armitage_eval: Armitage In Vitro Distribution Model
In httk: High-Throughput Toxicokinetics
armitage_eval R Documentation
Armitage In Vitro Distribution Model
Description
Evaluate the Armitage model for chemical distributon in vitro. Takes input
as data table or vectors of values. Outputs a data table. Updates over
the model published in Armitage et al. (2014) include binding to plastic walls
and lipid and protein compartments in cells.
Usage
armitage_eval(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
casrn.vector = NA_character_,
nomconc.vector = 1,
this.well_number = 384,
this.FBSf = NA_real_,
tcdata = NA,
user_assay_parameters = NA,
this.sarea = NA_real_,
this.v_total = NA_real_,
this.v_working = NA_real_,
this.cell_yield = NA_real_,
this.Tsys = 37,
this.Tref = 298.15,
this.option.kbsa2 = FALSE,
this.option.swat2 = FALSE,
this.option.kpl2 = FALSE,
this.option.bottom = TRUE,
this.pseudooct = 0.01,
this.memblip = 0.04,
this.nlom = 0.05,
this.P_nlom = 0.035,
this.P_dom = 0.05,
this.P_cells = 1,
this.cell_pH = 7.4,
this.Anionic_VF = 0.175,
this.A_Prop_acid = 0.05,
this.A_Prop_base = 20,
this.Lyso_VF = 0.0068,
this.Lyso_Diam = 500,
this.Lyso_pH = 5.1,
this.csalt = 0.15,
this.celldensity = 1,
this.cellmass = 3,
this.f_oc = 1,
this.conc_ser_alb = 24,
this.conc_ser_lip = 1.9,
this.Vdom = 0,
this.pH = 7,
restrict.ion.partitioning = FALSE,
surface.area.switch = TRUE
)
Arguments
chem.cas
A single or vector of Chemical Abstracts Service Registry
Number(s) (CAS-RN) of desired chemical(s).
chem.name
A single or vector of name(s)) of desired chemical(s).
dtxsid
A single or vector ofEPA's DSSTox Structure ID(s)
(https://comptox.epa.gov/dashboard)
casrn.vector
A deprecated argument specifying a single or vector of
Chemical Abstracts Service Registry
Number(s) (CAS-RN) of desired chemical(s).
nomconc.vector
For vector or single value, micromolar (uM = mol/L) nominal
concentration (e.g. AC50 value)
this.well_number
For single value, plate format default is 384, used
if is.na(tcdata)==TRUE. This value chooses default surface area settings for
armitage_estimate_sarea based on the number of wells per plate.
this.FBSf
Fraction fetal bovine serum, must be entered by user.
tcdata
A data.table with casrn, nomconc, MP, gkow, gkaw, gswat, sarea,
v_total, v_working. Otherwise supply single values to this.params (e.g., this.sarea,
this.v_total, etc.). Chemical parameters are taken from
chem.physical_and_invitro.data.
user_assay_parameters
option to fill in your own assay parameters (data table)
this.sarea
Surface area per well (m^2)
this.v_total
Total volume per well (uL)
this.v_working
Working volume per well (uL)
this.cell_yield
Number of cells per well
this.Tsys
System temperature (degrees C)
this.Tref
Reference temperature (degrees K)
this.option.kbsa2
Use alternative bovine-serum-albumin partitioning
model
this.option.swat2
Use alternative water solubility correction
this.option.kpl2
Use alternative plastic-water partitioning model
this.option.bottom
Include the bottom of the well in surface area calculation
this.pseudooct
Pseudo-octanol cell storage lipid content
this.memblip
Membrane lipid content of cells
this.nlom
Structural protein content of cells
this.P_nlom
Proportionality constant to octanol structural protein
this.P_dom
Proportionality constant to dissolve organic material
this.P_cells
Proportionality constant to octanol storage lipid
this.cell_pH
7.4, pH of cell
this.Anionic_VF
Anionic phospholipid fraction
this.A_Prop_acid
Sorption to anionic lipids - acidic chemicals
this.A_Prop_base
Sorption to anionic lipids - basic chemicals
this.Lyso_VF
lysosome volume fraction
this.Lyso_Diam
diameter of lysosome (500 nm)
this.Lyso_pH
pH of lysosome (5.1)
this.csalt
Ionic strength of buffer (M = mol/L)
this.celldensity
Cell density kg/L, g/mL
this.cellmass
Mass per cell, ng/cell
this.f_oc
Everything assumed to be like proteins
this.conc_ser_alb
Mass concentration of albumin in serum (g/L)
this.conc_ser_lip
Mass concentration of lipids in serum (g/L)
this.Vdom
0 ml, the volume of dissolved organic matter (DOM)
this.pH
pH of cell culture
restrict.ion.partitioning
FALSE, Should we restrict the chemical available to partition to only the neutral fraction?
