Env is compressed

NAMESPACE

@@ -71,12 +71,14 @@ S3method(nmObjGet,dataSav)
 S3method(nmObjGet,default)
 S3method(nmObjGet,env)
 S3method(nmObjGet,estimationModel)
+S3method(nmObjGet,finalUi)
 S3method(nmObjGet,foceiControl)
 S3method(nmObjGet,foceiThetaEtaParameters)
 S3method(nmObjGet,hini)
 S3method(nmObjGet,hmax)
 S3method(nmObjGet,hmin)
 S3method(nmObjGet,idLvl)
+S3method(nmObjGet,iniUi)
 S3method(nmObjGet,innerModel)
 S3method(nmObjGet,innerModelForce)
 S3method(nmObjGet,ipredModel)
@@ -109,6 +111,7 @@ S3method(nmObjGet,saemTransformedData)
 S3method(nmObjGet,seed)
 S3method(nmObjGet,sigma)
 S3method(nmObjGet,simInfo)
+S3method(nmObjGet,ui)
 S3method(nmObjGet,warnings)
 S3method(nmObjGetControl,default)
 S3method(nmObjGetControl,fo)

R/focei.R

@@ -1662,6 +1662,7 @@ attr(rxUiGet.foceiOptEnv, "desc") <- "Get focei optimization environment"
         rm(list=.item, envir=.env)
       }
     }
+    assign("ui", rxode2::rxUiCompress(.env$ui), envir=.env)
   })
   if (any(names(.ret) == "CWRES") && regexpr("^fo", est) == -1) {
     # focei is available; add objective function

R/nlmixr2.R

@@ -119,6 +119,7 @@ nlmixr2 <- function(object, data, est = NULL, control = list(),
                     envir = parent.frame()) {
   rxode2::rxUnloadAll()
   assignInMyNamespace(".nlmixr2Time", proc.time())
+  assignInMyNamespace(".finalUiCompressed", FALSE)
   .objectName <- try(as.character(substitute(object)), silent=TRUE)
   if (inherits(.objectName, "try-error")) .objectName <- "object"
   if (!identical(.objectName, "object")) {
@@ -156,6 +157,7 @@ nlmixr <- nlmixr2
   assignInMyNamespace(".nlmixr2pipeControl", NULL)
   assignInMyNamespace(".nlmixr2pipeTable", NULL)
   assignInMyNamespace(".nlmixr2pipeEst", NULL)
+  assignInMyNamespace(".finalUiCompressed", TRUE)
   rxode2::rxSetCovariateNamesForPiping(NULL)
 }
 
@@ -165,7 +167,8 @@ nlmixr2.function <- function(object, data=NULL, est = NULL, control = NULL, tabl
                              save = NULL, envir = parent.frame()) {
   on.exit(.nlmixr2clearPipe())
   .args <- as.list(match.call(expand.dots = TRUE))[-1]
-  .uif <- rxode2::rxode(object)
+  .uif <- rxode2::rxode2(object)
+  .uif <- rxode2::rxUiDecompress(.uif)
   if (!is.null(.nlmixr2objectName)) {
     if (!identical(.nlmixr2objectName, "object")) {
       assign("modelName", .nlmixr2objectName, envir=.uif)
@@ -220,6 +223,7 @@ nlmixr2.rxUi <- function(object, data=NULL, est = NULL, control = NULL, table =
   .modelName <- try(as.character(substitute(object)), silent=TRUE)
   if (inherits(.modelName, "try-error")) .modelName <- NULL
   .uif <- object
+  .uif <- rxode2::rxUiDecompress(.uif)
   if (is.null(.uif$modelName)) assign("modelName", .modelName, envir=.uif)
   if (is.null(data) && missing(est)) {
     return(.uif)
@@ -306,7 +310,8 @@ nlmixr2.nlmixr2FitCore <- function(object, data=NULL, est = NULL, control = NULL
     table <- getValidNlmixrControl(table, "tableControl")
   }
   .env <- new.env(parent=emptyenv())
-  .env$ui <- .nlmixrPreprocessUi(object$ui)
+  .ui <- rxode2::rxUiDecompress(object$ui)
+  .env$ui <- .nlmixrPreprocessUi(.ui)
   .env$data <- data
   .env$control <- control
   .env$table <- table

