nlmixr2 / nlmixr2data

nlmixr2 data

nlmixr2

The vision of nlmixr2 is to develop a R-based open-source nonlinear mixed-effects modeling software package that can compete with commercial pharmacometric tools and is suitable for regulatory submissions.

In short, the goal of nlmixr2 is to support easy and robust nonlinear mixed effects models in R. This is supported by our team and advisory committee

Blog for more information

For more information about ongoing development, best practices, and news about nlmixr2, please see the nlmixr2 blog.

Installation

For all versions of R, we need to have a compiler setup to run nlmixr2 and rxode2

Windows compilation tools setup

For Windows the compilers come from RTools. Download and the install the version of RTools for your version of R from https://cran.r-project.org/bin/windows/Rtools/

Mac compilation tools setup

To setup the mac compilers, simply

1. Install Xcode from app store

2. Install gfortran:

   1. Download and install from https://mac.r-project.org/tools/

   2. Add gfortran directory to the path with: export PATH=$PATH:/usr/local/gfortran/bin

R package installation

Installation nlmixr2 itself is easiest the latest version of R because no further compilation is required and all supporting packages are available. From R, run:

install.packages("nlmixr2",dependencies = TRUE)

For R-4.0.x and R-4.1.x, the symengine package will need to be downgraded to run in those earlier R versions. This can be done by:

# install.packages("remotes")
remotes::install_version("symengine", version = "0.1.6")

followed by:

install.packages("nlmixr2",dependencies = TRUE)

Checking installation

You can check that your installation is likely setup correctly with the following command after installing the nlmixr2 package:

nlmixr2::nlmixr2CheckInstall()

Development version installation

Once the compilers are setup and a compatible version of symengine is installed, you can install the development version of nlmixr2 and its nlmixr2-family dependencies either by using the r-universe or by installing manually.

Install using the R universe

For many people this is the fastest way to install the development version of nlmixr2 since it provides binaries for mac, windows for the latest and last version of R (no need to wait for a compile).

install.packages(c("dparser", "nlmixr2data", "lotri", "rxode2ll",
                   "rxode2parse", "rxode2random", "rxode2et",
                   "rxode2", "nlmixr2est", "nlmixr2extra", "nlmixr2plot",
                   "nlmixr2"),
                 repos = c('https://nlmixr2.r-universe.dev',
                           'https://cloud.r-project.org'))

If you are using a Ubuntu latest flavor (at the time of this writing jammy) you can also use the binaries (though if you use bspm you should install any dependencies first to reduce your computation time)

# bspm::disable() # if you are using r2u or other ubuntu binary for CRAN
oldOptions <- options()

options(repos=c(
  linux = 'https://nlmixr2.r-universe.dev/bin/linux/jammy/4.2/',
  sources = 'https://nlmixr2.r-universe.dev',
  cran = 'https://cloud.r-project.org'
))
install.packages(c("dparser", "nlmixr2data", "lotri", "rxode2ll",
                   "rxode2parse", "rxode2random", "rxode2et",
                   "rxode2", "nlmixr2est", "nlmixr2extra", "nlmixr2plot",
                   "nlmixr2"))

options(oldOptions)
#bspm::enable()

Support packages from the R universe can also be installed for the packages in the nlmixr2 domain:

install.packages(c("xpose.nlmixr2", # Additional goodness of fit plots
                                    # baesd on xpose
                   "nlmixr2targets", # Simplify work with the
                                     # `targets` package
                   "babelmixr2", # Convert/run from nlmixr2-based
                                 # models to NONMEM, Monolix, and
                                 # initialize models with PKNCA
                   "nonmem2rx", # Convert from NONMEM to
                                # rxode2/nlmixr2-based models
                   "nlmixr2lib", # a model library and model
                                 # modification functions that
                                 # complement model piping
                   "nlmixr2rpt" # Automated Microsoft Word and
                                # PowerPoint reporting for nlmixr2
                   ),
                 repos = c('https://nlmixr2.r-universe.dev',
                           'https://cloud.r-project.org'))

# Some additional packages outside of the `nlmixr2.r-univers.dev`
# install.packages("remotes")
remotes::install_github("ggPMXdevelopment/ggPMX") # Goodness of fit plots
remotes::install_github("RichardHooijmaijers/shinyMixR") # Shiny run manager (like Piranha)

For Ubuntu latest it is similar

# bspm::disable() # if you are using r2u or other ubuntu binary for CRAN
oldOptions <- options()

options(repos=c(
  linux = 'https://nlmixr2.r-universe.dev/bin/linux/jammy/4.2/',
  sources = 'https://nlmixr2.r-universe.dev',
  cran = 'https://cloud.r-project.org'
))
install.packages(c("xpose.nlmixr2", "nlmixr2targets", "babelmixr2", "nonmem2rx", "nlmixr2lib", "nlmixr2rpt"))

options(oldOptions)
#bspm::enable()
# install.packages("remotes")
remotes::install_github("ggPMXdevelopment/ggPMX") # Goodness of fit plots
remotes::install_github("RichardHooijmaijers/shinyMixR") # Shiny run manager (like Piranha)

Install using remotes

This is sure to give the latest development version

# install.packages("remotes")
remotes::install_github("nlmixr2/dparser-R")
remotes::install_github("nlmixr2/nlmixr2data")
remotes::install_github("nlmixr2/lotri")
remotes::install_github("nlmixr2/rxode2ll")
remotes::install_github("nlmixr2/rxode2parse")
remotes::install_github("nlmixr2/rxode2random")
remotes::install_github("nlmixr2/rxode2et")
remotes::install_github("nlmixr2/rxode2")
remotes::install_github("nlmixr2/nlmixr2est")
remotes::install_github("nlmixr2/nlmixr2extra")
remotes::install_github("nlmixr2/nlmixr2plot")
remotes::install_github("nlmixr2/nlmixr2")