surface.area.switch
TRUE, automatically calculates surface area, switch to FALSE if user provided
Value
Param Description Units
casrn Chemical Abstracts Service Registry Number character
nomconc Nominal Concentration uM=umol/L
well_number Number of wells in plate (used to set default surface area) unitless
sarea Surface area of well m^2
v_total Total volume of well uL
v_working Filled volume of well uL
cell_yield Number of cells cells
assay_component_endpoint_name link to invitro.assay.params table character
gkow The log10 octanol to water (PC) (logP) log10 unitless ratio
logHenry The log10 Henry's law constant ' log10 unitless ratio
gswat The log10 water solubility (logWSol) log10 mg/L
MP_C The chemical compound melting point degrees Celcius
MP_K The chemical compound melting point degrees Kelvin
MW The chemical compound molecular weight g/mol
gkaw The air to water PC unitless ratio
duow internal energy of phase change for octanol-water J/mol
duaw internal energy of phase change for air-water J/mol
gkmw The log10 membrane to water PC log10 unitless ratio
gkcw The log10 cell/tissue to water PC log10 unitless ratio
gkbsa The log10 bovine serum albumin to water PC log10 unitless ratio
gkpl The log10 plastic to water PC log10 m2/m2
ksalt Setschenow constant L/mol
Tsys System temperature degrees C
Tref Reference temperature degrees K
option.kbsa2 Use alternative bovine-serum-albumin partitioning model logical
option.swat2 Use alternative water solubility correction logical
option.kpl2 Use alternative plastic-water partitioning model logical
FBSf Fraction fetal bovine serum unitless
pseudooct Pseudo-octanol cell storage lipid content
memblip Membrane lipid content of cells unitless
nlom Structural protein content of cells unitless
P_nlom Proportionality constant to octanol structural protein unitless
P_dom Proportionality constant to dissolved organic material (DOM) unitless
P_cells Proportionality constant to octanol storage lipid unitless
Anionic_VF Anionic phospholipid fraction unitless
A_Prop_acid Sorption to anionic lipids - acidic chemicals unitless
A_Prop_base Sorption to anionic lipids - basic chemicals unitless
Lyso_VF Lysosome volume fraction unitless
Lyso_Diam Diameter of lysosome nm
Lyso_pH pH of lysosome unitless
csalt Ionic strength of buffer M=mol/L
celldensity Cell density kg/L, g/mL
cellmass Mass per cell ng/cell
f_oc Indicates fraction of dissolved organic matter to be treated like proteins unitless
cellwat Fraction of the cell made up of water unitless
Tcor Temperature correction
Vm Volume of media L
Vwell Volume of medium (aqueous phase only) L
Vair Volume of head space L
Vcells Volume of cells/tissue L
Valb Volume of serum albumin L
Vslip Volume of serum lipids L
Vdom Volume of dissolved organic matter L
F_ratio Fugacity ratio unitless
kmw The membrane to water PC (i.e., 10^gkmow unitless
kow The octanol to water PC (i.e., 10^gkow) unitless
kaw The air to water PC (i.e., 10^gkaw) unitless
swat The intrinsic water solubility (i.e., 10^gswat) mg/L
kpl The plastic to water PC (i.e., 10^gkpl) m3/m2
kcw The cell/tissue to water PC (i.e., 10^gkcw) unitless
