Usage

add_chemtable(new.table, data.list, current.table=NULL, 
              reference=NULL,species=NULL, overwrite=F)

Arguments

new.table	Object of class data.frame containing one row per chemical, with each chemical minimally by described by a CAS number.
data.list	This list identifies which properties are to be read from the table. Each item in the list should point to a column in the table new.table. Valid names in the list are: 'Compound', 'CAS', 'DSSTox.GSID' 'SMILES.desalt', 'Reference', 'Species', 'MW', 'logP', 'pKa_Donor', 'pKa_Accept', 'logMA', 'Clint', 'Clint.pValue', 'Funbound.plasma', 'Fgutabs', 'Rblood2plasma'. Note that Rblood2plasma (Ratio blood to plasma) is currently not used.
current.table	This is the table to which data is being added.
reference	This is the reference for the data in the new table. This may be omitted if a column in data.list gives the reference value for each chemical.
species	This is the species for the data in the new table. This may be omitted if a column in data.list gives the species value for each chemical or if the data is not species-specific (e.g., MW).
overwrite	If overwrite=TRUE then data in current.table will be replaced by any data in new.table that is for the same chemical and property. If overwrite=FALSE (DEFAULT) then new data for the same chemical and property is ignored.

Value

data.frame

A new data.frame containing the data in current.table augmented by new.table

Author(s)

John Wambaugh

Examples

my.new.data <- as.data.frame(c("A","B","C"),stringsAsFactors=FALSE)
my.new.data <- cbind(my.new.data,as.data.frame(c("111-11-5","222-22-0","333-33-5"),
                     stringsAsFactors=FALSE))
my.new.data <- cbind(my.new.data,as.data.frame(c(200,200,200)))
my.new.data <- cbind(my.new.data,as.data.frame(c(2,3,4)))
my.new.data <- cbind(my.new.data,as.data.frame(c(0.01,0.02,0.3)))
my.new.data <- cbind(my.new.data,as.data.frame(c(0,10,100)))
colnames(my.new.data) <- c("Name","CASRN","MW","LogP","Fup","CLint")

chem.physical_and_invitro.data <- add_chemtable(my.new.data,
                                  current.table=chem.physical_and_invitro.data,
                                  data.list=list(
                                  Compound="Name",
                                  CAS="CASRN",
                                  MW="MW",
                                  logP="LogP",
                                  Funbound.plasma="Fup",
                                  Clint="CLint"),
                                  species="Human",
                                  reference="MyPaper 2015")
parameterize_steadystate(chem.name="C")                                  
calc_mc_oral_equiv(10,chem.name="B")

wwiecek/httkgui documentation built on May 15, 2019, 6:31 p.m.