convert_solve_x: convert_solve_x

In httk: High-Throughput Toxicokinetics

convert_solve_x

Description

This function is designed to convert compartment values estimated from one of the HTTK models (e.g. "1compartment) using the solve_model function. It takes the HTTK model output matrix, model name, desired output units, and compound information to perform the conversion default model units to user specified units.

Usage

convert_solve_x(
  model.output.mat,
  model = NULL,
  output.units = NULL,
  MW = NULL,
  vol = NULL,
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  parameters = NULL,
  monitor.vars = NULL,
  suppress.messages = FALSE,
  verbose = FALSE,
  ...
)

Arguments

model.output.mat	Matrix of results from HTTK solve_model function.
model	Specified model to use in simulation: "pbtk", "3compartment", "3compartmentss", "1compartment", "schmitt", ...
output.units	Output units of interest for the compiled components. Defaults to NULL, and will provide values in model units if unspecified.
MW	Molecular weight of substance of interest in g/mole
vol	Volume for the target tissue of interest in liters (L). NOTE: Volume should not be in units of per BW, i.e. "kg".
chem.cas	Either the chemical name, CAS number, or the parameters must be specified.
chem.name	Either the chemical name, CAS number, or the parameters must be specified.
dtxsid	EPA's DSSTox Structure ID . (https://comptox.epa.gov/dashboard) the chemical must be identified by either CAS, name, or DTXSIDs.
parameters	A set of model parameters, especially a set that includes MW (molecular weight) for our conversions.
monitor.vars	A vector of character strings indicating the model component variables to retain in the conversion factor table (assuming suppress.messages == FALSE). It should also be noted this option does NOT exclude columns from the input matrix provided in the 'model.output.mat' parameter. (Default is NULL, i.e. conversion factors for all model components are included in the reporting matrix.)
suppress.messages	Whether or not the output messages are suppressed. (Default is FALSE, i.e. show messages.)
verbose	Whether or not to display the full conversion factor table. (Default is FALSE, i.e. only include rows where the conversion factor is 1.)
...	Other parameters that can be passed to convert_units, e.g. temperature and compound state. See details in convert_units.

Details

The function can be used to convert all compartments to a single unit, only units for a single model compartment, or units for a set of model compartments.

More details on the unit conversion can be found in the documentation for convert_units.

Value

'new.ouput.matrix' A matrix with a column for time (in days), each compartment, and the area under the curve (AUC) and a row for each time point. The compartment and AUC columns are converted from model specified units to user specified units.

'output.units.vector' A vector of character strings providing the model compartments and their corresponding units after convert_solve_x.

Author(s)

Sarah E. Davidson

See Also

convert_units

Examples

output.mat <- solve_1comp(dtxsid = "DTXSID0020573",days=1)
new.output.mat <- convert_solve_x(output.units = "mg",
                                  model.output.mat = output.mat,
                                  model = "1compartment",
                                  dtxsid = "DTXSID0020573")

httk documentation built on Sept. 11, 2024, 9:32 p.m.