Package 'nlmixr2lib'

Title: A Model Library for 'nlmixr2'
Description: A model library for 'nlmixr2'. The models include (and plan to include) pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. Where applicable, references for each model are included in the meta-data for each individual model. The package also includes model composition and modification functions to make model updates easier.
Authors: Richard Hooijmaijers [aut], Matthew Fidler [aut] , Bill Denney [aut, cre]
Maintainer: Bill Denney <[email protected]>
License: GPL (>= 2)
Version: 0.2.0.9000
Built: 2024-09-04 13:23:36 UTC
Source: https://github.com/nlmixr2/nlmixr2lib

Help Index

Add baseline that decays exponential with time

Description

Add baseline that decays exponential with time

Usage

addBaseline1exp(ui, effect = "effect", eb = "Eb", time = "time", kb = "kb")

Arguments

ui

rxode2 model
effect

the effect variable that will be modeled
eb

baseline constant parameter
time

the time or other variable used for baseline decay
kb

the first order baseline decay constant

Value

model with baseline constant

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaselineConst(), addBaselineExp(), addBaselineLin(), addDirectLin(), convertEmax(), convertLogLin(), convertQuad()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertQuad() |>
  addBaseline1exp()

Add an estimated baseline constant

Description

Add an estimated baseline constant

Usage

addBaselineConst(ui, effect = "effect", eb = "Eb")

Arguments

ui

rxode2 model
effect

the effect variable that will be modeled
eb

baseline constant parameter

Value

model with baseline constant

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineExp(), addBaselineLin(), addDirectLin(), convertEmax(), convertLogLin(), convertQuad()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertQuad() |>
  addBaselineConst()

Add baseline that decays exponential with time

Description

Add baseline that decays exponential with time

Usage

addBaselineExp(ui, effect = "effect", eb = "Eb", time = "time", kb = "kb")

Arguments

ui

rxode2 model
effect

the effect variable that will be modeled
eb

baseline constant parameter
time

the time or other variable used for baseline decay
kb

the first order baseline decay constant

Value

model with baseline constant

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineConst(), addBaselineLin(), addDirectLin(), convertEmax(), convertLogLin(), convertQuad()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertQuad() |>
  addBaselineExp()

Add an estimated baseline linear constant

Description

Add an estimated baseline linear constant

Usage

addBaselineLin(ui, effect = "effect", eb = "Eb", time = "time")

Arguments

ui

rxode2 model
effect

the effect variable that will be modeled
eb

baseline constant parameter
time

the time or other variable used for baseline decay

Value

model with baseline linear constant

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineConst(), addBaselineExp(), addDirectLin(), convertEmax(), convertLogLin(), convertQuad()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertQuad() |>
  addBaselineLin()

Add a property to a compartment

Description

Add a property to a compartment

Usage

addCmtProp(ui, prop = c("f", "lag", "dur", "rate", "ini"), cmt)

addBioavailability(ui, cmt)

addLag(ui, cmt)

addDur(ui, cmt)

addRate(ui, cmt)

addIni(ui, cmt)

Arguments

ui

rxode2 ui object
prop

property to add to a compartment:

- F: bioavailability

- lag: absorption lag time

- dur: modeled duration of infusion

- rate: modeled infusion rate

- ini: initial value of the compartment
cmt

compartment to apply the property to

Value

rxode2 ui object with property applied

Functions

  • addBioavailability(): Adds the bioavailability to a compartment in the model

  • addLag(): Adds the lag-time to a compartment in the model

  • addDur(): Adds the modeled duration to a compartment in the model

  • addRate(): Adds the modeled rate to a compartment in the model

  • addIni(): Adds the inital value to the compartment

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_3cmt_des") |> addCmtProp("f", "depot")

readModelDb("PK_3cmt_des") |> addBioavailability(depot)

readModelDb("PK_3cmt_des") |> addLag(depot)

readModelDb("PK_3cmt_des") |> addDur(depot)

readModelDb("PK_3cmt_des") |> addRate(depot)

readModelDb("PK_3cmt_des") |> addIni(depot)

To convert from infusion/intravenous administration to first-order oral absorption

Description

To convert from infusion/intravenous administration to first-order oral absorption

