Control for nlmer estimation method in nlmixr2

Control for nlmer estimation method in nlmixr2

Usage

nlmixr2NlmerControl(
  optimizer = "bobyqa",
  tolPwrss = 1e-07,
  optCtrl = list(),
  returnNlmer = FALSE,
  muRefCovAlg = TRUE,
  eventSens = c("jump", "fd"),
  eventType = c("central", "forward"),
  shiErr = (.Machine$double.eps)^(1/3),
  shi21maxFD = 20L,
  stickyRecalcN = 4,
  maxOdeRecalc = 5,
  odeRecalcFactor = 10^(0.5),
  useColor = NULL,
  printNcol = NULL,
  print = 1L,
  optExpression = TRUE,
  literalFix = TRUE,
  sumProd = FALSE,
  rxControl = NULL,
  calcTables = TRUE,
  compress = TRUE,
  adjObf = TRUE,
  ci = 0.95,
  sigdig = 4,
  sigdigTable = NULL,
  addProp = c("combined2", "combined1"),
  ...
)

nlmerControl(
  optimizer = "bobyqa",
  tolPwrss = 1e-07,
  optCtrl = list(),
  returnNlmer = FALSE,
  muRefCovAlg = TRUE,
  eventSens = c("jump", "fd"),
  eventType = c("central", "forward"),
  shiErr = (.Machine$double.eps)^(1/3),
  shi21maxFD = 20L,
  stickyRecalcN = 4,
  maxOdeRecalc = 5,
  odeRecalcFactor = 10^(0.5),
  useColor = NULL,
  printNcol = NULL,
  print = 1L,
  optExpression = TRUE,
  literalFix = TRUE,
  sumProd = FALSE,
  rxControl = NULL,
  calcTables = TRUE,
  compress = TRUE,
  adjObf = TRUE,
  ci = 0.95,
  sigdig = 4,
  sigdigTable = NULL,
  addProp = c("combined2", "combined1"),
  ...
)

Arguments

optimizer

passed to lme4::nlmerControl(): optimizer to use

tolPwrss

passed to lme4::nlmerControl(): tolerance for the penalized, weighted residual sum-of-squares (PWRSS) inner iterations

optCtrl

a list of additional control parameters passed to the nonlinear optimizer via lme4::nlmerControl()

returnNlmer

logical; when TRUE return the raw lme4 nlmerMod object instead of the nlmixr2 fit

muRefCovAlg

logical; when TRUE apply mu2 covariate referencing algebraic transformation (same as saem)

eventSens

method used for the dosing-parameter (alag/F/rate/dur) sensitivities in the analytic gradient model: "jump" routes them through rxode2's analytic event jumps; "fd" falls back to Shi2021 finite differences. See nlmixr2est::nlmControl().

eventType

finite-difference type ("central" or "forward") used for event-related parameters when eventSens = "fd"

shiErr

epsilon used when optimizing the ideal finite-difference step size with the Shi2021 method

shi21maxFD

maximum number of Shi2021 step-size optimization iterations for the gradient

stickyRecalcN

number of bad ODE solves tolerated before the per-subject tolerance is stickily relaxed

maxOdeRecalc

maximum number of times to retry a bad ODE solve with a relaxed tolerance

odeRecalcFactor

factor by which atol/rtol are relaxed on an ODE solve retry

useColor

Logical (or `NULL`) emit ANSI bold/color escapes in the iteration print. `NULL` (default) defers to [crayon::has_color()].

printNcol

Integer (or `NULL`) parameter columns per row before wrapping. `NULL` (default) uses `floor((getOption("width") - 23) / 12)`.

print

Either a scalar print-frequency (`0` = suppress, `1` (default) = every evaluation, `N` = every Nth), OR a pre-built [iterPrintControl()] object. Equivalent to `iterPrintControl(every = print, ncol = printNcol, useColor = useColor)`.

optExpression

Optimize the rxode2 expression to speed up calculation. By default this is turned on.

literalFix

boolean, substitute fixed population values as literals and re-adjust ui and parameter estimates after optimization; Default is `TRUE`.