kbsa The bovine serum albumin to water PC unitless
swat_L Water solubility limit used for Fugacity ratio calculation
mtot Total micromoles umol
cwat Total concentration in water uM=umol/L
cwat_s Dissolved concentration in water uM=umol/L
csat Is the solution saturated (1/0) logical
activity Chemical activity; indicates the potential for baseline toxicity to occur
cair Concentration in head space uM=umol/L
calb Concentration in serum albumin uM=umol/L
cslip Concentration in serum lipids uM=umol/L
cdom Concentration in dissolved organic matter uM=umol/L
ccells Concentration in cells uM=umol/L
cplastic Concentration in plastic uM=umol/m^2
mwat_s Mass dissolved in water umols
mair Mass in air/head space umols
mbsa Mass bound to bovine serum albumin umols
mslip Mass bound to serum lipids umols
mdom Mass bound to dissolved organic matter umols
mcells Mass in cells umols
mplastic Mass bond to plastic umols
mprecip Mass precipitated out of solution umols
xwat_s Fraction dissolved in water fraction
xair Fraction in the air fraction
xbsa Fraction bound to bovine serum albumin fraction
xslip Fraction bound to serum lipids fraction
xdom Fraction bound to dissolved organic matter fraction
xcells Fraction within cells fraction
xplastic Fraction bound to plastic fraction
xprecip Fraction precipitated out of solution fraction
eta_free Effective availability ratio fraction
cfree.invitro Free concentration in the in vitro media (use for Honda1 and Honda2) fraction
Author(s)
Greg Honda, Meredith Scherer adapted from code by James Armitage, Jon Arnot
References
\insertRefarmitage2014applicationhttk
\insertRefhonda2019usinghttk
Examples
library(httk)
# Check to see if we have info on the chemical:
"80-05-7" %in% get_cheminfo()
#We do:
temp <- armitage_eval(casrn.vector = c("80-05-7", "81-81-2"), this.FBSf = 0.1,
this.well_number = 384, nomconc = 10)
print(temp$cfree.invitro)
# Check to see if we have info on the chemical:
"793-24-8" %in% get_cheminfo()
# Since we don't have any info, let's look up phys-chem from dashboard:
cheminfo <- data.frame(
Compound="6-PPD",
CASRN="793-24-8",
DTXSID="DTXSID9025114",
logP=4.27,
logHenry=log10(7.69e-8),
logWSol=log10(1.58e-4),
MP= 99.4,
MW=268.404
)
# Add the information to HTTK's database:
chem.physical_and_invitro.data <- add_chemtable(
cheminfo,
current.table=chem.physical_and_invitro.data,
data.list=list(
Compound="Compound",
CAS="CASRN",
DTXSID="DTXSID",
MW="MW",
logP="logP",
logHenry="logHenry",
logWSol="logWSol",
MP="MP"),
species="Human",
reference="CompTox Dashboard 31921")
# Run the Armitage et al. (2014) model:
out <- armitage_eval(
casrn.vector = "793-24-8",
this.FBSf = 0.1,
this.well_number = 384,
nomconc = 10)
print(out)
httk documentation built on Aug. 29, 2025, 5:16 p.m.
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| armitage_eval | R Documentation |
Armitage In Vitro Distribution Model
Description
Evaluate the Armitage model for chemical distributon in vitro. Takes input as data table or vectors of values. Outputs a data table. Updates over the model published in Armitage et al. (2014) include binding to plastic walls and lipid and protein compartments in cells.
