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nonmemControl.R
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nonmemControl.R
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#' NONMEM estimation control
#'
#' @param est NONMEM estimation method
#' @param advanOde The ODE solving method for NONMEM
#' @param cov The NONMEM covariance method
#' @param maxeval NONMEM's maxeval (for non posthoc methods)
#' @param tol NONMEM tolerance for ODE solving advan
#' @param sigl NONMEM sigl estimation option
#' @param sigdig the significant digits for NONMEM
#' @param print The print number for NONMEM
#' @param extension NONMEM file extensions
#' @param protectZeros Add methods to protect divide by zero
#' @param noabort Add the `NOABORT` option for `$EST`
#'
#' @return babelmixr control option for generating NONMEM control stream and reading it back into
#' `babelmixr2`/`nlmixr2`
#'
#' @author Matthew L. Fidler
#'
#' @export
#'
#' @examples
#' nonmemControl()
nonmemControl <- function(est=c("focei", "imp", "its", "posthoc"),
advanOde=c("advan13", "advan8", "advan6"),
cov=c("r,s", "r", "s", ""),
maxeval=100000,
tol=6,
sigl=12,
sigdig=3,
print=1,
extension=getOption("babelmixr2.nmModelExtension", ".nmctl"),
outputExtension=getOption("babelmixr2.nmOutputExtension", ".lst"),
runCommand=getOption("babelmixr2.nonmem", ""),
iniSigDig=5,
protectZeros=TRUE,
muRef=TRUE,
addProp = c("combined2", "combined1"),
rxControl=NULL,
sumProd = FALSE,
optExpression = TRUE,
calcTables = TRUE,
compress = TRUE,
ci = 0.95,
sigdigTable=NULL,
readRounding=FALSE,
readBadOpt=FALSE,
niter=100L,
isample=1000L,
iaccept=0.4,
iscaleMin=0.1,
iscaleMax=10,
df=4,
seed=14456,
mapiter=1,
mapinter=0,
noabort=TRUE, ...) {
# nonmem manual slides suggest tol=6, sigl=6 sigdig=2
checkmate::assertIntegerish(maxeval, lower=100, len=1, any.missing=FALSE)
checkmate::assertIntegerish(sigdig, lower=1, len=1, any.missing=FALSE)
checkmate::assertIntegerish(print, lower=1, len=1, any.missing=FALSE)
checkmate::assertLogical(noabort, len=1, any.missing=FALSE)
checkmate::assertIntegerish(tol, lower=1, len=1, any.missing=FALSE)
checkmate::assertIntegerish(sigl, lower=1, upper=14, len=1, any.missing=FALSE)
checkmate::assertIntegerish(iniSigDig, lower=1, len=1, any.missing=FALSE)
checkmate::assertLogical(protectZeros, len=1, any.missing=FALSE)
checkmate::assertLogical(muRef, len=1, any.missing=FALSE)
checkmate::assertLogical(readRounding, len=1, any.missing=FALSE)
checkmate::assertLogical(readBadOpt, len=1, any.missing=FALSE)
checkmate::assertIntegerish(niter, lower=1, len=1, any.missing=FALSE)
checkmate::assertIntegerish(isample, lower=1, len=1, any.missing=FALSE)
checkmate::assertNumeric(iaccept, lower=0, upper=1, len=1, any.missing=FALSE)
checkmate::assertNumeric(iscaleMin, lower=0, len=1, any.missing=FALSE)
checkmate::assertNumeric(iscaleMax, lower=0, len=1, any.missing=FALSE)
checkmate::assertNumeric(df, lower=0, len=1, any.missing=FALSE)
checkmate::assertIntegerish(seed, lower=1, len=1, any.missing=FALSE)
checkmate::assertIntegerish(mapiter, len=1, any.missing=FALSE)
if (runCommand != "") checkmate::assertCharacter(runCommand, pattern="%s", min.len=1, max.len=1)
.xtra <- list(...)