Usage

addDepot(ui, central = "central", depot = "depot", ka = "ka")

Arguments

ui

The model as a function (or something convertible to an rxUi object)
central

central compartment name
depot

depot compartment name
ka

absorption rate parameter name

Value

a model with the depot added

Examples

# most of the examples in the model library already have a depot
# the PK_2cmt_no_depot is an exception
readModelDb("PK_2cmt_no_depot")  |> addDepot()

Add direct linear effect with baseline=0

Description

Add direct linear effect with baseline=0

Usage

addDirectLin(ui, ek = "Ek", cc = c("Ce", "Cc"), effect = "effect")

Arguments

ui

rxode2 model
ek

simulation linear constant
cc

the concentration value
effect

the effect variable that will be modeled

Value

model with direct linear effect added (baseline=0)

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineConst(), addBaselineExp(), addBaselineLin(), convertEmax(), convertLogLin(), convertQuad()

Examples

# Direct linear model
readModelDb("PK_2cmt_no_depot") |>
  addDirectLin()

# Direct emax model
readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertEmax()

Add a directory to the modeldb

Description

Add a directory to the modeldb

Usage

addDirToModelDb(dir, modeldb = data.frame())

addFileToModelDb(dir, file, modeldb)

Arguments

dir

Directory name containing model files
modeldb

The starting modeldb data.frame
file

The file name (without the directory name)

Value

The updated modeldb data.frame

the model database

Functions

  • addFileToModelDb(): Add a file to the modeldb

Add effect compartment

Description

Add effect compartment

Usage

addEffectCmtLin(
  ui,
  ke0 = "ke0",
  cc = "Cc",
  ce = "Ce",
  ek = "Ek",
  effect = "effect"
)

Arguments

ui

rxode2 model
ke0

This is the effect compartment keo rate
cc

the concentration value
ce

This is the concentration in the effect compartment
ek

simulation linear constant
effect

the effect variable that will be modeled

Value

a model with an effect compartment attached

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_2cmt_no_depot") |>
   addEffectCmtLin()

# Can also be changed to the more typical Emax with constant (estimated) baselie
readModelDb("PK_2cmt_no_depot") |>
  addEffectCmtLin() |>
  convertEmaxHill() |>
  addBaselineConst()

Add random effects to a model

Description

Add random effects to a model

Usage

addEta(
  ui,
  eta,
  priorName = getOption("nlmixr2lib.priorEta", TRUE),
  etaCombineType = c("default", "snake", "camel", "dot", "blank")
)

Arguments

ui

The model as a function
eta

vector with the parameters to add random effects (sometimes referred to as inter-individual variability, IIV) on
priorName

logical, if TRUE, the parameter name specified in 'eta' will be used to add the eta value prior name is used instead of the left handed side of the equation.
etaCombineType

the option for the how to ccombine the eta with the parameter name. Can be: "default", "snake", "camel", "dot", "blank"

Value

The model with eta added to the requested parameters

Author(s)

Bill Denney, Richard Hooijmaijers & Matthew L. Fidler

Examples

library(rxode2)
readModelDb("PK_1cmt") |> addEta("ka")

Add an indirect response model to a PK model

Description

Add an indirect response model to a PK model

Usage

addIndirect(
  ui,
  stim = c("in", "out"),
  inhib = c("in", "out"),
  hill = FALSE,
  ek = "Ek",
  ik = "Ik",
  emax = "Emax",
  ec50 = "EC50",
  imax = "Imax",
  ic50 = "IC50",
  kin = "kin",
  kout = "kout",
  g = "g",
  cc = "Cc",
  R = "R",
  effect = "effect"
)

Arguments

ui

rxode2 model
stim

what type of stimulation indirect response model:

- 'in': stimulation of input

- 'out': stimulation of output
inhib

what type of inhibition indirect response model:

- 'in': inhibition of input

- 'out': inhibition of output
hill

boolean stating if a hill sigmoid cofficient will be added
ek

simulation linear constant
ik

inhibition linear constant
emax

Emax parameter
ec50

EC50 parameter
imax

maximum inhibitory concentration
ic50

concentration where half of the imax occurs
kin

this is the kin parameter name
kout

this is the kout parameter name
g

hill coefficient
cc

the concentration value
R

drug response compartment
effect

the effect variable that will be modeled

Value

pk model with indirect response model added

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_2cmt_no_depot") |>
  addIndirect(stim="in",hill=TRUE)

readModelDb("PK_2cmt_no_depot") |>
  addIndirect(inhib="out", imax=1)

