armitage_eval: Evaluate the updated Armitage model
In httk: High-Throughput Toxicokinetics
armitage_eval R Documentation
Evaluate the updated Armitage 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(
casrn.vector = NA_character_,
nomconc.vector = 1,
this.well_number = 384,
this.FBSf = NA_real_,
tcdata = 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.pseudooct = 0.01,
this.memblip = 0.04,
this.nlom = 0.2,
this.P_nlom = 0.035,
this.P_dom = 0.05,
this.P_cells = 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
)
Arguments
casrn.vector
For vector or single value, CAS number
nomconc.vector
For vector or single value, micromolar nominal
concentration (e.g. AC50 value)
this.well_number
For single value, plate format default is 384, used
if is.na(tcdata)==TRUE
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.
this.sarea
Surface area per well (m^2)
this.v_total
Total volume per well (m^3)
this.v_working
Working volume per well (m^3)
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.pseudooct
Pseudo-octanol cell storage lipid content
this.memblip
Membrane lipid content of cells
this.nlom
Structural protein conent 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.csalt
Ionic strength of buffer, mol/L
this.celldensity
Cell density kg/L, g/mL
this.cellmass
Mass per cell, ng/cell
this.f_oc
1, everything assumed to be like proteins
this.conc_ser_alb
24 g/L, mass concentration of albumin in serum.
this.conc_ser_lip
1.9 g/L, mass concentration of lipids in serum.
this.Vdom
0 ml, the volume of dissolved organic matter (DOM)
Value
Column Description units
casrn Chemical Abstracts Service Registry Number
nomconc Nominal Concentration mol/L
well_number Number of wells in plate unitless
sarea Surface area of well m^2
v_total Total volume of well m^3
v_working Filled volume of well m^3
cell_yield Number of cells cells
gkow log10 octanol to water partition coefficient (PC) log10
logHenry log10 Henry's law constant ' log10 atm-m3/mol
gswat log10 Water solubility log10 mol/L
MP Melting Point degrees Celsius
MW Molecular Weight g/mol
gkaw air-water partition coefficient (mol/m3)/(mol/m3)
dsm
duow
duaw
dumw
gkmw
gkcw
gkbsa
gkpl
ksalt
Tsys
Tref
option.kbsa2
option.swat2
FBSf
pseudooct
memblip
nlom
P_nlom
P_dom dissolved organic matter to water PC Dimensionless
P_cells
csalt
celldensity
cellmass
f_oc
cellwat
Tcor
Vm Volume of media L
Vwell volume of medium (aqueous phase only) L
Vair volume of head space L
Vcells volume of cells/tissue
Valb volume of serum albumin
Vslip volume of serum lipids
Vdom volume of dissolved organic matter
F_ratio
gs1.GSE
s1.GSE
gss.GSE
ss.GSE
kmw
kow octanol to water PC
kaw the air towater PC dimensionless
swat
kpl
kcw cell/tissue to water PC dimensionless
kbsa
swat_L
oct_L
scell_L
cinit Initial concentration mol
mtot Total moles mol
cwat Total concentration in water mol/L
cwat_s Dissolved concentration in water mol/L
csat Is the solution saturated (1/0) Boolean
activity
cair mol/L
calb mol/L
cslip mol/L
cdom concentration of/in dissolved organic matter mol/L
ccells mol/L
cplastic mol/L
mwat_s Mass dissolved in water mols
mair Mass in air mols
mbsa Mass bound to bovine serum albumin mols
mslip Mass bound to serum lipids mols
mdom Mass bound to dissolved organic matter mols
mcells Mass in cells mols
mplastic Mass bond to plastic mols
mprecip Mass precipitated out of solution
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) micromolar
Author(s)
Greg Honda
References
Armitage, J. M.; Wania, F.; Arnot, J. A. Environ. Sci. Technol.