Usage
armitage_eval(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
casrn.vector = NA_character_,
nomconc.vector = 1,
this.well_number = 384,
this.FBSf = NA_real_,
tcdata = NA,
user_assay_parameters = NA,
this.sarea = NA_real_,
this.v_total = NA_real_,
this.v_working = NA_real_,
this.cell_yield = NA_real_,
this.Tsys = 37,
this.Tref = 298.15,
this.option.kbsa2 = FALSE,
this.option.swat2 = FALSE,
this.option.kpl2 = FALSE,
this.option.bottom = TRUE,
this.pseudooct = 0.01,
this.memblip = 0.04,
this.nlom = 0.05,
this.P_nlom = 0.035,
this.P_dom = 0.05,
this.P_cells = 1,
this.cell_pH = 7.4,
this.Anionic_VF = 0.175,
this.A_Prop_acid = 0.05,
this.A_Prop_base = 20,
this.Lyso_VF = 0.0068,
this.Lyso_Diam = 500,
this.Lyso_pH = 5.1,
this.csalt = 0.15,
this.celldensity = 1,
this.cellmass = 3,
this.f_oc = 1,
this.conc_ser_alb = 24,
this.conc_ser_lip = 1.9,
this.Vdom = 0,
this.pH = 7,
restrict.ion.partitioning = FALSE,
surface.area.switch = TRUE
)
Arguments
chem.cas |
A single or vector of Chemical Abstracts Service Registry Number(s) (CAS-RN) of desired chemical(s). |
chem.name |
A single or vector of name(s)) of desired chemical(s). |
dtxsid |
A single or vector ofEPA's DSSTox Structure ID(s) (https://comptox.epa.gov/dashboard) |
casrn.vector |
A deprecated argument specifying a single or vector of Chemical Abstracts Service Registry Number(s) (CAS-RN) of desired chemical(s). |
nomconc.vector |
For vector or single value, micromolar (uM = mol/L) nominal concentration (e.g. AC50 value) |
this.well_number |
For single value, plate format default is 384, used
if is.na(tcdata)==TRUE. This value chooses default surface area settings for
|
this.FBSf |
Fraction fetal bovine serum, must be entered by user. |
tcdata |
A data.table with casrn, nomconc, MP, gkow, gkaw, gswat, sarea,
v_total, v_working. Otherwise supply single values to this.params (e.g., this.sarea,
this.v_total, etc.). Chemical parameters are taken from
|
user_assay_parameters |
option to fill in your own assay parameters (data table) |
this.sarea |
Surface area per well (m^2) |
this.v_total |
Total volume per well (uL) |
this.v_working |
Working volume per well (uL) |
this.cell_yield |
Number of cells per well |
this.Tsys |
System temperature (degrees C) |
this.Tref |
Reference temperature (degrees K) |
this.option.kbsa2 |
Use alternative bovine-serum-albumin partitioning model |
this.option.swat2 |
Use alternative water solubility correction |
this.option.kpl2 |
Use alternative plastic-water partitioning model |
this.option.bottom |
Include the bottom of the well in surface area calculation |
this.pseudooct |
Pseudo-octanol cell storage lipid content |
this.memblip |
Membrane lipid content of cells |
this.nlom |
Structural protein content of cells |
this.P_nlom |
Proportionality constant to octanol structural protein |
this.P_dom |
Proportionality constant to dissolve organic material |
this.P_cells |
Proportionality constant to octanol storage lipid |
this.cell_pH |
7.4, pH of cell |
this.Anionic_VF |
Anionic phospholipid fraction |
this.A_Prop_acid |
Sorption to anionic lipids - acidic chemicals |
this.A_Prop_base |
Sorption to anionic lipids - basic chemicals |
this.Lyso_VF |
lysosome volume fraction |
this.Lyso_Diam |
diameter of lysosome (500 nm) |
this.Lyso_pH |
pH of lysosome (5.1) |
this.csalt |
Ionic strength of buffer (M = mol/L) |
this.celldensity |
Cell density kg/L, g/mL |
this.cellmass |
Mass per cell, ng/cell |
this.f_oc |
Everything assumed to be like proteins |
