pkmodel.Rd
Use to create a PK model
pkmodel(
isPopulation = TRUE,
parameterization = "Clearance",
absorption = "Intravenous",
numCompartments = 1,
isClosedForm = TRUE,
isTlag = FALSE,
hasEliminationComp = FALSE,
isFractionExcreted = FALSE,
isSaturating = FALSE,
infusionAllowed = FALSE,
isDuration = FALSE,
isStdevFrozen = FALSE,
data = NULL,
columnMap = TRUE,
modelName = "",
workingDir = "",
...
)
Is this a population model TRUE
or individual model FALSE
?
Type of parameterization. Options are "Clearance"
, "Micro"
,
"Macro"
, or "Macro1"
.
Type of absorption. Options are "Intravenous"
, "FirstOrder"
,
"Gamma"
, "InverseGaussian"
, "Weibull"
.
Value of either 1
, 2
, or 3
.
Set to TRUE
to convert model from a differential equation to close form.
Set to TRUE
to add a lag time parameter to the model.
Set to TRUE
to add an elimination compartment to the model.
Set to TRUE
if elimination compartment (hasEliminationComp = TRUE
)
contains a fraction excreted parameter.
Set to TRUE
to use Michaelis-Menten kinetics for elimination.
Only applicable to models with paramteterization = "Clearance"
Set to TRUE
if infusions allowed.
Set to TRUE
if infusions use duration instead of rate
(must also set infusionAllowed = TRUE
).
Set to TRUE
to freeze value of standard deviation of residual error variable.
Input dataset
If TRUE
(default) column mapping arguments are required.
Set to FALSE
to manually map columns after defining model using colMapping
.
Model name for subdirectory created for model output in current working directory.
Working directory to run the model. Current working directory will be used
if workingDir
not specified.
Arguments passed on to pkmodel_MappingParameters
ID
Column mapping argument for input dataset column(s) that identify
individual data profiles. Only applicable to population models isPopulation = TRUE
.
Time
Column mapping argument that represents the input dataset column for the relative time used in a study and only applicable to time-based models.
A1
Column mapping argument that represents the input dataset column for the amount of drug administered. Only applicable to the following types of models:
Models with absorption = "Intravenous"
and parameterization set
to either "Clearance"
,"Micro"
, or "Macro"
Models with
absorption
set to either "Gamma"
, "InverseGaussian"
, or "Weibull"
Aa
Column mapping argument that represents the input dataset column
for the amount of drug administered and only applicable to models with absorption = "FirstOrder"
.
A
Column mapping argument that represents the input dataset column
for the amount of drug administered and only applicable to models with
absorption = "Intravenous"
and parameterization = "Macro1"
.
A1_Rate
Column mapping argument that represents the input dataset column for the rate of drug administered. Only applicable to the following types of models:
Models with absorption = "Intravenous"
, infusionAllowed = TRUE
and parameterization set to either "Clearance"
,"Micro"
or "Macro"
Models with absorption
set to either "Gamma"
, "InverseGaussian"
,
or "Weibull"
and infusionAllowed = TRUE
A1_Duration
Column mapping argument that represents the input dataset column for the duration of drug administered. Only applicable to the following types of models:
Models with absorption = "Intravenous"
,
infusionAllowed = TRUE
with isDuration = TRUE
and
parameterization set to either "Clearance"
,"Micro"
or "Macro"
Models with absorption
set to either "Gamma"
, "InverseGaussian"
, or "Weibull"
and infusionAllowed = TRUE
with isDuration = TRUE
Aa_Rate
Column mapping argument that represents the input dataset column
for the rate of drug administered and only applicable to models with absorption = "FirstOrder"
,
infusionAllowed = TRUE
.
Aa_Duration
Column mapping argument that represents the input dataset column
for the duration of drug administered and only applicable to models with absorption = "FirstOrder"
,
infusionAllowed = TRUE
, and isDuration = TRUE
.
A_Rate
Column mapping argument that represents the input dataset column
for the rate of drug administered and only applicable to models with absorption = "Intravenous"
,
infusionAllowed = TRUE
, and parameterization = "Macro1"
.
A_Duration
Column mapping argument that represents the input dataset column
for the duration of drug administered and only applicable to models with absorption = "Intravenous"
,
infusionAllowed = TRUE
, isDuration = TRUE
, and parameterization = "Macro1"
.
A1Strip
Column mapping argument that represents the input dataset column
for the stripping dose and only applicable to models with parameterization = "Macro"
.
CObs
Column mapping argument that represents the input dataset column
for the observations of drug concentration in the central compartment and only applicable
to models with parameterization
being either set to either "Clearance"
or "Micro"
.
C1Obs
Column mapping argument that represents the input dataset column
for the observations of drug concentration in the central compartment and only applicable
to models with parameterization
being either set to either "Macro"
or "Macro1"
.
A0Obs
Column mapping argument that represents the input dataset column
for the observed amount of drug in the elimination compartment. (hasEliminationComp = TRUE
).
Note that quoted and unquoted column names are supported. Please see colMapping
.
if (FALSE) {
model <- pkmodel(
parameterization = "Clearance",
numCompartments = 2,
data = pkData,
ID = "Subject",
Time = "Act_Time",
A1 = "Amount",
CObs = "Conc"
)
# View the model as well as its associated column mappings
print(model)
}