Add linear indirect response model

Description

Add linear indirect response model

Usage

addIndirectLin(
  ui,
  stim = c("in", "out"),
  inhib = c("in", "out"),
  ek = "Ek",
  ik = "Ik",
  kin = "kin",
  kout = "kout",
  cc = "Cc",
  R = "R",
  effect = "effect"
)

Arguments

ui

rxode2 model
stim

what type of stimulation indirect response model:

- 'in': stimulation of input

- 'out': stimulation of output
inhib

what type of inhibition indirect response model:

- 'in': inhibition of input

- 'out': inhibition of output
ek

simulation linear constant
ik

inhibition linear constant
kin

this is the kin parameter name
kout

this is the kout parameter name
cc

the concentration value
R

drug response compartment
effect

the effect variable that will be modeled

Value

model with linear indirect effect added;

note that while linear indirect effects are not common, it allows an easier hook to produce all sorts of standard effect curves, like Emax/Imax, Hill, etc.

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_2cmt_no_depot") |> addIndirectLin(stim="in")

readModelDb("PK_2cmt_no_depot") |> addIndirectLin(stim="out")

readModelDb("PK_2cmt_no_depot") |> addIndirectLin(inhib="in")

readModelDb("PK_2cmt_no_depot") |> addIndirectLin(inhib="out")

Add log estimates to a model

Description

Add log estimates to a model

Usage

addLogEstimates(ui, vars, extraLines = NULL, beforeCmt = NULL)

Arguments

ui

rxode2 model
vars

estimates to add they will be parameterized as:

var <- exp(lvar)

where var is the variable name in the model and lvar is the log transformed variable that will be estimated
extraLines

this is a list of additional lines to add to the model just after the variables are defined. It must be NULL or a list of language objects.
beforeCmt

if the model is compartmental you can specify the preferred names where the estimates and extra lines are added before

Value

rxode2 model with log estimates added (and possibly extra lines)

Author(s)

Matthew L. Fidler

Examples

# Change the transformation of the PK model from cl to k

readModelDb("PK_3cmt_des") |>
  removeLinesAndInis(c("kel", "k12", "k21", "k13", "k31", "vc")) |>
  addLogEstimates(c("kel", "k12", "k21", "k13", "k31", "vc"))

# You can also label the parameters by using a named character
# vector with the names of the parameters representing the
# variables and the values representing the labels:

readModelDb("PK_3cmt_des") |>
  removeLinesAndInis(c("kel", "k12", "k21", "k13", "k31", "vc")) |>
  addLogEstimates(c(kel="elimination", k12="k12 constant",
                    k21="k21 constant",
                    k13="k13 constant",
                    k31="k31 constant",
                    vc="volume of central compartment"))

Add residual error to a model

Description

Add residual error to a model

Usage

addResErr(ui, reserr, endpoint)

Arguments

ui

The model as a function
reserr

The type or types of residual error (currently "addSd", "propSd", and "lnormSd" are accepted)
endpoint

the endpoint to apply the error; will default to the first error in the model

Details

For reserr, the parameter will be named with the dependent variable from the model as a prefix. For example, if the dependent variable in the model is Cc, the parameter name for propSd will become CcpropSd.

Value

The model with residual error modified

Examples

library(rxode2)
readModelDb("PK_1cmt") |> addResErr("addSd")
readModelDb("PK_1cmt") |> addResErr("lnormSd")
readModelDb("PK_1cmt") |> addResErr(c("addSd", "propSd"))

To add transit compartments to the model

Description

To add transit compartments to the model

Usage

addTransit(
  ui,
  ntransit,
  central = "central",
  depot = "depot",
  transit = "transit",
  ktr = "ktr",
  ka = "ka"
)

Arguments

ui

The model as a function
ntransit

the number of transit compartments to be added
central

central compartment name
depot

depot compartment name
transit

the transit compartment prefix
ktr

the parameter name for the transit compartment rate
ka

absorption rate parameter name

Value

a model with transit compartment added

This matches

'dose->a0->a1->abs cmt->central'