R/nlmixr2Est.R

@@ -113,6 +113,8 @@ nlmixr2Est.default <- function(env, ...) {
 #' @noRd
 nlmixr2Est0 <- function(env, ...) {
   rxode2::rxUnloadAll()
+  .ui <- rxode2::rxUiDecompress(env$ui)
+  assign("ui", .ui, envir=env)
   if (!exists("missingTable", envir=env)) {
     assign("missingTable", FALSE, envir=env)
   }
@@ -127,7 +129,9 @@ nlmixr2Est0 <- function(env, ...) {
   }
   if (inherits(env$ui, "rxUi")) {
     .modelName <- env$ui$modelName
-    assign("ui", env$ui$fun(), envir=env) # re-evaluate so it doesn't overwrite inital ui
+    assign("ui",
+           rxode2::rxUiDecompress(env$ui$fun()),
+           envir=env) # re-evaluate so it doesn't overwrite inital ui
     assign("modelName", .modelName, envir=env$ui)
   }
   .doIt <- TRUE

R/nlmixr2output.R

@@ -355,7 +355,7 @@ VarCorr.nlmixr2FitCoreSilent <- VarCorr.nlmixr2FitCore
 .sigma <- function(x) {
   .ret <- x$nlme
   if (is.null(.ret)) {
-    if (exists("uif", envir = x$env)) {
+    if (exists("ui", envir = x$env)) {
       .df <- as.data.frame(x$uif$ini)
       .errs <- paste(.df[which(!is.na(.df$err)), "name"])
       return(fixef(x)[.errs])
@@ -521,7 +521,7 @@ vcov.nlmixr2FitCoreSilent <- vcov.nlmixr2FitCore
   # Update initial estimates to match current initial estimates
   .ui <- x$ui
   .iniDf <- .ui$iniDf
-
+  assign("iniDf0", .iniDf, envir=x)
   if (exists("fullTheta", x)) {
     .thetas <- x$fullTheta
   } else if (exists("fixef", x)) {

R/nmObjGet.R

@@ -23,6 +23,33 @@ nmObjGet <- function(x, ...) {
   UseMethod("nmObjGet")
 }
 
+#' @export
+nmObjGet.iniUi <- function(x, ...) {
+  .env <- x[[1]]
+  .ui <- .cloneEnv(rxode2::rxUiDecompress(get("ui", .env)))
+  .iniDf <- get("iniDf0", envir=.env)
+  if (is.null(.iniDf)) return(NULL)
+  assign("iniDf", .iniDf, envir=.ui)
+  rxode2::rxUiCompress(.ui)
+}
+attr(nmObjGet.iniUi, "desc") <- "The initial ui used to run the model"
+
+.finalUiCompressed <- TRUE
+#' @export
+nmObjGet.finalUi <- function(x, ...) {
+  .env <- x[[1]]
+  .ui <- .cloneEnv(rxode2::rxUiDecompress(get("ui", .env)))
+  if (.finalUiCompressed) {
+    rxode2::rxUiCompress(.ui)
+  } else {
+    rxode2::rxUiDecompress(.ui)
+  }
+}
+attr(nmObjGet.finalUi, "desc") <- "The final ui used to run the model"
+
+#' @export
+nmObjGet.ui <- nmObjGet.finalUi
+
 #' Get an item from a nlmixr2FitData object
 #'
 #' @param x A specialized list with:
@@ -104,6 +131,10 @@ nmObjGet.default <- function(x, ...) {
   }
   # Now get the ui, install the control object temporarily and use `rxUiGet`
   .ui <- get("ui", envir=.env)
+  .ui <- rxode2::rxUiDecompress(.ui)
+  on.exit({
+    assign("ui", rxode2::rxUiCompress(.ui), envir=.env)
+  })
   .ctl <- nmObjGetControl(.createEstObject(x[[1]]), ...)
   if (!is.null(.ctl)) {
     assign("control", .ctl, envir=.ui)

R/preProcessModel.R

@@ -120,7 +120,7 @@
   .ret <- ui
   .zeroEtas <- .getZeroEtasFromModel(.ret)
   if (length(.zeroEtas) > 0) {
-    assignInMyNamespace(".nlmixrPureInputUi", .ret)
+    assignInMyNamespace(".nlmixrPureInputUi", rxode2::rxUiDecompress(.ret))
     .minfo(paste0("the following etas are removed from the model since their initial estimates are zero: ",
            paste(.zeroEtas, collapse=", ")))
     .ret <- .downgradeEtas(ui, zeroEtas=.zeroEtas)