sumProd

Is a boolean indicating if the model should change multiplication to high precision multiplication and sums to high precision sums using the PreciseSums package. By default this is FALSE.

rxControl

`rxode2` ODE solving options during fitting, created with `rxControl()`

calcTables

This boolean is to determine if the foceiFit will calculate tables. By default this is TRUE

compress

Should the object have compressed items

adjObf

is a boolean to indicate if the objective function should be adjusted to be closer to NONMEM's default objective function. By default this is TRUE

ci

Confidence level for some tables. By default this is 0.95 or 95% confidence.

sigdig

Optimization significant digits; controls the inner/outer optimization tolerance (10^-sigdig), ODE solver tolerance (0.5*10^(-sigdig-2), or 0.5*10^(-sigdig-1.5) for sensitivity/steady-state with liblsoda), and boundary check tolerance (5*10^(-sigdig+1)).

sigdigTable

Significant digits in the final output table. If not specified, then it matches the significant digits in the `sigdig` optimization algorithm. If `sigdig` is NULL, use 3.

addProp

Type of additive-plus-proportional error: `"combined1"`, where standard deviations add: $$y = f + (a + b\times f^c) \times \varepsilon$$; or `"combined2"`, where variances add: $$y = f + \sqrt{a^2 + b^2\times f^{2\times c}} \times \varepsilon$$. Here y = observed, f = predicted, a = additive sd, b = proportional/power sd, c = power exponent (1 in the proportional case).

...