But 'a0' is depot so dosing records labeled depot do not need to be changed

The abs cmt becomes the last "transit" compartment

This is simply for convienience

See Also

Other absorption: addWeibullAbs(), removeTransit()

Examples

readModelDb("PK_1cmt_des") |> addTransit(3)

Converts first order absorption model to Weibull absorption model

Description

Converts first order absorption model to Weibull absorption model

Usage

addWeibullAbs(
  ui,
  ntransit,
  central = "central",
  depot = "depot",
  transit = "transit",
  wa = "wa",
  wb = "wb",
  ka = "ka",
  ktr = "ktr"
)

Arguments

ui

The model as a function
ntransit

the number of transit compartments to be added
central

central compartment name
depot

depot compartment name
transit

the transit compartment prefix
wa

weibull alpha parameter name
wb

weibull beta parameter name
ka

absorption rate parameter name
ktr

the parameter name for the transit compartment rate

Value

model where first order absorption is changed to weibull absorption model

Author(s)

Matthew L. Fidler

See Also

Other absorption: addTransit(), removeTransit()

Examples

readModelDb("PK_1cmt_des") |>
  addWeibullAbs()

Combine two strings using a naming convention

Description

Combine two in a manner similar to 'paste()' strings using the default combine type

Usage

combinePaste2(
  a,
  b,
  combineType = c("default", "snake", "camel", "dot", "blank")
)

Arguments

a

first string to combine
b

second string to combine
combineType

is the type of combination; can be:

- "default": default combine (set with 'setDefualtCombine()')

- "camel": camelCase combine

- "snake": snake_case combine

- "dot": dot combine (i.e. "a.b")

- "blank": no separator (i.e. "ab")

Value

combined strings separated with defautCombine

Author(s)

Matthew L. Fidler

Examples

combinePaste2("f", "depot")

combinePaste2("f", "depot", "snake")

combinePaste2("f", "depot", "dot")

combinePaste2("f", "depot", "blank")

Convert linear effect to Emax effect

Description

Convert linear effect to Emax effect

Usage

convertEmax(
  ui,
  emax = "Emax",
  ec50 = "EC50",
  imax = "Imax",
  ic50 = "IC50",
  ek = c("Ik", "Ek"),
  cc = c("Ec", "Cc")
)

Arguments

ui

rxode2 model
emax

Emax parameter
ec50

EC50 parameter
imax

Imax parameter used when input model contains "Ik" instead of "Ek"
ic50

IC50 parameter used when input model contains "Ik" instead of "Ek"
ek

simulation linear constant
cc

the concentration value

Value

Model with the linear effect converted to an Emax effect

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineConst(), addBaselineExp(), addBaselineLin(), addDirectLin(), convertLogLin(), convertQuad()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addIndirectLin(stim="in") |>
  convertEmax()

# When emax=1
readModelDb("PK_2cmt_no_depot") |>
  addIndirectLin(stim="in") |>
  convertEmax(emax=1)

Convert linear effect to Emax-Hill effect

Description

Convert linear effect to Emax-Hill effect

Usage

convertEmaxHill(
  ui,
  emax = "Emax",
  ec50 = "EC50",
  g = "g",
  imax = "Imax",
  ic50 = "IC50",
  ek = c("Ik", "Ek"),
  cc = c("Ec", "Cc")
)

Arguments

ui

rxode2 model
emax

Emax parameter
ec50

EC50 parameter
g

hill coefficient
imax

Imax parameter used when input model contains "Ik" instead of "Ek"
ic50

IC50 parameter used when input model contains "Ik" instead of "Ek"
ek

simulation linear constant
cc

the concentration value

Value

Model with the linear effect converted to an Emax effect

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_2cmt_no_depot") |>
  addIndirectLin(stim="in") |>
  convertEmaxHill()

# can also specify as emax=1

readModelDb("PK_2cmt_no_depot") |>
  addIndirectLin(stim="in") |>
  convertEmaxHill(emax=1)

Convert a kin/kout indirect response model to R0 and kout

Description

This replaces the kin/kout parametrization to the R0 and kout parametrization

Usage

convertKinR0(ui, kin = "kin", kout = "kout", R = "R", R0 = "R0")

