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
Examples
# \donttest{
# Three compartment model translations
readModelDb("PK_3cmt_des") |>
pkTrans("k")
#>
#>
#> ── rxode2-based free-form 4-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lk12 lk21 lk13 lk31 lkel lvc
#> 0.45 0.50 0.10 0.10 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> 4 4 peripheral2
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lk12 <- 0.1
#> label("Central->Periph1 constant (k12)")
#> lk21 <- 0.1
#> label("Periph1->Central constant (k21)")
#> lk13 <- 0.1
#> label("Central->Periph2 constant (k13)")
#> lk31 <- 0.1
#> label("Periph2->Central constant (k31)")
#> lkel <- 0.1
#> label("Elimination from central (kel)")
#> lvc <- 0.1
#> label("Central compartment volume (vc)")
#> })
#> model({
#> ka <- exp(lka)
#> k12 <- exp(lk12)
#> k21 <- exp(lk21)
#> k13 <- exp(lk13)
#> k31 <- exp(lk31)
#> kel <- exp(lkel)
#> vc <- exp(lvc)
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1 - k13 * central + k31 * peripheral2
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> d/dt(peripheral2) <- k13 * central - k31 * peripheral2
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_3cmt_des") |>
pkTrans("k21")
#>
#>
#> ── rxode2-based free-form 4-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lk21 lk31 lalpha lbeta lgam lvc
#> 0.45 0.50 0.10 0.10 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> 4 4 peripheral2
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lk21 <- 0.1
#> label("Periph1->Central constant (k21)")
#> lk31 <- 0.1
#> label("Periph2->Central constant (k31)")
#> lalpha <- 0.1
#> label("alpha macro constant (alpha)")
#> lbeta <- 0.1
#> label("beta macro constant (beta)")
#> lgam <- 0.1
#> label("gam macro constant (gam)")
#> lvc <- 0.1
#> label("Volume of central compartment (vc)")
#> })
#> model({
#> ka <- exp(lka)
#> k21 <- exp(lk21)
#> k31 <- exp(lk31)
#> alpha <- exp(lalpha)
#> beta <- exp(lbeta)
#> gam <- exp(lgam)
#> vc <- exp(lvc)
#> kel <- alpha * beta * gam/(k21 * k31)
#> s <- alpha + beta + gam
#> p <- alpha * beta + alpha * gam + beta * gam
#> k13 <- (p + k31 * k31 - k31 * s - kel * k21)/(k21 - k31)
#> k12 <- s - kel - k13 - k21 - k31
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1 - k13 * central + k31 * peripheral2
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> d/dt(peripheral2) <- k13 * central - k31 * peripheral2
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_3cmt_des") |>
pkTrans("alpha")
#>
#>
#> ── rxode2-based free-form 4-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lalpha lbeta lgam lA lB lC
#> 0.45 0.50 0.10 0.10 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> 4 4 peripheral2
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lalpha <- 0.1
#> label("alpha macro constant (alpha)")
#> lbeta <- 0.1
#> label("beta macro constant (beta)")
#> lgam <- 0.1
#> label("gam macro constant (gam)")
#> lA <- 0.1
#> label("A coefficient (A)")
#> lB <- 0.1
#> label("B coefficient (B)")
#> lC <- 0.1
#> label("C coefficent (C)")
#> })
#> model({
#> ka <- exp(lka)
#> alpha <- exp(lalpha)
#> beta <- exp(lbeta)
#> gam <- exp(lgam)
#> A <- exp(lA)
#> B <- exp(lB)
#> C <- exp(lC)
#> vc <- 1/(A + B + C)
#> s <- -(alpha * C + alpha * B + gam * A + gam * B + beta *
#> A + beta * C) * vc
#> p <- (alpha * beta * C + alpha * gam * B + beta * gam *
#> A) * vc
#> tmp <- sqrt(p * p - 4 * s)
#> k21 <- 0.5 * (-p + tmp)
#> k31 <- 0.5 * (-p - tmp)
#> kel <- alpha * beta * gam/(k21 * k31)
#> k12 <- ((beta * gam + alpha * beta + alpha * gam) - k21 *
#> (alpha + beta + gam) - kel * k31 + k21 * k21)/(k31 -
#> k21)
#> k13 <- alpha + beta + gam - (kel + k12 + k21 + k31)
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1 - k13 * central + k31 * peripheral2
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> d/dt(peripheral2) <- k13 * central - k31 * peripheral2
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
# The most types of transformations are
# available for 2 compartment models
readModelDb("PK_2cmt_des") |>
pkTrans("k")
#>
#>
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lk12 lk21 lkel lvc
#> 0.45 0.50 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lk12 <- 0.1
#> label("Central->Periph1 constant (k12)")
#> lk21 <- 0.1
#> label("Periph1->Central constant (k21)")
#> lkel <- 0.1
#> label("Elimination from central (kel)")
#> lvc <- 0.1
#> label("Central compartment volume (vc)")
#> })
#> model({
#> ka <- exp(lka)
#> k12 <- exp(lk12)
#> k21 <- exp(lk21)
#> kel <- exp(lkel)
#> vc <- exp(lvc)
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_2cmt_des") |>
pkTrans("vss")
#>
#>
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lcl lvc lq lvss
#> 0.45 0.50 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lcl <- 0.1
#> label("Clearance (cl)")
#> lvc <- 0.1
#> label("Central compartment volume (vc)")
#> lq <- 0.1
#> label("Periph1<->Central inter-compartmental clearance (q)")
