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Merge pull request #105 from nlmixr2/105-as.nlmixr2.monolix2rx
`as.nlmixr2` for `monolix2rx` objects
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -39,6 +39,7 @@ Imports: | |
| lotri, | ||
| nlmixr2est (>= 2.1.6), | ||
| nonmem2rx (>= 0.1.3), | ||
| monolix2rx, | ||
| methods, | ||
| qs, | ||
| rex, | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| #' @export | ||
| nmObjGetControl.monolix2rx <- function(x, ...) { | ||
| .env <- x[[1]] | ||
| if (exists("control", .env)) { | ||
| .control <- get("control", .env) | ||
| if (inherits(.control, "foceiControl")) return(.control) | ||
| } | ||
| if (exists("foceiControl0", .env)) { | ||
| .control <- get("foceiControl0", .env) | ||
| if (inherits(.control, "foceiControl")) return(.control) | ||
| } | ||
| stop("cannot find monolix2rx related control object", call.=FALSE) | ||
| } | ||
|
|
||
| .monolix2rxToFoceiControl <- function(env, model, assign=FALSE) { | ||
| ## maxSS=nbSSDoses + 1, | ||
| ## minSS=nbSSDoses, | ||
| ## ssAtol=100, | ||
| ## ssRtol=100, | ||
| ## atol=ifelse(stiff, 1e-9, 1e-6), | ||
| ## rtol=ifelse(stiff, 1e-6, 1e-3), | ||
| ## method=ifelse(stiff, "liblsoda", "dop853") | ||
| .nbSsDoses <- monolix2rx::.getNbdoses(model) | ||
| .stiff <- monolix2rx::.getStiff(model) | ||
| .rxControl <- rxode2::rxControl(covsInterpolation="locf", | ||
| atol=ifelse(.stiff, 1e-9, 1e-6), | ||
| rtol=ifelse(.stiff, 1e-6, 1e-3), | ||
| ssRtol=100, | ||
| ssAtol=100, | ||
| maxSS=.nbSsDoses + 1, | ||
| minSS=.nbSsDoses, | ||
| method=ifelse(.stiff, "liblsoda", "dop853"), | ||
| safeZero=FALSE) | ||
| .foceiControl <- nlmixr2est::foceiControl(rxControl=.rxControl, | ||
| maxOuterIterations = 0L, maxInnerIterations = 0L, | ||
| etaMat = env$etaMat, | ||
| covMethod=0L, | ||
| interaction = 1L) | ||
| if (assign) | ||
| env$control <- .foceiControl | ||
| .foceiControl | ||
| } | ||
|
|
||
| #' @export | ||
| as.nlmixr2.monolix2rx <- function(x, ..., table=nlmixr2est::tableControl(), rxControl=rxode2::rxControl(), ci=0.95) { | ||
| #need x$nonmemData | ||
| # need x to have at least one endpoint | ||
| # The environment needs: | ||
| env <- new.env(parent=emptyenv()) | ||
| x <- rxode2::rxUiDecompress(x) | ||
| nlmixr2est::nlmixrWithTiming("as.nlmixr2", { | ||
| .ui <- new.env(parent=emptyenv()) | ||
| .oldUi <- x | ||
| for (n in ls(envir=.oldUi, all.names=TRUE)) { | ||
| assign(n, get(n, envir=.oldUi), envir=.ui) | ||
| } | ||
| class(.ui) <- class(.oldUi) | ||
| # - $table for table options -- already present | ||
| env$table <- table | ||
| env$origData <- x$monolixData | ||
| nlmixr2est::.foceiPreProcessData(env$origData, env, .ui, rxControl) | ||
| # - $origData -- Original Data -- already present | ||
| # - $dataSav -- Processed data from .foceiPreProcessData --already present | ||
| # - $idLvl -- Level information for ID factor added -- already present | ||
| env$ui <- .ui | ||
| # - $ui for ui fullTheta Full theta information | ||
| env$fullTheta <- .ui$monolixFullTheta | ||
| # - $etaObf data frame with ID, etas and OBJI | ||
| env$etaObf <- .ui$monolixEtaObf | ||
| if (is.null(env$etaObf)) { | ||
| .df <- data.frame(ID=unique(env$dataSav$ID)) | ||
| for (.n in .getEtaNames(.ui)) { | ||
| .df[[.n]] <- 0 | ||
| } | ||
| .df[["OBJI"]] <- NA_real_ | ||
| env$etaObf <- .df | ||
| warning("since Monolix did not output between subject variability, assuming all ETA(#) are zero", | ||
| call.=FALSE) | ||
| } | ||
| # - $cov For covariance | ||
| .cov <- .ui$monolixCovariance | ||
| if (!is.null(.cov)) { | ||
| env$cov <- .cov | ||
| # - $covMethod for the method of calculating the covariance | ||
| env$covMethod <- "monolix2rx" | ||
| } | ||
| # - $objective objective function value | ||
| env$objective <- .ui$monolixObjf | ||
| # - $extra Extra print information | ||
| env$extra <- paste0(" reading Monolix ver ", env$ui$monolixOutputVersion) | ||
| # - $method Estimation method (for printing) | ||
| env$method <- "monolix2rx" | ||
| # - $omega Omega matrix | ||
| env$omega <- .ui$monolixOmega | ||
| # - $theta Is a theta data frame | ||
| env$theta <- .ui$monolixTheta | ||
| # - $model a list of model information for table generation. Needs a `predOnly` model | ||
| env$model <- .ui$ebe | ||
| # - $message Message for display | ||
| env$message <- "" | ||
| # - $est estimation method | ||
| env$est <- "monolix2rx" | ||
| # - $ofvType (optional) tells the type of ofv is currently being used | ||
| #env$ofvType | ||
| env$ofvType <- .ui$monolixObjfType | ||
| # Add parameter history | ||
| env$nobs <- x$dfObs | ||
| env$nobs2<- x$dfObs | ||
| # Run before converting to nonmemControl | ||
| .objf <- .ui$monolixObjf | ||
| # When running the focei problem to create the nlmixr object, you also need a | ||
| # foceiControl object | ||
| .monolix2rxToFoceiControl(env, x, TRUE) | ||
| .ret <- nlmixr2est::nlmixr2CreateOutputFromUi(env$ui, data=env$origData, | ||
| control=env$control, table=env$table, | ||
| env=env, est="monolix2rx") | ||
| if (inherits(.ret, "nlmixr2FitData")) { | ||
| assign("monolixControl", list(ci=ci), .ret$env) | ||
| .msg <- .monolixMergePredsAndCalcRelativeErr(.ret) | ||
| rm("monolixControl", envir=.ret$env) | ||
| .msg$message <- c(.msg$message) | ||
| .tmp <- .ret$ui$monolixParHistory | ||
| assign("message", paste(.msg$message, collapse="\n "), envir=.ret$env) | ||
| if (is.null(.tmp)) { | ||
| .minfo("monolix parameter history needs exported charts, please export charts") | ||
| } else { | ||
| .tmp$type <- "Unscaled" | ||
| assign("parHistData", .tmp, .ret$env) | ||
| .minfo("monolix parameter history integrated into fit object") | ||
| } | ||
| } | ||
| ## .time <- get("time", .ret$env) | ||
| ## .time <- .time[,!(names(.time) %in% c("optimize", "covariance"))] | ||
| ## assign("time", | ||
| ## cbind(.time, data.frame(NONMEM=.ui$nonmemRunTime)), | ||
| ## .ret$env) | ||
| .ret | ||
| }, env=env) | ||
| } |
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