Arguments

ui

a rxode2 user function
kin

the kin variable (by default is "kin")
kout

the kout variable (by default is "kout")
R

the compartment variable (by default is "R")
R0

the R0 variable (by default is "R0")

Value

a model where the estimated kin is changed to the estimated R0

Author(s)

Matthew L. Fidler

Examples

addIndirect(stim="in") |> convertKinR0()

Converts a linear effect to a log-linear effect

Description

Converts a linear effect to a log-linear effect

Usage

convertLogLin(ui, ek = c("Ik", "Ek"), cc = c("Ce", "Cc"))

Arguments

ui

rxode2 model
ek

simulation linear constant
cc

the concentration value

Value

model converted from linear to log-linear effect

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineConst(), addBaselineExp(), addBaselineLin(), addDirectLin(), convertEmax(), convertQuad()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertLogLin()

readModelDb("PK_2cmt_no_depot") |>
  addIndirectLin(stim="out") |>
  convertLogLin()

Convert models from linear elimination to Michaelis-Menten elimination

Description

Convert models from linear elimination to Michaelis-Menten elimination

Usage

convertMM(
  ui,
  central = "central",
  elimination = "kel",
  vm = "vm",
  km = "km",
  vc = "vc"
)

Arguments

ui

model to convert
central

the central compartment where the elimination is present
elimination

variable for the elimination constant in the model
vm

variable name for Vmax in the model
km

variable name for Km in the model
vc

variable name for Vc in the model

Value

new model changing linear elimination to Michaelis-Menten elimination

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_1cmt_des") |> convertMM()

readModelDb("PK_2cmt_des") |> convertMM()

readModelDb("PK_3cmt_des") |> convertMM()

readModelDb("PK_3cmt_des") |> removeDepot() |> convertMM()

Convert linear elimination to quadratic elimination

Description

Convert linear elimination to quadratic elimination

Usage

convertQuad(ui, ek = c("Ik", "Ek"), cc = c("Ce", "Cc"), ek2 = "Ek2")

Arguments

ui

rxode2 model
ek

simulation linear constant
cc

the concentration value
ek2

quadratic coeffficent

Value

model with linear effect converted to quadratic effect

Author(s)

Matthew L. Fidler

See Also

Other PD: addBaseline1exp(), addBaselineConst(), addBaselineExp(), addBaselineLin(), addDirectLin(), convertEmax(), convertLogLin()

Examples

readModelDb("PK_2cmt_no_depot") |>
  addIndirectLin(stim="out") |>
  convertQuad()

readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertQuad()

readModelDb("PK_2cmt_no_depot") |>
 addEffectCmtLin() |>
 convertQuad()

Default combine strings

Description

Default combine strings

Usage

defaultCombine(...)

snakeCombine(...)

camelCombine(...)

dotCombine(...)

blankCombine(...)

Arguments

...

uses default to combine strings

Value

combined strings

Functions

  • snakeCombine(): use snake_case to combine 2 strings

  • camelCombine(): use camelCase to combine strings

  • dotCombine(): use the default method for combining two strings

  • blankCombine(): combine using a blank separator

Author(s)

Matthew L. Fidler

Examples

# default combine

defaultCombine("f", "depot")

defaultCombine(list(c("a", "funny", "c")))

defaultCombine(c("a", "funny", "c"))

# snake combine

snakeCombine("f", "depot")

snakeCombine(list(c("a", "funny", "c")))

snakeCombine(c("a", "funny", "c"))

# dot combine

dotCombine("f", "depot")

dotCombine(list(c("a", "funny", "c")))

dotCombine(c("a", "funny", "c"))

# blank combine

blankCombine("f", "depot")

blankCombine(list(c("a", "funny", "c")))

blankCombine(c("a", "funny", "c"))

Fake blank Cc for creating PD only models

Description

Fake blank Cc for creating PD only models

Usage

fakeCc(fun, ..., cc = "Cc")

Arguments

fun

function to that requires Cc
...

arguments sent PD function
cc

character name of the concentration in the central compartment that will be faked to allow models that require Cc to change to models with Cc as a covariate

Value

Model where Cc is a covariate

Author(s)

Matthew L. Fidler

Examples

fakeCc(addDirectLin) |> convertEmaxHill()

Model library for nlmixr2

Description

This is a data frame of the available models in nlmixr2lib, it is generated with the package. Custom modeldb may be used.