this.conc_ser_alb |
Mass concentration of albumin in serum (g/L) |
this.conc_ser_lip |
Mass concentration of lipids in serum (g/L) |
this.Vdom |
0 ml, the volume of dissolved organic matter (DOM) |
this.pH |
pH of cell culture |
restrict.ion.partitioning |
FALSE, Should we restrict the chemical available to partition to only the neutral fraction? |
surface.area.switch |
TRUE, automatically calculates surface area, switch to FALSE if user provided |
Value
| Param | Description | Units |
| casrn | Chemical Abstracts Service Registry Number | character |
| nomconc | Nominal Concentration | uM=umol/L |
| well_number | Number of wells in plate (used to set default surface area) | unitless |
| sarea | Surface area of well | m^2 |
| v_total | Total volume of well | uL |
| v_working | Filled volume of well | uL |
| cell_yield | Number of cells | cells |
| assay_component_endpoint_name | link to invitro.assay.params table | character |
| gkow | The log10 octanol to water (PC) (logP) | log10 unitless ratio |
| logHenry | The log10 Henry's law constant ' | log10 unitless ratio |
| gswat | The log10 water solubility (logWSol) | log10 mg/L |
| MP_C | The chemical compound melting point | degrees Celcius |
| MP_K | The chemical compound melting point | degrees Kelvin |
| MW | The chemical compound molecular weight | g/mol |
| gkaw | The air to water PC | unitless ratio |
| duow | internal energy of phase change for octanol-water | J/mol |
| duaw | internal energy of phase change for air-water | J/mol |
| gkmw | The log10 membrane to water PC | log10 unitless ratio |
| gkcw | The log10 cell/tissue to water PC | log10 unitless ratio |
| gkbsa | The log10 bovine serum albumin to water PC | log10 unitless ratio |
| gkpl | The log10 plastic to water PC | log10 m2/m2 |
| ksalt | Setschenow constant | L/mol |
| Tsys | System temperature | degrees C |
| Tref | Reference temperature | degrees K |
| option.kbsa2 | Use alternative bovine-serum-albumin partitioning model | logical |
| option.swat2 | Use alternative water solubility correction | logical |
| option.kpl2 | Use alternative plastic-water partitioning model | logical |
| FBSf | Fraction fetal bovine serum | unitless |
| pseudooct | Pseudo-octanol cell storage lipid content | |
| memblip | Membrane lipid content of cells | unitless |
| nlom | Structural protein content of cells | unitless |
| P_nlom | Proportionality constant to octanol structural protein | unitless |
| P_dom | Proportionality constant to dissolved organic material (DOM) | unitless |
| P_cells | Proportionality constant to octanol storage lipid | unitless |
| Anionic_VF | Anionic phospholipid fraction | unitless |
| A_Prop_acid | Sorption to anionic lipids - acidic chemicals | unitless |
| A_Prop_base | Sorption to anionic lipids - basic chemicals | unitless |
| Lyso_VF | Lysosome volume fraction | unitless |
| Lyso_Diam | Diameter of lysosome | nm |
| Lyso_pH | pH of lysosome | unitless |
| csalt | Ionic strength of buffer | M=mol/L |
| celldensity | Cell density | kg/L, g/mL |
| cellmass | Mass per cell | ng/cell |
| f_oc | Indicates fraction of dissolved organic matter to be treated like proteins | unitless |
| cellwat | Fraction of the cell made up of water | unitless |
| Tcor | Temperature correction | |
| Vm | Volume of media | L |
| Vwell | Volume of medium (aqueous phase only) | L |
| Vair | Volume of head space | L |
| Vcells | Volume of cells/tissue | L |
| Valb | Volume of serum albumin | L |
