Plot a nlmixr2 data object

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

Usage

# S3 method for 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))
#>  
#>  
#>  
#>  
#>  
#>  
#> → 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 11.4.0-1ubuntu1~22.04) 11.4.0’
#> 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 phiM in nlmixr2 object, save 2832
#> → compress parHistData in nlmixr2 object, save 2488
#> → compress saem0 in nlmixr2 object, save 23920

# 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.


# }