Ignored parameters

Value

nlmer control structure

Author

Matthew L. Fidler

Examples

nlmerControl()
#> $optimizer
#> [1] "bobyqa"
#> 
#> $tolPwrss
#> [1] 1e-07
#> 
#> $optCtrl
#> list()
#> 
#> $returnNlmer
#> [1] FALSE
#> 
#> $muRefCovAlg
#> [1] TRUE
#> 
#> $eventSens
#> [1] "jump"
#> 
#> $eventType
#> [1] "central"
#> 
#> $shiErr
#> [1] 6.055454e-06
#> 
#> $shi21maxFD
#> [1] 20
#> 
#> $stickyRecalcN
#> [1] 4
#> 
#> $maxOdeRecalc
#> [1] 5
#> 
#> $odeRecalcFactor
#> [1] 3.162278
#> 
#> $iterPrintControl
#> $every
#> [1] 1
#> 
#> $ncol
#> [1] 4
#> 
#> $headerEvery
#> [1] 10
#> 
#> $useColor
#> [1] TRUE
#> 
#> $simple
#> [1] FALSE
#> 
#> attr(,"class")
#> [1] "iterPrintControl" "list"            
#> 
#> $optExpression
#> [1] TRUE
#> 
#> $literalFix
#> [1] TRUE
#> 
#> $sumProd
#> [1] FALSE
#> 
#> $rxControl
#> $scale
#> NULL
#> 
#> $method
#> liblsoda 
#>        2 
#> 
#> $atol
#> [1] 5e-07
#> 
#> $rtol
#> [1] 5e-07
#> 
#> $maxsteps
#> [1] 70000
#> 
#> $hmin
#> [1] 0
#> 
#> $hmax
#> [1] NA
#> 
#> $hini
#> [1] 0
#> 
#> $maxordn
#> [1] 12
#> 
#> $maxords
#> [1] 5
#> 
#> $covsInterpolation
#> locf 
#>    1 
#> 
#> $addCov
#> [1] TRUE
#> 
#> $returnType
#> rxSolve 
#>       0 
#> 
#> $sigma
#> NULL
#> 
#> $sigmaDf
#> NULL
#> 
#> $nCoresRV
#> [1] 1
#> 
#> $sigmaIsChol
#> [1] FALSE
#> 
#> $sigmaSeparation
#> [1] "auto"
#> 
#> $sigmaXform
#> identity 
#>        4 
#> 
#> $nDisplayProgress
#> [1] 10000
#> 
#> $amountUnits
#> [1] NA
#> 
#> $timeUnits
#> [1] "hours"
#> 
#> $addDosing
#> [1] FALSE
#> 
#> $stateTrim
#> [1] Inf
#> 
#> $updateObject
#> [1] FALSE
#> 
#> $omega
#> NULL
#> 
#> $omegaDf
#> NULL
#> 
#> $omegaIsChol
#> [1] FALSE
#> 
#> $omegaSeparation
#> [1] "auto"
#> 
#> $omegaXform
#> variance 
#>        6 
#> 
#> $nSub
#> [1] 1
#> 
#> $thetaMat
#> NULL
#> 
#> $thetaDf
#> NULL
#> 
#> $thetaIsChol
#> [1] FALSE
#> 
#> $nStud
#> [1] 1
#> 
#> $dfSub
#> [1] 0
#> 
#> $dfObs
#> [1] 0
#> 
#> $seed
#> NULL
#> 
#> $nsim
#> NULL
#> 
#> $minSS
#> [1] 10
#> 
#> $maxSS
#> [1] 10000
#> 
#> $strictSS
#> [1] 1
#> 
#> $infSSstep
#> [1] 12
#> 
#> $istateReset
#> [1] TRUE
#> 
#> $subsetNonmem
#> [1] TRUE
#> 
#> $hmaxSd
#> [1] 0
#> 
#> $maxAtolRtolFactor
#> [1] 0.1
#> 
#> $from
#> NULL
#> 
#> $to
#> NULL
#> 
#> $by
#> NULL
#> 
#> $length.out
#> NULL
#> 
#> $iCov
#> NULL
#> 
#> $keep
#> NULL
#> 
#> $keepF
#> character(0)
#> 
#> $drop
#> NULL
#> 
#> $warnDrop
#> [1] TRUE
#> 
#> $omegaLower
#> [1] -Inf
#> 
#> $omegaUpper
#> [1] Inf
#> 
#> $sigmaLower
#> [1] -Inf
#> 
#> $sigmaUpper
#> [1] Inf
#> 
#> $thetaLower
#> [1] -Inf
