httk (version 2.7.0)

get_2023pfasinfo: Retrieve chemical information on 2023 EPA PFAS Chemicals

Description

This function is a wrapper for get_cheminfo that only lists chemicals from the Smeltz, Kreutz, and Crizer data sets collected on PFAS between 2019 and 2022. Plasma protein binding (fraction unbound) data were collected using ultracentrifugation (UC) instead of rapid equilibrium dialysis. Intrsinsic hepatic clearance (Clint) data were collected with substrate depletion (over time) assays.

Usage

get_2023pfasinfo(
  info = "CAS",
  species = "Human",
  fup.lod.default = 0.005,
  model = "3compartmentss",
  default.to.human = FALSE,
  median.only = FALSE,
  fup.ci.cutoff = FALSE,
  clint.pvalue.threshold = 0.05,
  suppress.messages = FALSE
)

Value

vector/data.table

Table (if info has multiple entries) or vector containing a column for each valid entry specified in the argument "info" and a row for each chemical with sufficient data for the model specified by argument "model":

Column	Description	units
Compound	The preferred name of the chemical compound	none
CAS	The preferred Chemical Abstracts Service Registry Number	none
DTXSID	DSSTox Structure ID (http://comptox.epa.gov/dashboard)	none
logP	The log10 octanol:water partition coefficient	log10 unitless ratio
MW	The chemical compound molecular weight	g/mol
pKa_Accept	The hydrogen acceptor equilibria concentrations	logarithm
pKa_Donor	The hydrogen donor equilibria concentrations	logarithm
[SPECIES].Clint	(Primary hepatocyte suspension) intrinsic hepatic clearance	uL/min/10^6 hepatocytes
[SPECIES].Clint.pValue	Probability that there is no clearance observed.	none
[SPECIES].Funbound.plasma	Chemical fraction unbound in presence of plasma proteins	unitless fraction
[SPECIES].Rblood2plasma	Chemical concentration blood to plasma ratio	unitless ratio

Arguments

info

A single character vector (or collection of character vectors) from "Compound", "CAS", "DTXSID, "logP", "pKa_Donor"," pKa_Accept", "MW", "Clint", "Clint.pValue", "Funbound.plasma","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").

fup.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.

median.only

Use median values only for fup and clint. Default is FALSE.

fup.ci.cutoff

Cutoff for the level of uncertainty in fup estimates. This value should be between (0,1). Default is `NULL` specifying no filtering.

clint.pvalue.threshold

Hepatic clearance for chemicals where the in vitro clearance assay result has a p-values greater than the threshold are set to zero.

suppress.messages

Whether or not the output messages are suppressed.

Author

John Wambaugh

Details

Note that in some cases the Funbound.plasma and the intrinsic clearance are provided as a series of numbers separated by commas. These values are the result of Bayesian analysis and characterize a distribution: the first value is the median of the distribution, while the second and third values are the lower and upper 95th percentile (that is qunatile 2.5 and 97.5) respectively. For intrinsic clearance a fourth value indicating a p-value for a decrease is provided. Typically 4000 samples were used for the Bayesian analusis, such that a p-value of "0" is equivale to "<0.00025". See Wambaugh et al. (2019) for more details. If argument meadian.only == TRUE then only the median is reported for parameters with Bayesian analysis distributions. If the 95 credible interval is larger than fup.ci.cutoff (defaults to NULL) then the Fup is treated as too uncertain and the value NA is given.

Examples

# \donttest{
PFASCssTable <- NULL
for (this.id in get_2023pfasinfo(info="dtxsid"))
{
  PFASCssTable <- rbind(PFASCssTable, data.frame(
    DTXSID = this.id,
    Css = try(calc_analytic_css(dtxsid=this.id, 
                                  model="sumclearancespfas",
                                  suppress.messages=TRUE
   ))))
}
# }