Model block for rxode2/nlmixr models

Usage

# S3 method for class '`function`'
model(
  x,
  ...,
  append = NULL,
  auto = getOption("rxode2.autoVarPiping", TRUE),
  cov = NULL,
  envir = parent.frame()
)

# S3 method for class 'rxUi'
model(
  x,
  ...,
  append = NULL,
  auto = getOption("rxode2.autoVarPiping", TRUE),
  cov = NULL,
  envir = parent.frame()
)

# S3 method for class 'rxode2'
model(
  x,
  ...,
  append = NULL,
  auto = getOption("rxode2.autoVarPiping", TRUE),
  cov = NULL,
  envir = parent.frame()
)

# S3 method for class 'rxModelVars'
model(
  x,
  ...,
  append = NULL,
  auto = getOption("rxode2.autoVarPiping", TRUE),
  cov = NULL,
  envir = parent.frame()
)

model(
  x,
  ...,
  append = FALSE,
  auto = getOption("rxode2.autoVarPiping", TRUE),
  cov = NULL,
  envir = parent.frame()
)

# Default S3 method
model(x, ..., append = FALSE, cov = NULL, envir = parent.frame())

Arguments

x

model expression

...

Other arguments

append

This is a boolean to determine if the lines are appended in piping. The possible values for this is:

TRUE which is when the lines are appended to the model instead of replaced
FALSE when the lines are replaced in the model (default)
NA is when the lines are pre-pended to the model instead of replaced
lhs expression, which will append the lines after the last observed line of the expression lhs

auto

This boolean tells if piping automatically selects the parameters should be characterized as a population parameter, between subject variability, or a covariate. When TRUE this automatic selection occurs. When FALSE this automatic selection is turned off and everything is added as a covariate (which can be promoted to a parameter with the ini statement). By default this is TRUE, but it can be changed by options(rxode2.autoVarPiping=FALSE).

cov

is a character vector of variables that should be assumed to be covariates. This will override automatic promotion to a population parameter estimate (or an eta)

envir

the environment in which unevaluated model expressions is to be evaluated. May also be NULL, a list, a data frame, a pairlist or an integer as specified to sys.call.

Value

Model block with ini information included. ini must be called before model block

Author

Matthew Fidler

Examples

# \donttest{
mod <- function() {
  ini({
    tka <- log(1.1)
    tcl <- log(3)
    tv <- log(30)
    eta.cl ~ 0.1
    add.sd <- 0.7
  })
  model({
    ka <- exp(tka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv)
    d/dt(depot) <- -ka * depot
    d/dt(central) <- ka * depot - cl / v * central
    cp <- central / v
    cp ~ add(add.sd)
  })
}
# extract the model block
model(mod)
#>  
#>  
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> model({
#>     ka <- exp(tka)
#>     cl <- exp(tcl + eta.cl)
#>     v <- exp(tv)
#>     d/dt(depot) <- -ka * depot
#>     d/dt(central) <- ka * depot - cl/v * central
#>     cp <- central/v
#>     cp ~ add(add.sd)
#> })
# replace a line; the new parameter tcl.wt is added to ini()
mod |> model(cl <- exp(tcl + eta.cl) * (WT / 70)^tcl.wt)
#>  
#>  
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> ℹ add covariate `WT`
#> ℹ add population parameter `tcl.wt` and set estimate to 1
#>  ── rxode2-based free-form 2-cmt ODE model ────────────────────────────────────── 
#>  ── Initalization: ──  
#> Fixed Effects ($theta): 
#>        tka        tcl         tv     add.sd     tcl.wt 
#> 0.09531018 1.09861229 3.40119738 0.70000000 1.00000000 
#> 
#> Omega ($omega): 
#>        eta.cl
#> eta.cl    0.1
#> 
#> States ($state or $stateDf): 
#>   Compartment Number Compartment Name
#> 1                  1            depot
#> 2                  2          central
#>  ── μ-referencing ($muRefTable): ──  
#>   theta    eta level
#> 1   tcl eta.cl    id
#> 
#>  ── Model (Normalized Syntax): ── 
#> function() {
#>     ini({
#>         tka <- 0.0953101798043249
#>         tcl <- 1.09861228866811
#>         tv <- 3.40119738166216
#>         add.sd <- c(0, 0.7)
#>         tcl.wt <- 1
#>         eta.cl ~ 0.1
#>     })
#>     model({
#>         ka <- exp(tka)
#>         cl <- exp(tcl + eta.cl) * (WT/70)^tcl.wt
#>         v <- exp(tv)
#>         d/dt(depot) <- -ka * depot
#>         d/dt(central) <- ka * depot - cl/v * central
#>         cp <- central/v
#>         cp ~ add(add.sd)
#>     })
#> }
# append a line after cp
mod |> model(auc <- cp * 12, append = cp)
#>  
#>  
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#>  ── rxode2-based free-form 2-cmt ODE model ────────────────────────────────────── 
#>  ── Initalization: ──  
#> Fixed Effects ($theta): 
#>        tka        tcl         tv     add.sd 
#> 0.09531018 1.09861229 3.40119738 0.70000000 
#> 
#> Omega ($omega): 
#>        eta.cl
#> eta.cl    0.1
#> 
#> States ($state or $stateDf): 
#>   Compartment Number Compartment Name
#> 1                  1            depot
#> 2                  2          central
#>  ── μ-referencing ($muRefTable): ──  
#>   theta    eta level
#> 1   tcl eta.cl    id
#> 
#>  ── Model (Normalized Syntax): ── 
#> function() {
#>     ini({
#>         tka <- 0.0953101798043249
#>         tcl <- 1.09861228866811
#>         tv <- 3.40119738166216
#>         add.sd <- c(0, 0.7)
#>         eta.cl ~ 0.1
#>     })
#>     model({
#>         ka <- exp(tka)
#>         cl <- exp(tcl + eta.cl)
#>         v <- exp(tv)
#>         d/dt(depot) <- -ka * depot
#>         d/dt(central) <- ka * depot - cl/v * central
#>         cp <- central/v
#>         cp ~ add(add.sd)
#>         auc <- cp * 12
#>     })
#> }
# }