#> 
#> $thetaUpper
#> [1] Inf
#> 
#> $indLinPhiM
#> [1] 0
#> 
#> $indLinPhiTol
#> [1] 1e-07
#> 
#> $indLinMatExpType
#> expokit 
#>       2 
#> 
#> $indLinMatExpOrder
#> [1] 6
#> 
#> $idFactor
#> [1] TRUE
#> 
#> $mxhnil
#> [1] 0
#> 
#> $hmxi
#> [1] 0
#> 
#> $warnIdSort
#> [1] TRUE
#> 
#> $ssAtol
#> [1] 5e-05
#> 
#> $ssRtol
#> [1] 5e-05
#> 
#> $safeZero
#> [1] 1
#> 
#> $sumType
#> pairwise 
#>        1 
#> 
#> $prodType
#> long double 
#>           1 
#> 
#> $resample
#> NULL
#> 
#> $resampleID
#> [1] TRUE
#> 
#> $maxwhile
#> [1] 100000
#> 
#> $cores
#> [1] 0
#> 
#> $atolSens
#> [1] 1.581139e-06
#> 
#> $rtolSens
#> [1] 1.581139e-06
#> 
#> $ssAtolSens
#> [1] 0.0002108483
#> 
#> $ssRtolSens
#> [1] 0.0002108483
#> 
#> $simVariability
#> [1] NA
#> 
#> $nLlikAlloc
#> NULL
#> 
#> $useStdPow
#> [1] 0
#> 
#> $naTimeHandle
#> ignore 
#>      1 
#> 
#> $addlKeepsCov
#> [1] FALSE
#> 
#> $addlDropSs
#> [1] TRUE
#> 
#> $ssAtDoseTime
#> [1] TRUE
#> 
#> $ss2cancelAllPending
#> [1] FALSE
#> 
#> $naInterpolation
#> locf 
#>    1 
#> 
#> $keepInterpolation
#> na 
#>  2 
#> 
#> $safeLog
#> [1] 1
#> 
#> $safePow
#> [1] 1
#> 
#> $ssSolved
#> [1] TRUE
#> 
#> $linCmtSensType
#> auto 
#>  100 
#> 
#> $linCmtSensH
#> [1] 1e-04
#> 
#> $linCmtGillFtol
#> [1] 0
#> 
#> $linCmtGillK
#> [1] 20
#> 
#> $linCmtGillStep
#> [1] 4
#> 
#> $linCmtGillRtol
#> [1] 1.490116e-08
#> 
#> $linCmtShiErr
#> [1] 1.490116e-08
#> 
#> $linCmtShiMax
#> [1] 20
#> 
#> $linCmtScale
#> [1] 0 0 0 0 0 0 0
#> 
#> $linCmtHcmt
#> [1] 1
#> 
#> $linCmtHmeanI
#> geometric 
#>         2 
#> 
#> $linCmtHmeanO
#> geometric 
#>         2 
#> 
#> $linCmtSuspect
#> [1] 1e-06
#> 
#> $linCmtForwardMax
#> [1] 2
#> 
#> $indOwnAlloc
#> [1] -1
#> 
#> $maxExtra
#> [1] 1000
#> 
#> $tolFactor
#> NULL
#> 
#> $serializeFile
#> NULL
#> 
#> $dense
#> [1] FALSE
#> 
#> $cvodeLinSolver
#> dense 
#>     1 
#> 
#> $stiff2
#> [1] 0
#> 
#> $autoSwitchMaxStiff
#> [1] 10
#> 
#> $autoSwitchMaxNonstiff
#> [1] 3
#> 
#> $autoSwitchStiffFirst
#> [1] 0
#> 
#> $autoSwitchNonstifftol
#> [1] 0.9
#> 
#> $autoSwitchStifftol
#> [1] 0.9
#> 
#> $autoSwitchDtfac
#> [1] 2
#> 
#> $autoSwitchSwitchMax
#> [1] 5
#> 
#> $useLinCmt
#> [1] TRUE
#> 
#> $file
#> NULL
#> 
#> $chunkSize
#> NULL
#> 
#> $parallel
#> [1] 0
#> 
#> $.zeros
#> NULL
#> 
#> attr(,"class")
#> [1] "rxControl"
#> 
#> $calcTables
#> [1] TRUE
#> 
#> $compress
#> [1] TRUE
#> 
#> $adjObf
#> [1] TRUE
#> 
#> $ci
#> [1] 0.95
#> 
#> $sigdig
#> [1] 4
#> 
#> $sigdigTable
#> [1] 4
#> 
#> $addProp
#> [1] "combined2"
#> 
#> $genRxControl
#> [1] TRUE
#> 