#> lvss <- 0.1
#> label("Volume of distribution at steady state (vss)")
#> })
#> model({
#> ka <- exp(lka)
#> cl <- exp(lcl)
#> vc <- exp(lvc)
#> q <- exp(lq)
#> vss <- exp(lvss)
#> kel <- cl/vc
#> k12 <- q/vc
#> k21 <- q/(vss - vc)
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_2cmt_des") |>
pkTrans("aob")
#>
#>
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd laob lalpha lbeta lvc
#> 0.45 0.50 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> laob <- 0.1
#> label("A/B (aob)")
#> lalpha <- 0.1
#> label("alpha macro constant (alpha)")
#> lbeta <- 0.1
#> label("beta macro constant (beta)")
#> lvc <- 0.1
#> label("Volume of central compartment (vc)")
#> })
#> model({
#> ka <- exp(lka)
#> aob <- exp(laob)
#> alpha <- exp(lalpha)
#> beta <- exp(lbeta)
#> vc <- exp(lvc)
#> k21 <- (aob * beta + alpha)/(aob + 1)
#> kel <- (alpha * beta)/k21
#> k12 <- alpha + beta - k21 - kel
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_2cmt_des") |>
pkTrans("k21")
#>
#>
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lk21 lalpha lbeta lvc
#> 0.45 0.50 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lk21 <- 0.1
#> label("Periph1->Central constant (k21)")
#> lalpha <- 0.1
#> label("alpha macro constant (alpha)")
#> lbeta <- 0.1
#> label("beta macro constant (beta)")
#> lvc <- 0.1
#> label("Volume of central compartment (vc)")
#> })
#> model({
#> ka <- exp(lka)
#> k21 <- exp(lk21)
#> alpha <- exp(lalpha)
#> beta <- exp(lbeta)
#> vc <- exp(lvc)
#> kel <- alpha * beta/k21
#> k12 <- alpha + beta - k21 - kel
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_2cmt_des") |>
pkTrans("alpha")
#>
#>
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lalpha lbeta lA lB
#> 0.45 0.50 0.10 0.10 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 peripheral1
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lalpha <- 0.1
#> label("alpha macro constant (alpha)")
#> lbeta <- 0.1
#> label("beta macro constant (beta)")
#> lA <- 0.1
#> label("A coefficient (A)")
#> lB <- 0.1
#> label("B coefficient (B)")
#> })
#> model({
#> ka <- exp(lka)
#> alpha <- exp(lalpha)
#> beta <- exp(lbeta)
#> A <- exp(lA)
#> B <- exp(lB)
#> vc <- 1/(A + B)
#> k21 <- (A * beta + B * alpha) * vc
#> kel <- alpha * beta/k21
#> k12 <- alpha + beta - k21 - kel
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central - k12 * central +
#> k21 * peripheral1
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
# One compartment transformations are also available:
readModelDb("PK_1cmt_des") |>
pkTrans("k")
#>
#>
#> ── rxode2-based free-form 2-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lkel lvc
#> 0.45 0.50 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> ── Model (Normalized Syntax): ──
#> function() {
#> dosing <- c("central", "depot")
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lkel <- 0.1
#> label("Elimination from central (kel)")
#> lvc <- 0.1
#> label("Central compartment volume (vc)")
#> })
#> model({
#> ka <- exp(lka)
#> kel <- exp(lkel)
#> vc <- exp(lvc)
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
readModelDb("PK_1cmt_des") |>
pkTrans("alpha")
#>
#>
#> ── rxode2-based free-form 2-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka propSd lalpha lA
#> 0.45 0.50 0.10 0.10
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> ── Model (Normalized Syntax): ──
#> function() {
#> dosing <- c("central", "depot")
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lalpha <- 0.1
#> label("alpha macro constant (alpha)")
#> lA <- 0.1
#> label("A coefficient (A)")
#> })
#> model({
#> ka <- exp(lka)
#> alpha <- exp(lalpha)
#> A <- exp(lA)
#> kel <- alpha
#> vc <- 1/A
#> d/dt(depot) <- -ka * depot
#> d/dt(central) <- ka * depot - kel * central
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
# also works without depot:
readModelDb("PK_3cmt_des") |>
removeDepot() |>
pkTrans("k")
#>
#>
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> propSd lk12 lk21 lk13 lk31 lkel lvc
#> 0.5 0.1 0.1 0.1 0.1 0.1 0.1
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 central
#> 2 2 peripheral1
#> 3 3 peripheral2
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lk12 <- 0.1
#> label("Central->Periph1 constant (k12)")
#> lk21 <- 0.1
#> label("Periph1->Central constant (k21)")
#> lk13 <- 0.1
#> label("Central->Periph2 constant (k13)")
#> lk31 <- 0.1
#> label("Periph2->Central constant (k31)")
#> lkel <- 0.1
#> label("Elimination from central (kel)")
#> lvc <- 0.1
#> label("Central compartment volume (vc)")
#> })
#> model({
#> k12 <- exp(lk12)
#> k21 <- exp(lk21)
#> k13 <- exp(lk13)
#> k31 <- exp(lk31)
#> kel <- exp(lkel)
#> vc <- exp(lvc)
#> d/dt(central) <- -kel * central - k12 * central + k21 *
#> peripheral1 - k13 * central + k31 * peripheral2
#> d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#> d/dt(peripheral2) <- k13 * central - k31 * peripheral2
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }
# }