Optional supporting packages can be installed like so:

# install.packages("remotes")
# Goodness of fit plots
remotes::install_github("ggPMXdevelopment/ggPMX")
# Additional goodness of fit plots
remotes::install_github("nlmixr2/xpose.nlmixr2")
# Shiny run manager (like Piranha)
remotes::install_github("RichardHooijmaijers/shinyMixR")
# Simplify work with the `targets` package
remotes::install_github("nlmixr2/nlmixr2targets")
# Convert/run from nlmixr2-based models to NONMEM, Monolix, and initialize
# models with PKNCA
remotes::install_github("nlmixr2/babelmixr2")
# Convert from NONMEM to rxode2/nlmixr2-based models
remotes::install_github("nlmixr2/nonmem2rx")
# A library of models and model modification functions
remotes::install_github("nlmixr2/nlmixr2lib")
# Automated Microsoft Word and PowerPoint reporting for nlmixr2
remotes::install_github("nlmixr2/nlmixr2rpt")

Refreshing the installation with the latest CRAN version

If you have difficulties due to errors while compiling models, it may be useful to re-install all of nlmixr2 and its dependencies. For development versions, please use the remotes::install_github() or the install.package() with the r-universe above. For the stable version, please use the following command:

install.packages(c("dparser", "lotri", "rxode2ll", "rxode2parse",
                   "rxode2random", "rxode2et", "rxode2",
                   "nlmixr2data", "nlmixr2est", "nlmixr2extra",
                   "nlmixr2plot", "nlmixr2"))

Example

This is a basic example which shows you how to solve a common problem:

library(nlmixr2)

## The basic model consists of an ini block that has initial estimates
one.compartment <- function() {
  ini({
    tka <- log(1.57); label("Ka")
    tcl <- log(2.72); label("Cl")
    tv <- log(31.5); label("V")
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  # and a model block with the error specification and model specification
  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/nlmixr2 specifying the model, data and estimate
fit <- nlmixr2(one.compartment, theo_sd,  est="saem", saemControl(print=0))
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00 
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print(fit)
#> ── nlmixr² SAEM OBJF by FOCEi approximation ──
#> 
#>  Gaussian/Laplacian Likelihoods: AIC() or $objf etc. 
#>  FOCEi CWRES & Likelihoods: addCwres() 
#> 
#> ── Time (sec $time): ──
#> 
#>            setup covariance  saem table compress    other
#> elapsed 0.000891   0.020004 2.792 0.043    0.017 2.397105
#> 
#> ── Population Parameters ($parFixed or $parFixedDf): ──
#> 
#>        Parameter  Est.     SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)%
#> tka           Ka  0.46  0.196 42.7       1.58 (1.08, 2.33)     71.9    -0.291% 
#> tcl           Cl  1.01 0.0839 8.29       2.75 (2.34, 3.25)     27.0      3.42% 
#> tv             V  3.45 0.0469 1.36       31.6 (28.8, 34.7)     14.0      10.7% 
#> add.sd           0.694                               0.694                     
#>  
#>   Covariance Type ($covMethod): linFim
#>   No correlations in between subject variability (BSV) matrix
#>   Full BSV covariance ($omega) or correlation ($omegaR; diagonals=SDs) 
#>   Distribution stats (mean/skewness/kurtosis/p-value) available in $shrink 
#>   Censoring ($censInformation): No censoring
#> 
#> ── Fit Data (object is a modified tibble): ──
#> # A tibble: 132 × 19
#>   ID     TIME    DV  PRED    RES IPRED   IRES  IWRES eta.ka eta.cl   eta.v    cp
#>   <fct> <dbl> <dbl> <dbl>  <dbl> <dbl>  <dbl>  <dbl>  <dbl>  <dbl>   <dbl> <dbl>
#> 1 1      0     0.74  0     0.74   0     0.74   1.07  0.0988 -0.484 -0.0843  0   
#> 2 1      0.25  2.84  3.27 -0.433  3.87 -1.03  -1.49  0.0988 -0.484 -0.0843  3.87
#> 3 1      0.57  6.57  5.85  0.718  6.82 -0.247 -0.356 0.0988 -0.484 -0.0843  6.82
#> # ℹ 129 more rows
#> # ℹ 7 more variables: depot <dbl>, center <dbl>, ka <dbl>, cl <dbl>, v <dbl>,
#> #   tad <dbl>, dosenum <dbl>

Plotting outputs

Base R Graphics

You can use the built-in plot with the fit and it will produce a standard set of goodness of fit plots:

pdf(file="myplots.pdf")
plot(fit)
dev.off()

xpose.nlmixr2

The {xpose.nlmixr2} package extends xpose support for nlmixr2. You simply need to convert the fit results into an xpose database:

library(xpose.nlmixr2)
xpdb = xpose_data_nlmixr(fit)

Then you can use any of the xpose functions for generating goodness of fit plots:

library(xpose)
plt <- dv_vs_ipred(xpdb)

ggPMX

Another option is to use the ggPMX package. You first create a ggPMX controller object from the nlmixr fit object. Then that controller object can be used to generate figures:

library(ggPMX)
ctr = pmx_nlmixr(fit)
pmx_plot_dv_ipred(ctr)

nlmixr2data's Issues

Some datasets use less standard EVID values

Looking at the theo_sd dataset, I see that the EVID column is set to 101 instead of the value of 1 that I expected. Is it okay to change this to 1? Alternatively, should I accept 101 as a dosing EVID for the PKNCA link?