Plot a nlmixr2 data object

Plot some standard goodness of fit plots for the focei fitted object

Usage

# S3 method for class 'nlmixr2FitData'
plot(x, ...)

Arguments

x

a focei fit object

...

additional arguments (currently ignored)

Value

An nlmixr2PlotList object (a list of ggplot2 objects with easier plotting for all of them at the same time)

Author

Wenping Wang & Matthew Fidler

Examples

# \donttest{
library(nlmixr2est)
one.compartment <- function() {
  ini({
    tka <- 0.45
    tcl <- 1
    tv <- 3.45
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv + eta.v)
    d/dt(depot) = -ka * depot
    d/dt(center) = ka * depot - cl / v * center
    cp = center / v
    cp ~ add(add.sd)
  })
}

## The fit is performed by the function nlmixr/nlmix2 specifying the model, data and estimate
fit <- nlmixr2(one.compartment, theo_sd,  est="saem", saemControl(print=0, nBurn = 10, nEm = 20))
#>  
#>  
#>  
#>  
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#>  
#>  
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem model...
#> → optimizing duplicate expressions in saem model...
#> ✔ done
#> using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
#> ℹ calculate uninformed etas
#> ℹ done
#> Calculating covariance matrix
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem predOnly model 0...
#> → finding duplicate expressions in saem predOnly model 1...
#> → optimizing duplicate expressions in saem predOnly model 1...
#> → finding duplicate expressions in saem predOnly model 2...
#> ✔ done
#>  
#>  
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 5952
#> → compress parHistData in nlmixr2 object, save 2456
#> → compress phiM in nlmixr2 object, save 3712

# This shows many goodness of fit plots
plot(fit)


#> Warning: log-10 transformation introduced infinite values.
#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


#> Warning: log-10 transformation introduced infinite values.


# }