nlmixr2save

The goal of nlmixr2save is to save a nlmixr2 fit in file formats that can be read outside R, avoiding .rds or other formats as much as possible.

Installation

You can install the development version of nlmixr2save from GitHub with:

# install.packages("remotes")
remotes::install_github("nlmixr2/nlmixr2save")

Example

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

library(nlmixr2)
#> ── Attaching packages ───────────────────────────────────────── nlmixr2 5.0.0 ──
#> ✔ lotri         1.0.2          ✔ monolix2rx    0.0.6     
#> ✔ nlmixr2data   2.0.9          ✔ nlmixr2lib    0.3.2     
#> ✔ nlmixr2est    5.0.2.9000     ✔ nlmixr2rpt    0.2.2     
#> ✔ nlmixr2extra  5.0.0          ✔ nonmem2rx     0.1.9     
#> ✔ nlmixr2plot   5.0.0          ✔ posologyr     1.2.8     
#> ✔ rxode2        5.0.1.9000     ✔ shinyMixR     0.5.3     
#> ✔ babelmixr2    0.1.11         ✔ xpose.nlmixr2 0.4.1     
#> ✔ ggPMX         1.3.2
#> ── Optional Packages Loaded/Ignored ─────────────────────────── nlmixr2 5.0.0 ──
#> ✔ babelmixr2        ✔ nonmem2rx    
#> ✔ ggPMX             ✔ posologyr    
#> ✔ monolix2rx        ✔ shinyMixR    
#> ✔ nlmixr2lib        ✔ xpose.nlmixr2
#> ✔ nlmixr2rpt
#> ── Conflicts ───────────────────────────────────────────── nlmixr2conflicts() ──
#> ✖ rxode2::boxCox()     masks nlmixr2est::boxCox()
#> ✖ rxode2::yeoJohnson() masks nlmixr2est::yeoJohnson()
library(nlmixr2save) # eventually nlmixr2 will include this if available
one.cmt <- function() {
  ini({
    ## You may label each parameter with a comment
    tka <- 0.45 # Log Ka
    tcl <- log(c(0, 2.7, 100)) # Log Cl
    ## This works with interactive models
    ## You may also label the preceding line with label("label text")
    tv <- 3.45; label("log V")
    ## the label("Label name") works with all models
    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)
    linCmt() ~ add(add.sd)
  })
}

fitF <- suppressMessages(nlmixr(one.cmt, theo_sd, est="focei",
                                control=list(print=0, compress=FALSE)))
#> calculating covariance matrix
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00 
#> done

saveFit(fitF)
#> ℹ saving fit item: .rownum
#> ℹ saving fit item: AIC
#> ℹ saving fit item: aqHi
#> ℹ saving fit item: aqLow
#> ℹ saving fit item: aqn
#> ℹ saving fit item: BIC
#> ℹ saving fit item: censInformation
#> ℹ saving fit item: cholR
#> ℹ saving fit item: cholS
#> ℹ saving fit item: conditionNumberCor
#> ℹ saving fit item: conditionNumberCov
#> ℹ saving fit item: convergence
#> ℹ saving fit item: cov
#> ℹ saving fit item: covLvl
#> ℹ saving fit item: covMethod
#> ℹ saving fit item: covR
#> ℹ saving fit item: covRS
#> ℹ saving fit item: covS
#> ℹ saving fit item: eigenCor
#> ℹ saving fit item: eigenCov
#> ℹ saving fit item: eigenVecCor
#> ℹ saving fit item: eigenVecCov
#> ℹ saving fit item: est
#> ℹ saving fit item: etaObf
#> ℹ saving fit item: extra
#> ℹ saving fit item: fixef
#> ℹ saving fit item: foceiControl0
#> ℹ saving fit item: foceiModel
#> ℹ saving fit item: fullCor
#> ℹ saving fit item: iniDf0
#> ℹ saving fit item: llikObs
#> ℹ saving fit item: logLik
#> ℹ saving fit item: message
#> ℹ saving fit item: method
#> ℹ saving fit item: mixIdx
#> ℹ saving fit item: nAGQ
#> ℹ saving fit item: nEstOmega
#> ℹ saving fit item: nobs
#> ℹ saving fit item: nsub
#> ℹ saving fit item: objDf
#> ℹ saving fit item: objective
#> ℹ saving fit item: ofvType
#> ℹ saving fit item: omega
#> ℹ saving fit item: optReturn
#> ℹ saving fit item: origData
#> ℹ saving fit item: parFixed
#> ℹ saving fit item: parFixedDf
#> ℹ saving fit item: parHistData
#> ℹ saving fit item: phiC
#> ℹ saving fit item: phiH
#> ℹ saving fit item: qfirst
#> ℹ saving fit item: qw
#> ℹ saving fit item: qx
#> ℹ saving fit item: R
#> ℹ saving fit item: R.0
#> ℹ saving fit item: R.E
#> ℹ saving fit item: R.pd
#> ℹ saving fit item: ranef
#> ℹ saving fit item: Rinv
#> ℹ saving fit item: runInfo
#> ℹ saving fit item: S
#> ℹ saving fit item: S.E
#> ℹ saving fit item: S.pd
#> ℹ saving fit item: S0
#> ℹ saving fit item: scaleInfo
#> ℹ saving fit item: sessioninfo
#> ℹ saving fit item: shrink
#> ℹ saving fit item: Sper
#> ℹ saving fit item: table
#> ℹ saving fit item: time
#> ℹ saving fit item: ui
#> ℹ zipping fit files
#> ℹ removing unzipped fit files

This creates a “.zip” file that includes a “fitF.R” file. This fit builds the fit from (mostly) csv and R source files.

The reason for this extra package saving models:

• The model properties and results can be examined outside of R

• This model can be saved without worrying how data are serialized and/or compressed

• This saved model version should be independent of the version of rxode2 and nlmixr2, whereas other methods of saving are dependent on the version of nlmixr2/rxode2

In the future, this could be used in conjunction with vroom, altrep and other similar tools to partially load fit without loading the corresponding datasets.