create_mc_samples: Create a data table of draws of parameter values for Monte Carlo

Description

This function creates a data table of draws of parameter values for use with Monte Carlo methods

Usage

create_mc_samples(
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  parameters = NULL,
  samples = 1000,
  species = "Human",
  suppress.messages = FALSE,
  model = "3compartmentss",
  httkpop = TRUE,
  invitrouv = TRUE,
  calcrb2p = TRUE,
  censored.params = list(),
  vary.params = list(),
  return.samples = FALSE,
  tissue = NULL,
  httkpop.dt = NULL,
  invitro.mc.arg.list = list(adjusted.Funbound.plasma = TRUE, poormetab = TRUE,
    fup.censored.dist = FALSE, fup.lod = 0.01, fup.meas.cv = 0.4, clint.meas.cv = 0.3,
    fup.pop.cv = 0.3, clint.pop.cv = 0.3),
  httkpop.generate.arg.list = list(method = "direct resampling", gendernum = NULL,
    agelim_years = NULL, agelim_months = NULL, weight_category = c("Underweight",
    "Normal", "Overweight", "Obese"), gfr_category = c("Normal", "Kidney Disease",
    "Kidney Failure"), reths = c("Mexican American", "Other Hispanic",
    "Non-Hispanic White", "Non-Hispanic Black", "Other")),
  convert.httkpop.arg.list = list(),
  propagate.invitrouv.arg.list = list(),
  parameterize.arg.list = list(restrictive.clearance = TRUE, default.to.human = FALSE,
    clint.pvalue.threshold = 0.05, regression = TRUE)
)

Value

A data table where each column corresponds to parameters needed for the specified model and each row represents a different Monte Carlo sample of parameter values.

Arguments

chem.cas: Chemical Abstract Services Registry Number (CAS-RN) -- if parameters is not specified then the chemical must be identified by either CAS, name, or DTXISD
chem.name: Chemical name (spaces and capitalization ignored) -- if parameters is not specified then the chemical must be identified by either CAS, name, or DTXISD
dtxsid: EPA's DSSTox Structure ID (https://comptox.epa.gov/dashboard) -- if parameters is not specified then the chemical must be identified by either CAS, name, or DTXSIDs
parameters: Parameters from the appropriate parameterization function for the model indicated by argument model
samples: Number of samples generated in calculating quantiles.
species: Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human"). Species must be set to "Human" to run httkpop model.
suppress.messages: Whether or not to suppress output message.
model: Model used in calculation: 'pbtk' for the multiple compartment model,'3compartment' for the three compartment model, '3compartmentss' for the three compartment steady state model, and '1compartment' for one compartment model. This only applies when httkpop=TRUE and species="Human", otherwise '3compartmentss' is used.
httkpop: Whether or not to use the Ring et al. (2017) "httkpop" population generator. Species must be 'Human'.
invitrouv: Logical to indicate whether to include in vitro parameters such as intrinsic hepatic clearance rate and fraction unbound in plasma in uncertainty and variability analysis
calcrb2p: Logical determining whether or not to recalculate the chemical ratio of blood to plasma
censored.params: The parameters listed in censored.params are sampled from a normal distribution that is censored for values less than the limit of detection (specified separately for each parameter). This argument should be a list of sub-lists. Each sublist is named for a parameter in "parameters" and contains two elements: "CV" (coefficient of variation) and "LOD" (limit of detection, below which parameter values are censored. New values are sampled with mean equal to the value in "parameters" and standard deviation equal to the mean times the CV. Censored values are sampled on a uniform distribution between 0 and the limit of detection. Not used with httkpop model.
vary.params: The parameters listed in vary.params are sampled from a normal distribution that is truncated at zero. This argument should be a list of coefficients of variation (CV) for the normal distribution. Each entry in the list is named for a parameter in "parameters". New values are sampled with mean equal to the value in "parameters" and standard deviation equal to the mean times the CV. Not used with httkpop model.
return.samples: Whether or not to return the vector containing the samples from the simulation instead of the selected quantile.
tissue: Desired steady state tissue conentration.
httkpop.dt: A data table generated by httkpop_generate. This defaults to NULL, in which case httkpop_generate is called to generate this table.
invitro.mc.arg.list: Additional parameters passed to invitro_mc.
httkpop.generate.arg.list: Additional parameters passed to httkpop_generate.
convert.httkpop.arg.list: Additional parameters passed to the convert_httkpop_* function for the model.
propagate.invitrouv.arg.list: Additional parameters passed to model's associated in vitro uncertainty and variability propagation function
parameterize.arg.list: Additional parameters passed to the parameterize_* function for the model.

Author

Caroline Ring, Robert Pearce, and John Wambaugh

References

Wambaugh, John F., et al. "Toxicokinetic triage for environmental chemicals." Toxicological Sciences 147.1 (2015): 55-67.

Ring, Caroline L., et al. "Identifying populations sensitive to environmental chemicals by simulating toxicokinetic variability." Environment international 106 (2017): 105-118.

Examples

Run this code


# \donttest{
sample_set = create_mc_samples(chem.name = 'bisphenol a')
# }

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