Add direct linear effect with baseline=0

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)

See also

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

Author

Matthew L. Fidler

Examples

# Direct linear model
readModelDb("PK_2cmt_no_depot") |>
  addDirectLin()
#>  
#>  
#>  ── rxode2-based free-form 2-cmt ODE model ────────────────────────────────────── 
#>  ── Initalization: ──  
#> Fixed Effects ($theta): 
#>      lcl      lvc      lvp       lq   propSd      uEk effectSd 
#>      1.0      3.0      5.0      0.1      0.5      0.1      0.1 
#> 
#> States ($state or $stateDf): 
#>   Compartment Number Compartment Name
#> 1                  1          central
#> 2                  2      peripheral1
#>  ── Multiple Endpoint Model ($multipleEndpoint): ──  
#>     variable                   cmt                   dvid*
#> 1     Cc ~ …     cmt='Cc' or cmt=3     dvid='Cc' or dvid=1
#> 2 effect ~ … cmt='effect' or cmt=4 dvid='effect' or dvid=2
#>   * If dvids are outside this range, all dvids are re-numered sequentially, ie 1,7, 10 becomes 1,2,3 etc
#> 
#>  ── Model (Normalized Syntax): ── 
#> function() {
#>     ini({
#>         lcl <- 1
#>         label("Clearance (CL)")
#>         lvc <- 3
#>         label("Central volume of distribution (V)")
#>         lvp <- 5
#>         label("Peripheral volume of distribution (Vp)")
#>         lq <- 0.1
#>         label("Intercompartmental clearance (Q)")
#>         propSd <- c(0, 0.5)
#>         label("Proportional residual error (fraction)")
#>         uEk <- 0.1
#>         label("untransformed slope (Ek)")
#>         effectSd <- c(0, 0.1)
#>         label("additive error for effect")
#>     })
#>     model({
#>         Ek <- uEk
#>         cl <- exp(lcl)
#>         vc <- exp(lvc)
#>         vp <- exp(lvp)
#>         q <- exp(lq)
#>         kel <- cl/vc
#>         k12 <- q/vc
#>         k21 <- q/vp
#>         d/dt(central) <- -kel * central - k12 * central + k21 * 
#>             peripheral1
#>         d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#>         Cc <- central/vc
#>         Cc ~ prop(propSd)
#>         effect <- Ek * Cc
#>         effect ~ add(effectSd)
#>     })
#> }

# Direct emax model
readModelDb("PK_2cmt_no_depot") |>
  addDirectLin() |>
  convertEmax()
#>  
#>  
#>  ── rxode2-based free-form 2-cmt ODE model ────────────────────────────────────── 
#>  ── Initalization: ──  
#> Fixed Effects ($theta): 
#>      lcl      lvc      lvp       lq   propSd effectSd    lEmax    lEC50 
#>      1.0      3.0      5.0      0.1      0.5      0.1      0.1      0.1 
#> 
#> States ($state or $stateDf): 
#>   Compartment Number Compartment Name
#> 1                  1          central
#> 2                  2      peripheral1
#>  ── Multiple Endpoint Model ($multipleEndpoint): ──  
#>     variable                   cmt                   dvid*
#> 1     Cc ~ …     cmt='Cc' or cmt=3     dvid='Cc' or dvid=1
#> 2 effect ~ … cmt='effect' or cmt=4 dvid='effect' or dvid=2
#>   * If dvids are outside this range, all dvids are re-numered sequentially, ie 1,7, 10 becomes 1,2,3 etc
#> 
#>  ── Model (Normalized Syntax): ── 
#> function() {
#>     ini({
#>         lcl <- 1
#>         label("Clearance (CL)")
#>         lvc <- 3
#>         label("Central volume of distribution (V)")
#>         lvp <- 5
#>         label("Peripheral volume of distribution (Vp)")
#>         lq <- 0.1
#>         label("Intercompartmental clearance (Q)")
#>         propSd <- c(0, 0.5)
#>         label("Proportional residual error (fraction)")
#>         effectSd <- c(0, 0.1)
#>         label("additive error for effect")
#>         lEmax <- 0.1
#>         label("Maximum effect (Emax)")
#>         lEC50 <- 0.1
#>         label("Concentration of 50% Emax (Emax)")
#>     })
#>     model({
#>         Emax <- exp(lEmax)
#>         EC50 <- exp(lEC50)
#>         cl <- exp(lcl)
#>         vc <- exp(lvc)
#>         vp <- exp(lvp)
#>         q <- exp(lq)
#>         kel <- cl/vc
#>         k12 <- q/vc
#>         k21 <- q/vp
#>         d/dt(central) <- kel * central - k12 * central + k21 * 
#>             peripheral1
#>         d/dt(peripheral1) <- k12 * central - k21 * peripheral1
#>         Cc <- central/vc
#>         Cc ~ prop(propSd)
#>         effect <- Emax * Cc/(Cc + EC50)
#>         effect ~ add(effectSd)
#>     })
#> }