convert_units: convert_units

In httk: High-Throughput Toxicokinetics

convert_units

Description

This function is designed to accept input units, output units, and the molecular weight (MW) of a substance of interest to then use a table lookup to return a scaling factor that can be readily applied for the intended conversion. It can also take chemical identifiers in the place of a specified molecular weight value to retrieve that value for its own use.

Usage

convert_units(
  input.units = NULL,
  output.units = NULL,
  MW = NULL,
  vol = NULL,
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  parameters = NULL,
  temp = 25,
  liquid.density = 1,
  state = "liquid"
)

Arguments

input.units	Assigned input units of interest
output.units	Desired output units
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
temp	Temperature for conversions (default = 25 degreees C)
liquid.density	Density of the specified chemical in liquid state, numeric value, (default 1.0 g/mL).
state	Chemical state (gas or default liquid).

Details

If input or output units not contained in the table are queried, it gives a corresponding error message. It gives a warning message about the handling of 'ppmv,' as the function is only set up to convert between ppmv and mass-based units (like mg/m³ or umol/L) in the context of ideal gases.

convert_units is not directly configured to accept and convert units based on BW, like mg/kg. For this purpose, see scale_dosing.

The function supports a limited set of most relevant units across toxicological models, currently including umol, uM, mg, mg/L, mg/m³ or umol/L), and in the context of gases assumed to be ideal, ppmv.

Andersen and Clewell's Rules of PBPK Modeling:

1. Check Your Units

2. Check Your Units

3. Check Mass Balance

Author(s)

Mark Sfeir, John Wambaugh, and Sarah E. Davidson

Examples

# MW BPA is 228.29 g/mol
# 1 mg/L -> 1/228.29*1000 = 4.38 uM
convert_units("mg/L","uM",chem.cas="80-05-7")

# MW Diclofenac is 296.148 g/mol
# 1 uM -> 296.148/1000 =  0.296
convert_units("uM","mg/L",chem.name="diclofenac")

# ppmv only works for gasses:
try(convert_units("uM","ppmv",chem.name="styrene"))
convert_units("uM","ppmv",chem.name="styrene",state="gas")

# Compare with https://www3.epa.gov/ceampubl/learn2model/part-two/onsite/ia_unit_conversion.html
# 1 ug/L Toluene -> 0.263 ppmv
convert_units("ug/L","ppmv",chem.name="toluene",state="gas")
# 1 pppmv Toluene, 0.0038 mg/L
convert_units("ppmv","mg/L",chem.name="toluene",state="gas")

MW_pyrene <- get_physchem_param(param='MW', chem.name='pyrene')
conversion_factor <- convert_units(input.units='mg/L', output.units ='uM',
  MW=MW_pyrene)

calc_mc_oral_equiv(15, parameters=p)

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