#> attr(,"class")
#> [1] "nlmerControl"
nlmixr2NlmerControl()
#> $optimizer
#> [1] "bobyqa"
#> 
#> $tolPwrss
#> [1] 1e-07
#> 
#> $optCtrl
#> list()
#> 
#> $returnNlmer
#> [1] FALSE
#> 
#> $muRefCovAlg
#> [1] TRUE
#> 
#> $eventSens
#> [1] "jump"
#> 
#> $eventType
#> [1] "central"
#> 
#> $shiErr
#> [1] 6.055454e-06
#> 
#> $shi21maxFD
#> [1] 20
#> 
#> $stickyRecalcN
#> [1] 4
#> 
#> $maxOdeRecalc
#> [1] 5
#> 
#> $odeRecalcFactor
#> [1] 3.162278
#> 
#> $iterPrintControl
#> $every
#> [1] 1
#> 
#> $ncol
#> [1] 4
#> 
#> $headerEvery
#> [1] 10
#> 
#> $useColor
#> [1] TRUE
#> 
#> $simple
#> [1] FALSE
#> 
#> attr(,"class")
#> [1] "iterPrintControl" "list"            
#> 
#> $optExpression
#> [1] TRUE
#> 
#> $literalFix
#> [1] TRUE
#> 
#> $sumProd
#> [1] FALSE
#> 
#> $rxControl
#> $scale
#> NULL
#> 
#> $method
#> liblsoda 
#>        2 
#> 
#> $atol
#> [1] 5e-07
#> 
#> $rtol
#> [1] 5e-07
#> 
#> $maxsteps
#> [1] 70000
#> 
#> $hmin
#> [1] 0
#> 
#> $hmax
#> [1] NA
#> 
#> $hini
#> [1] 0
#> 
#> $maxordn
#> [1] 12
#> 
#> $maxords
#> [1] 5
#> 
#> $covsInterpolation
#> locf 
#>    1 
#> 
#> $addCov
#> [1] TRUE
#> 
#> $returnType
#> rxSolve 
#>       0 
#> 
#> $sigma
#> NULL
#> 
#> $sigmaDf
#> NULL
#> 
#> $nCoresRV
#> [1] 1
#> 
#> $sigmaIsChol
#> [1] FALSE
#> 
#> $sigmaSeparation
#> [1] "auto"
#> 
#> $sigmaXform
#> identity 
#>        4 
#> 
#> $nDisplayProgress
#> [1] 10000
#> 
#> $amountUnits
#> [1] NA
#> 
#> $timeUnits
#> [1] "hours"
#> 
#> $addDosing
#> [1] FALSE
#> 
#> $stateTrim
#> [1] Inf
#> 
#> $updateObject
#> [1] FALSE
#> 
#> $omega
#> NULL
#> 
#> $omegaDf
#> NULL
#> 
#> $omegaIsChol
#> [1] FALSE
#> 
#> $omegaSeparation
#> [1] "auto"
#> 
#> $omegaXform
#> variance 
#>        6 
#> 
#> $nSub
#> [1] 1
#> 
#> $thetaMat
#> NULL
#> 
#> $thetaDf
#> NULL
#> 
#> $thetaIsChol
#> [1] FALSE
#> 
#> $nStud
#> [1] 1
#> 
#> $dfSub
#> [1] 0
#> 
#> $dfObs
#> [1] 0
#> 
#> $seed
#> NULL
#> 
#> $nsim
#> NULL
#> 
#> $minSS
#> [1] 10
#> 
#> $maxSS
#> [1] 10000
#> 
#> $strictSS
#> [1] 1
#> 
#> $infSSstep
#> [1] 12
#> 
#> $istateReset
#> [1] TRUE
#> 
#> $subsetNonmem
#> [1] TRUE
#> 
#> $hmaxSd
#> [1] 0
#> 
#> $maxAtolRtolFactor
#> [1] 0.1
#> 
#> $from
#> NULL
#> 
#> $to
#> NULL
#> 
#> $by
#> NULL
#> 
#> $length.out
#> NULL
#> 
#> $iCov
#> NULL
#> 
#> $keep
#> NULL
#> 
#> $keepF
#> character(0)
#> 
#> $drop
#> NULL
#> 
#> $warnDrop
#> [1] TRUE
#> 
#> $omegaLower
#> [1] -Inf
#> 
#> $omegaUpper
#> [1] Inf
#> 
#> $sigmaLower
#> [1] -Inf
#> 
#> $sigmaUpper
#> [1] Inf
#> 
#> $thetaLower
#> [1] -Inf
#> 
#> $thetaUpper
#> [1] Inf
#> 