Usage

modeldb

Format

An object of class data.frame with 17 rows and 9 columns.

Get the model from the model library

Description

This function gets a model from the available model library

Usage

modellib(name = NULL, eta = NULL, reserr = NULL)

Arguments

name

character with the name of the model to load (if NULL, lists all available base models)
eta

vector with the parameters to add random effects (sometimes referred to as inter-individual variability, IIV) on
reserr

The type or types of residual error (currently "addSd", "propSd", and "lnormSd" are accepted)

Details

This is a very first draft just to look at the proof of concept

Value

The function returns a function the model code (or NULL if the model = NULL)

Examples

modellib(name = "PK_1cmt")
modellib(name = "PK_1cmt", eta = c("ka", "vc"), reserr = "addSd")
modellib(name = "PK_1cmt", reserr = "addSd")

Change the transformation type for PK models

Description

Change the transformation type for PK models

Usage

pkTrans(
  ui,
  type = c("k", "k21", "vss", "aob", "alpha"),
  k13 = "k13",
  k31 = "k31",
  k12 = "k12",
  k21 = "k21",
  kel = "kel",
  vc = "vc",
  cl = "cl",
  vp = "vp",
  q = "q",
  vp2 = "vp2",
  q2 = "q2",
  vss = "vss",
  aob = "aob",
  alpha = "alpha",
  beta = "beta",
  gam = "gam",
  A = "A",
  B = "B",
  C = "C",
  s = "s",
  p = "p",
  tmp = "tmp",
  beforeCmt = c("depot", "central")
)

Arguments

ui

A model in terms of Clearance
type

the type of PK transformation to make:

- "k": Change to rate constants (kel, k12, k21, k13, k31)

- "vss": Change to volume of distribution at steady state (cl, vc, q, vss)

- "aob": Change to A/B ratio (aob, alpha, beta, vc)

- "k21": Change to k21 constant (k21, alpha, beta, vc) or (k21, k31, alpha, beta, gam, vc)

- "alpha": Change to macro constants (alpha, beta, gam, A, B, C, vc)
k13

name of rate constant from central to periph2
k31

name of rate constant from periph2 to central
k12

name of rate constant from central to periph1
k21

name of rate constant from periph1 to central
kel

name of elimination rate constant
vc

name of central compartment volume
cl

name of clearance
vp

name of volume of periph1
q

name of intercompartmental clearance between central and periph1
vp2

name of volume of periph2
q2

name of intercompartmental clearance between central and periph2
vss

name of volume of distribution at steady state
aob

A/B ratio
alpha

macro constant name for first exponential decay term
beta

macro constant name for second exponential decay term
gam

macro constant name for third exponential decay term
A

macro coefficient for the first exponential decay term (corresponds with alpha)
B

macro coefficient for the second exponential decay term (corresponds with beta)
C

macro coefficient for the third exponential decay term (corresponds with gam)
s

sum constant name for the k12 three compartment
p

product constant name for the k12 three compartment
tmp

name of temporary variable for the three compartment with 'A', 'B', 'C', 'alpha', 'beta' and 'gam'.
beforeCmt

if the model is compartmental you can specify the preferred names where the estimates and extra lines are added before

Value

ui with no PK parameters estimated

Author(s)

Matthew L. Fidler

Examples

# Three compartment model translations

readModelDb("PK_3cmt_des") |>
  pkTrans("k")

readModelDb("PK_3cmt_des") |>
  pkTrans("k21")

readModelDb("PK_3cmt_des") |>
  pkTrans("alpha")

# The most types of transformations are
# available for 2 compartment models

readModelDb("PK_2cmt_des") |>
  pkTrans("k")

readModelDb("PK_2cmt_des") |>
  pkTrans("vss")

readModelDb("PK_2cmt_des") |>
  pkTrans("aob")

readModelDb("PK_2cmt_des") |>
  pkTrans("k21")

readModelDb("PK_2cmt_des") |>
  pkTrans("alpha")

# One compartment transformations are also available:

readModelDb("PK_1cmt_des") |>
  pkTrans("k")

readModelDb("PK_1cmt_des") |>
  pkTrans("alpha")

