Writes a portable .zip copy of a saved fit that omits the original dataset
(the subject-level data), so a fitted model can be shared without its data.
The input may be a live fit object or the base name of an existing saved fit
.zip; either way the original is left unchanged and new sibling zips are
written. Names are resolved through getOption("nlmixr2save.dir") and
getOption("nlmixr2save.prefix") (as for the := cache).
Arguments
- x
a fitted model object, or the base name (no extension) of a saved fit
.zipto read.- noFit
Boolean; when
TRUE, also strip the output tables (the returned prediction/residual data.frame), writing<file>-noData-noFit.zipinstead of<file>-noData.zip.- file
optional output base name; defaults to the name of
x.
Details
nlmixr2saveShare("fit")writesfit-noData.zip– the full fit (predictions and tables intact) with the original data removed.nlmixr2saveShare("fit", noFit=TRUE)writesfit-noData-noFit.zip– the core fit only (model, parameter estimates, objective,omega,etaObf,parHistData), with both the original data and the returned prediction/residual table removed.
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) # fit.zip (with data)
nlmixr2saveShare("fit") # fit-noData.zip
nlmixr2saveShare("fit", noFit=TRUE) # fit-noData-noFit.zip
})
}
#>
#>
#>
#>
#> 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: 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: 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 removing unzipped fit files
#> ℹ loading fit from fit.R
#> lotri syntax error:
#> =================================================================================
#> :001: tka ~ c(tka = 0.0367813010669496)
#> :002: tcl ~ c(tka = -0.000782456725690811, tcl = 0.0069543545026029)
#> :003: tv ~ c(tka = 0.000952366834165392, tcl = -0.000489959598361193, tv = 0.00218330787936497)
#> :004: add.sd ~ c(tka = -6.41258631708858e-05, tcl = -5.67004131128066e-05, tv = 3.82936894597721e-05, add.sd = 0.00243929995816957)
#> lotri error:
#> matrix expression should be 'name ~ c(lower-tri)'
#> :005: om.eta.ka ~ c(tka = 0.000146993075376898, tcl = 0.000126165231341427, tv = -0.000127191366433412, add.sd = -0.000541130240379496, om.eta.ka = 0.0353763038424305)
#> lotri error:
#> number named variables and lower triangular matrix size do not match
#> did you mean something like:
#> 'om.eta.cl + varName2 + varName3 ~ c(-0.000117433625253258,
#> 0.000125380229779247, -6.81577112109223e-05,
#> 9.82139979915425e-06, -0.00012172625636792, 0.00118026544368931)
#> :006: om.eta.cl ~ c(tka = -0.000117433625253258, tcl = 0.000125380229779247, tv = -6.81577112109223e-05, add.sd = 9.82139979915425e-06, om.eta.ka = -0.00012172625636792, om.eta.cl = 0.00118026544368931)
#> lotri error:
#> matrix expression should be 'name ~ c(lower-tri)'
#> :007: om.eta.v ~ c(tka = 7.85881365155322e-05, tcl = -3.00853221214718e-05, tv = 5.01075513373757e-05, add.sd = -2.91997524119011e-05, om.eta.ka = 0.000117120738078429, om.eta.cl = -8.31373925204361e-05, om.eta.v = 0.000124134785919267)
#> =================================================================================
#> Error: lotri syntax errors above
# }