Save a fitted model object to a series of files
Usage
saveFit(fit, file, zip = TRUE, data = .nlmixr2saveData())
# S3 method for class 'nlmixr2FitCore'
saveFit(fit, file, zip = TRUE, data = .nlmixr2saveData())
# S3 method for class 'nlmixr2FitData'
saveFit(fit, file, zip = TRUE, data = .nlmixr2saveData())
# Default S3 method
saveFit(fit, file, zip = TRUE, data = .nlmixr2saveData())Arguments
- fit
the fitted model object
- file
the base name of the files to save the fit to. It may include a directory, e.g.
"path/to/fit": the files are written there (the directory is created if needed) and the archivepath/to/fit.zipholds them under the bare namefit, so it can be moved and loaded from anywhere.- zip
Boolean indicating if the files should be zipped.
- data
Boolean indicating whether the original dataset (
origData) is stored in the saved fit. WhenFALSEit is omitted, producing a fit that can be shared without the subject-level data (seenlmixr2saveShare()). Defaults togetOption("nlmixr2save.data", TRUE).
Examples
# \donttest{
if (requireNamespace("nlmixr2est", quietly=TRUE) &&
requireNamespace("nlmixr2data", quietly=TRUE) &&
requireNamespace("withr")) {
library(nlmixr2est)
library(nlmixr2data)
withr::with_tempdir({
one.cmt <- function() {
ini({
tka <- 0.45
tcl <- log(c(0, 2.7, 100))
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)
linCmt() ~ add(add.sd)
})
}
fit <- nlmixr2(one.cmt, theo_sd, est="focei")
saveFit(fit) # saved to fit.zip
fit2 <- loadFit(fit) # load fit.zip
if (file.exists("fit.zip")) {
unlink("fit.zip")
}
print(fit2)
})
}
#>
#>
#>
#>
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> → Calculating residuals/tables
#> ✔ done
#> ℹ saving fit item: .fdFullCov
#> ℹ saving fit item: .fdFullS
#> ℹ saving fit item: .rownum
#> ℹ saving fit item: AIC
#> ℹ saving fit item: BIC
#> 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: Rinv
#> 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: Sper
#> ℹ saving fit item: aqHi
#> ℹ saving fit item: aqLow
#> ℹ saving fit item: aqn
#> 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: covList
#> ℹ saving fit item: covLvl
#> ℹ saving fit item: covMethod
#> ℹ saving fit item: covOptions
#> 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: nConditionalInnerHessian
#> ℹ saving fit item: nEstOmega
#> ℹ saving fit item: nInnerRerank
#> ℹ saving fit item: nTrustInner
#> 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: ranef
#> ℹ saving fit item: runInfo
#> ℹ saving fit item: scaleInfo
#> ℹ saving fit item: sessioninfo
#> ℹ saving fit item: shrink
#> ℹ saving fit item: table
#> ℹ saving fit item: time
#> ℹ saving fit item: tolFactor
#> ℹ saving fit item: ui
#> ℹ zipping fit files
#> ℹ loading fit from fit.zip
#>
#>
#> ℹ parameter labels from comments are typically ignored in non-interactive mode
#> ℹ Need to run with the source intact to parse comments
#> ── nlmixr² FOCEi (outer: bobyqa) ──
#>
#> OBJF AIC BIC Log-likelihood Condition#(Cov) Condition#(Cor)
#> FOCEi 116.8076 373.4073 393.587 -179.7037 538873.5 3771.305
#>
#> ── Time (sec $time): ──
#>
#> setup optimize covariance preprocess postprocess table compress
#> elapsed 0.3862331 0.4304268 0.7344415 0.048 0.045 0.079 0.001
#> other
#> elapsed 0.2658987
#>
#> ── Population Parameters ($parFixed or $parFixedDf): ──
#>
#> Est. SE %RSE Back-transformed(95%CI) BSV(CV%) Shrink(SD)%
#> tka 0.472 0.208 44.1 1.60 (1.07, 2.41) 69.9 1.34
#> tcl 1.01 0.00728 0.719 2.75 (2.71, 2.79) 27.0 4.41
#> tv 3.46 0.0460 1.33 31.8 (29.1, 34.8) 13.9 10.4
#> add.sd 0.695 0.0940 13.5 0.695 (0.511, 0.880)
#>
#> Covariance Type ($covMethod): r,s (full)
#> other calculated covs (setCov()): r; s; r,s; r (full); s (full)
#> Some strong fixed parameter correlations exist ($cor) :
#> cor:tcl,tka cor:tv,tka cor:add.sd,tka
#> 0.316 0.288 -0.177
#> cor:om.eta.ka,tka cor:om.eta.cl,tka cor:om.eta.v,tka
#> 0.735 -0.163 -0.220
#> cor:tv,tcl cor:add.sd,tcl cor:om.eta.ka,tcl
#> -0.296 -0.281 0.260
#> cor:om.eta.cl,tcl cor:om.eta.v,tcl cor:add.sd,tv
#> -0.0127 0.178 -0.381
#> cor:om.eta.ka,tv cor:om.eta.cl,tv cor:om.eta.v,tv
#> 0.274 -0.102 -0.0694
#> cor:om.eta.ka,add.sd cor:om.eta.cl,add.sd cor:om.eta.v,add.sd
#> -0.411 -0.0705 -0.595
#> cor:om.eta.cl,om.eta.ka cor:om.eta.v,om.eta.ka cor:om.eta.v,om.eta.cl
#> -0.276 0.452 -0.0799
#>
#>
#> No correlations in between subject variability (BSV) matrix
#> Full BSV covariance ($omega) or correlation ($omegaR; diagonals=SDs)
#> Distribution stats (mean/skewness/kurtosis/p-value) available in $shrink
#> Information about run found ($runInfo):
#> • gradient problems with covariance; see $scaleInfo
#> • last objective function was not at minimum, possible problems in optimization
#> • ETAs were reset to zero during optimization; (Can control by foceiControl(resetEtaP=.))
#> Censoring ($censInformation): No censoring
#> Minimization message ($message):
#> Normal exit from bobyqa
#>
#> ── Fit Data (object is a modified tibble): ──
#> # A tibble: 132 × 22
#> ID TIME DV PRED RES WRES IPRED IRES IWRES CPRED CRES CWRES
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0 0.74 0 0.74 1.06 0 0.74 1.06 0 0.74 1.06
#> 2 1 0.25 2.84 3.28 -0.445 -0.237 3.85 -1.01 -1.45 3.24 -0.404 -0.190
#> 3 1 0.57 6.57 5.86 0.711 0.287 6.79 -0.216 -0.310 5.81 0.763 0.278
#> # ℹ 129 more rows
#> # ℹ 10 more variables: eta.ka <dbl>, eta.cl <dbl>, eta.v <dbl>, depot <dbl>,
#> # central <dbl>, ka <dbl>, cl <dbl>, v <dbl>, tad <dbl>, dosenum <int>
# }