# also works without depot:

readModelDb("PK_3cmt_des") |>
  removeDepot() |>
  pkTrans("k")

Read a model from the nlmixr2 model database

Description

Read a model from the nlmixr2 model database

Usage

readModelDb(name)

Arguments

name

The name of the model (must be one of modeldb$name)

Value

The model as a function

Examples

readModelDb("PK_1cmt")

To convert from first order oral absorption to IV/Intravenous

Description

To convert from first order oral absorption to IV/Intravenous

Usage

removeDepot(ui, central = "central", depot = "depot", ka = "ka")

Arguments

ui

The model as a function (or something convertible to an rxUi object)
central

central compartment name
depot

depot compartment name
ka

absorption rate parameter name

Value

Returns a model with the depot from a first order absorption model removed

Examples

readModelDb("PK_1cmt_des") |> removeDepot()

Removes lines and inis from a model

Description

Removes lines and inis from a model

Usage

removeLinesAndInis(ui, vars)

Arguments

ui

A rxode2 model
vars

A character vector of variables to remove

Value

model with rxode2 lines and any estimates associate with lines removed

Author(s)

Matthew L. Fidler

Examples

readModelDb("PK_3cmt_des") |> removeLinesAndInis(c("kel", "k12", "k21"))

To remove transit compartments from the model

Description

To remove transit compartments from the model

Usage

removeTransit(
  ui,
  ntransit,
  central = "central",
  depot = "depot",
  transit = "transit",
  ktr = "ktr",
  ka = "ka"
)

Arguments

ui

The model as a function
ntransit

the number of transit compartments to be added
central

central compartment name
depot

depot compartment name
transit

The number of transit compartments to remove
ktr

the parameter name for the transit compartment rate
ka

absorption rate parameter name

Value

rxode2 model with transit compartment removed

See Also

Other absorption: addTransit(), addWeibullAbs()

Examples

# In this example the transit is added and then a few are removed

readModelDb("PK_1cmt_des") |> addTransit(4) |> removeTransit(3)

readModelDb("PK_1cmt_des") |> addTransit(4) |> removeTransit()

Search within a model to replace part of the model

Description

Search within a model to replace part of the model

Usage

searchReplace(object, find, replace)

searchReplaceHelper(object, find, replace)

Arguments

object

function specifying the nlmixr2 model
find, replace

Character scalars of parts of the model to replace

Value

object with find replaced with replace

Functions

  • searchReplaceHelper(): A helper function for searchReplace (not intended for users to use directly)

Change the default combine type for the package

Description

Change the default combine type for the package

Usage

setCombineType(combineType = c("snake", "camel", "dot", "blank"))

Arguments

combineType

this is the default combine type: - "default": default combine - "snake": snake_case combine - "camel": camelCase combine - "dot": dot combine (i.e. "a.b") - "blank": no separator (i.e. "ab")

Author(s)

Matthew L. Fidler

Examples

# Change to the popular snake_case
setCombineType("snake")
defaultCombine("a", "b")

# Change back to nlmixr2/rxode2 default camelCase

setCombineType("camel")
defaultCombine("a", "b")

# This is used to change the naming convention for parameters
# produced by this package

Update an oncology xenograft model based on Simeoni 2004

Description

Update an oncology xenograft model based on Simeoni 2004

Usage

updateOncologyXenograftSimeoni2004(
  object,
  ncmt,
  damagedCmtName = "damagedCells",
  drugEffectName = "drugEffectCyclingCells",
  undamagedCmtName = "cyclingCells",
  tumorVolName = "tumorVol",
  transitRateName = "damageTransit"
)

Arguments

object

Fitted object or function specifying the model.
ncmt

The desired number of damaged cell compartments
damagedCmtName, undamagedCmtName, tumorVolName

character string names for the compartments for damaged cells, undamaged cells, and the calculated tumor volume (the sum of undamaged and damaged cells)
drugEffectName, transitRateName

character string names of the drug effect and transit rate (as used in the model block)

Value

An updated model with the new number of compartments

Examples

library(rxode2)
readModelDb("oncology_xenograft_simeoni_2004") %>%
  updateOncologyXenograftSimeoni2004(ncmt = 5)