.bad <- names(.xtra)
.bad <- .bad[!(.bad %in% c("genRxControl"))]
if (length(.bad) > 0) {
stop("unused argument: ", paste
(paste0("'", .bad, "'", sep=""), collapse=", "),
call.=FALSE)
}
if (checkmate::testIntegerish(addProp, lower=1, upper=1, len=1)) {
addProp <- c("combined1", "combined2")[addProp]
} else {
addProp <- match.arg(addProp)
}
checkmate::assertLogical(compress, any.missing=FALSE, len=1)
if (!is.null(.xtra$genRxControl)) {
genRxControl <- .xtra$genRxControl
} else {
genRxControl <- FALSE
if (is.null(rxControl)) {
#FIXME how to determine atol/rtol from NONMEM model
rxControl <- rxode2::rxControl(
covsInterpolation="nocb",
method="liblsoda"
)
genRxControl <- TRUE
} else if (is.list(rxControl)) {
rxControl$covsInterpolation <- "nocb"
rxControl$method <- "liblsoda"
rxControl <- do.call(rxode2::rxControl, rxControl)
}
if (!inherits(rxControl, "rxControl")) {
stop("rxControl needs to be ode solving options from rxode2::rxControl()",
call.=FALSE)
}
}
checkmate::assertLogical(sumProd, any.missing=FALSE, len=1)
checkmate::assertLogical(optExpression, any.missing=FALSE, len=1)
checkmate::assertNumeric(ci, any.missing=FALSE, len=1, lower=0, upper=1)
checkmate::assertLogical(calcTables, len=1, any.missing=FALSE)
.ret <- list(est=match.arg(est),
cov=match.arg(cov),
advanOde=match.arg(advanOde),
maxeval=maxeval,
print=print,
noabort=noabort,
iniSigDig=iniSigDig,
tol=tol,
sigl=sigl,
muRef=muRef,
sigdig=sigdig,
runCommand=runCommand,
outputExtension=outputExtension,
addProp=addProp,
rxControl=rxControl,
sumProd = sumProd,
optExpression=optExpression,
calcTables = calcTables,
compress = compress,
ci = ci,
sigdigTable=sigdigTable,
readRounding=readRounding,
readBadOpt=readBadOpt,
genRxControl=genRxControl,
niter=niter,
isample=isample,
iaccept=iaccept,
iscaleMin=iscaleMin,
iscaleMax=iscaleMax,
df=df,
seed=seed,
mapiter=mapiter
)
class(.ret) <- "nonmemControl"
.ret
}
#' @export
getValidNlmixrCtl.nonmem <- function(control) {
.ctl <- control[[1]]
.cls <- class(control)[1]
if (is.null(.ctl)) .ctl <- nonmemControl()
if (is.null(attr(.ctl, "class")) && is(.ctl, "list")) .ctl <- do.call("nonmemControl", .ctl)
if (!inherits(.ctl, "nonmemControl")) {
.minfo(paste0("invalid control for `est=\"", .cls, "\"`, using default"))
.ctl <- nonmemControl()
} else {
.ctl <- do.call(nonmemControl, .ctl)
}
.ctl
}
#' @export
nmObjHandleControlObject.nonmemControl <- function(control, env) {
assign("nonmemControl", control, envir=env)
}
#' @export
nmObjGetControl.nonmem <- function(x, ...) {
.env <- x[[1]]
if (exists("nonmemControl", .env)) {
.control <- get("nonmemControl", .env)
if (inherits(.control, "nonmemControl")) return(.control)
}
if (exists("control", .env)) {
.control <- get("control", .env)
if (inherits(.control, "nonmemControl")) return(.control)
}
stop("cannot find nonmem related control object", call.=FALSE)
}
#' @export
nmObjHandleControlObject.nonmemControl <- function(control, env) {
assign("nonmemControl", control, envir=env)
}
#' @export
nmObjGetControl.nonmem <- function(x, ...) {
.env <- x[[1]]
if (exists("nonmemControl", .env)) {
.control <- get("nonmemControl", .env)
if (inherits(.control, "nonmemControl")) return(.control)
}
if (exists("control", .env)) {
.control <- get("control", .env)
if (inherits(.control, "nonmemControl")) return(.control)
}
stop("cannot find nonmem related control object", call.=FALSE)
}
.nonmemControlToFoceiControl <- function(env, assign=FALSE) {
.nonmemControl <- env$nonmemControl
.ui <- env$ui
.foceiControl <- nlmixr2est::foceiControl(rxControl = env$nonmemControl$rxControl,
maxOuterIterations = 0L, maxInnerIterations = 0L, covMethod = 0L,
etaMat = env$etaMat, sumProd = .nonmemControl$sumProd,
optExpression = .nonmemControl$optExpression, scaleTo = 0,
calcTables = .nonmemControl$calcTables,
addProp = .nonmemControl$addProp,
skipCov = .ui$foceiSkipCov, interaction = 1L,
compress = .nonmemControl$compress,
ci = .nonmemControl$ci,
sigdigTable = .nonmemControl$sigdigTable)
if (assign)
env$control <- .foceiControl
.foceiControl
}