2014, 48, 9770-9779. https://doi.org/10.1021/es501955g
Honda et al. PloS one 14.5 (2019): e0217564. https://doi.org/10.1371/journal.pone.0217564
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 March 7, 2023, 7:26 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| armitage_eval | R Documentation |
Evaluate the updated Armitage 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( casrn.vector = NA_character_, nomconc.vector = 1, this.well_number = 384, this.FBSf = NA_real_, tcdata = 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.pseudooct = 0.01, this.memblip = 0.04, this.nlom = 0.2, this.P_nlom = 0.035, this.P_dom = 0.05, this.P_cells = 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 )
Arguments
casrn.vector |
For vector or single value, CAS number |
nomconc.vector |
For vector or single value, micromolar nominal concentration (e.g. AC50 value) |
this.well_number |
For single value, plate format default is 384, used if is.na(tcdata)==TRUE |
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. |
this.sarea |
Surface area per well (m^2) |
this.v_total |
Total volume per well (m^3) |
this.v_working |
Working volume per well (m^3) |
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.pseudooct |
Pseudo-octanol cell storage lipid content |
this.memblip |
Membrane lipid content of cells |
this.nlom |
Structural protein conent 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.csalt |
Ionic strength of buffer, mol/L |
this.celldensity |
Cell density kg/L, g/mL |
this.cellmass |
Mass per cell, ng/cell |
this.f_oc |
1, everything assumed to be like proteins |
this.conc_ser_alb |
24 g/L, mass concentration of albumin in serum. |
this.conc_ser_lip |
1.9 g/L, mass concentration of lipids in serum. |
this.Vdom |
0 ml, the volume of dissolved organic matter (DOM) |
Value
| Column | Description | units |
| casrn | Chemical Abstracts Service Registry Number | |
| nomconc | Nominal Concentration | mol/L |
| well_number | Number of wells in plate | unitless |
| sarea | Surface area of well | m^2 |
| v_total | Total volume of well | m^3 |
| v_working | Filled volume of well | m^3 |
| cell_yield | Number of cells | cells |
| gkow | log10 octanol to water partition coefficient (PC) | log10 |
| logHenry | log10 Henry's law constant ' | log10 atm-m3/mol |
| gswat | log10 Water solubility | log10 mol/L |
| MP | Melting Point | degrees Celsius |
| MW | Molecular Weight | g/mol |
| gkaw | air-water partition coefficient | (mol/m3)/(mol/m3) |
| dsm | ||
| duow | ||
| duaw | ||
| dumw | ||
| gkmw | ||
| gkcw | ||
| gkbsa | ||
| gkpl | ||
| ksalt | ||
| Tsys | ||
| Tref | ||
| option.kbsa2 | ||
| option.swat2 | ||
| FBSf | ||
| pseudooct | ||
| memblip | ||
| nlom | ||
| P_nlom | ||
| P_dom | dissolved organic matter to water PC | Dimensionless |
| P_cells | ||
| csalt | ||
| celldensity | ||
| cellmass | ||
| f_oc | ||
| cellwat | ||
| Tcor | ||
| Vm | Volume of media | L |
| Vwell | volume of medium (aqueous phase only) | L |
| Vair | volume of head space | L |
| Vcells | volume of cells/tissue | |
| Valb | volume of serum albumin | |
| Vslip | volume of serum lipids | |
| Vdom | volume of dissolved organic matter | |
| F_ratio | ||
| gs1.GSE | ||
| s1.GSE | ||
| gss.GSE | ||
| ss.GSE | ||
| kmw | ||
| kow | octanol to water PC | |
| kaw | the air towater PC | dimensionless |
| swat | ||
| kpl | ||
| kcw | cell/tissue to water PC | dimensionless |
| kbsa | ||
| swat_L | ||
| oct_L | ||
| scell_L | ||
| cinit | Initial concentration | mol |
| mtot | Total moles | mol |
| cwat | Total concentration in water | mol/L |
| cwat_s | Dissolved concentration in water | mol/L |
| csat | Is the solution saturated (1/0) | Boolean |
| activity | ||
| cair | mol/L | |
| calb | mol/L | |
| cslip | mol/L | |
| cdom | concentration of/in dissolved organic matter | mol/L |
| ccells | mol/L | |
| cplastic | mol/L | |
| mwat_s | Mass dissolved in water | mols |
| mair | Mass in air | mols |
| mbsa | Mass bound to bovine serum albumin | mols |
| mslip | Mass bound to serum lipids | mols |
| mdom | Mass bound to dissolved organic matter | mols |
| mcells | Mass in cells | mols |
| mplastic | Mass bond to plastic | mols |
| mprecip | Mass precipitated out of solution | |
| 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) | micromolar |
Author(s)
Greg Honda
References
Armitage, J. M.; Wania, F.; Arnot, J. A. Environ. Sci. Technol. 2014, 48, 9770-9779. https://doi.org/10.1021/es501955g
Honda et al. PloS one 14.5 (2019): e0217564. https://doi.org/10.1371/journal.pone.0217564
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.