| Vslip | Volume of serum lipids | L |
| Vdom | Volume of dissolved organic matter | L |
| F_ratio | Fugacity ratio | unitless |
| kmw | The membrane to water PC (i.e., 10^gkmow | unitless |
| kow | The octanol to water PC (i.e., 10^gkow) | unitless |
| kaw | The air to water PC (i.e., 10^gkaw) | unitless |
| swat | The intrinsic water solubility (i.e., 10^gswat) | mg/L |
| kpl | The plastic to water PC (i.e., 10^gkpl) | m3/m2 |
| kcw | The cell/tissue to water PC (i.e., 10^gkcw) | unitless |
| kbsa | The bovine serum albumin to water PC | unitless |
| swat_L | Water solubility limit used for Fugacity ratio calculation | |
| mtot | Total micromoles | umol |
| cwat | Total concentration in water | uM=umol/L |
| cwat_s | Dissolved concentration in water | uM=umol/L |
| csat | Is the solution saturated (1/0) | logical |
| activity | Chemical activity; indicates the potential for baseline toxicity to occur | |
| cair | Concentration in head space | uM=umol/L |
| calb | Concentration in serum albumin | uM=umol/L |
| cslip | Concentration in serum lipids | uM=umol/L |
| cdom | Concentration in dissolved organic matter | uM=umol/L |
| ccells | Concentration in cells | uM=umol/L |
| cplastic | Concentration in plastic | uM=umol/m^2 |
| mwat_s | Mass dissolved in water | umols |
| mair | Mass in air/head space | umols |
| mbsa | Mass bound to bovine serum albumin | umols |
| mslip | Mass bound to serum lipids | umols |
| mdom | Mass bound to dissolved organic matter | umols |
| mcells | Mass in cells | umols |
| mplastic | Mass bond to plastic | umols |
| mprecip | Mass precipitated out of solution | umols |
| xwat_s | Fraction dissolved in water | fraction |
| xair | Fraction in the air | fraction |
| xbsa | Fraction bound to bovine serum albumin | fraction |
| xslip | Fraction bound to serum lipids | fraction |
| xdom | Fraction bound to dissolved organic matter | fraction |
| xcells | Fraction within cells | fraction |
| xplastic | Fraction bound to plastic | fraction |
| xprecip | Fraction precipitated out of solution | fraction |
| eta_free | Effective availability ratio | fraction |
| cfree.invitro | Free concentration in the in vitro media (use for Honda1 and Honda2) | fraction |
Author(s)
Greg Honda, Meredith Scherer adapted from code by James Armitage, Jon Arnot
References
\insertRefarmitage2014applicationhttk
\insertRefhonda2019usinghttk
Examples
library(httk)
# Check to see if we have info on the chemical:
"80-05-7" %in% get_cheminfo()
#We do:
temp <- armitage_eval(casrn.vector = c("80-05-7", "81-81-2"), this.FBSf = 0.1,
this.well_number = 384, nomconc = 10)
print(temp$cfree.invitro)
# Check to see if we have info on the chemical:
"793-24-8" %in% get_cheminfo()
# Since we don't have any info, let's look up phys-chem from dashboard:
cheminfo <- data.frame(
Compound="6-PPD",
CASRN="793-24-8",
DTXSID="DTXSID9025114",
logP=4.27,
logHenry=log10(7.69e-8),
logWSol=log10(1.58e-4),
MP= 99.4,
MW=268.404
)
# Add the information to HTTK's database:
chem.physical_and_invitro.data <- add_chemtable(
cheminfo,
current.table=chem.physical_and_invitro.data,
data.list=list(
Compound="Compound",
CAS="CASRN",
DTXSID="DTXSID",
MW="MW",
logP="logP",
logHenry="logHenry",
logWSol="logWSol",
MP="MP"),
species="Human",
reference="CompTox Dashboard 31921")
# Run the Armitage et al. (2014) model:
out <- armitage_eval(
casrn.vector = "793-24-8",
this.FBSf = 0.1,
this.well_number = 384,
nomconc = 10)
print(out)
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