#> $indLinPhiM
#> [1] 0
#> 
#> $indLinPhiTol
#> [1] 1e-07
#> 
#> $indLinMatExpType
#> expokit 
#>       2 
#> 
#> $indLinMatExpOrder
#> [1] 6
#> 
#> $idFactor
#> [1] TRUE
#> 
#> $mxhnil
#> [1] 0
#> 
#> $hmxi
#> [1] 0
#> 
#> $warnIdSort
#> [1] TRUE
#> 
#> $ssAtol
#> [1] 5e-05
#> 
#> $ssRtol
#> [1] 5e-05
#> 
#> $safeZero
#> [1] 1
#> 
#> $sumType
#> pairwise 
#>        1 
#> 
#> $prodType
#> long double 
#>           1 
#> 
#> $resample
#> NULL
#> 
#> $resampleID
#> [1] TRUE
#> 
#> $maxwhile
#> [1] 100000
#> 
#> $cores
#> [1] 0
#> 
#> $atolSens
#> [1] 1.581139e-06
#> 
#> $rtolSens
#> [1] 1.581139e-06
#> 
#> $ssAtolSens
#> [1] 0.0002108483
#> 
#> $ssRtolSens
#> [1] 0.0002108483
#> 
#> $simVariability
#> [1] NA
#> 
#> $nLlikAlloc
#> NULL
#> 
#> $useStdPow
#> [1] 0
#> 
#> $naTimeHandle
#> ignore 
#>      1 
#> 
#> $addlKeepsCov
#> [1] FALSE
#> 
#> $addlDropSs
#> [1] TRUE
#> 
#> $ssAtDoseTime
#> [1] TRUE
#> 
#> $ss2cancelAllPending
#> [1] FALSE
#> 
#> $naInterpolation
#> locf 
#>    1 
#> 
#> $keepInterpolation
#> na 
#>  2 
#> 
#> $safeLog
#> [1] 1
#> 
#> $safePow
#> [1] 1
#> 
#> $ssSolved
#> [1] TRUE
#> 
#> $linCmtSensType
#> auto 
#>  100 
#> 
#> $linCmtSensH
#> [1] 1e-04
#> 
#> $linCmtGillFtol
#> [1] 0
#> 
#> $linCmtGillK
#> [1] 20
#> 
#> $linCmtGillStep
#> [1] 4
#> 
#> $linCmtGillRtol
#> [1] 1.490116e-08
#> 
#> $linCmtShiErr
#> [1] 1.490116e-08
#> 
#> $linCmtShiMax
#> [1] 20
#> 
#> $linCmtScale
#> [1] 0 0 0 0 0 0 0
#> 
#> $linCmtHcmt
#> [1] 1
#> 
#> $linCmtHmeanI
#> geometric 
#>         2 
#> 
#> $linCmtHmeanO
#> geometric 
#>         2 
#> 
#> $linCmtSuspect
#> [1] 1e-06
#> 
#> $linCmtForwardMax
#> [1] 2
#> 
#> $indOwnAlloc
#> [1] -1
#> 
#> $maxExtra
#> [1] 1000
#> 
#> $tolFactor
#> NULL
#> 
#> $serializeFile
#> NULL
#> 
#> $dense
#> [1] FALSE
#> 
#> $cvodeLinSolver
#> dense 
#>     1 
#> 
#> $stiff2
#> [1] 0
#> 
#> $autoSwitchMaxStiff
#> [1] 10
#> 
#> $autoSwitchMaxNonstiff
#> [1] 3
#> 
#> $autoSwitchStiffFirst
#> [1] 0
#> 
#> $autoSwitchNonstifftol
#> [1] 0.9
#> 
#> $autoSwitchStifftol
#> [1] 0.9
#> 
#> $autoSwitchDtfac
#> [1] 2
#> 
#> $autoSwitchSwitchMax
#> [1] 5
#> 
#> $useLinCmt
#> [1] TRUE
#> 
#> $file
#> NULL
#> 
#> $chunkSize
#> NULL
#> 
#> $parallel
#> [1] 0
#> 
#> $.zeros
#> NULL
#> 
#> attr(,"class")
#> [1] "rxControl"
#> 
#> $calcTables
#> [1] TRUE
#> 
#> $compress
#> [1] TRUE
#> 
#> $adjObf
#> [1] TRUE
#> 
#> $ci
#> [1] 0.95
#> 
#> $sigdig
#> [1] 4
#> 
#> $sigdigTable
#> [1] 4
#> 
#> $addProp
#> [1] "combined2"
#> 
#> $genRxControl
#> [1] TRUE
#> 
#> attr(,"class")
#> [1] "nlmerControl"