Merge branch 'main' into HEAD

.github/workflows/R-CMD-check.yaml

@@ -54,12 +54,12 @@ jobs:
           pak-version: stable
           extra-packages: |
             any::rcmdcheck
+            nlmixr2/n1qn1c
+            nlmixr2/lbfgsb3c
+            nlmixr2/PreciseSums
             nlmixr2/dparser-R
             nlmixr2/lotri
             nlmixr2/rxode2ll
-            nlmixr2/rxode2parse
-            nlmixr2/rxode2random
-            nlmixr2/rxode2et
             nlmixr2/rxode2
             nlmixr2/nlmixr2est
             nlmixr2/nlmixr2extra

.github/workflows/pkgdown.yaml

@@ -32,12 +32,14 @@ jobs:
         with:
           extra-packages: |
             any::pkgdown
+            any::mrgsolve
+            any::PKPDsim
+            nlmixr2/n1qn1c
+            nlmixr2/lbfgsb3c
+            nlmixr2/PreciseSums
             nlmixr2/lotri
             nlmixr2/dparser-R
             nlmixr2/rxode2ll
-            nlmixr2/rxode2parse
-            nlmixr2/rxode2random
-            nlmixr2/rxode2et
             nlmixr2/rxode2
             nlmixr2/nonmem2rx
             nlmixr2/nlmixr2est

.github/workflows/test-coverage.yaml

@@ -28,11 +28,12 @@ jobs:
           pak-version: devel
           extra-packages: |
             any::covr
+            nlmixr2/n1qn1c
+            nlmixr2/lbfgsb3c
+            nlmixr2/PreciseSums
+            nlmixr2/dparser-R
             nlmixr2/lotri
             nlmixr2/rxode2ll
-            nlmixr2/rxode2parse
-            nlmixr2/rxode2random
-            nlmixr2/rxode2et
             nlmixr2/rxode2
             nlmixr2/nlmixr2est
             nlmixr2/nlmixr2extra

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: babelmixr2
 Type: Package
 Title: Use 'nlmixr2' to Interact with Open Source and Commercial Software
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(person("Matthew","Fidler", role = c("aut", "cre"), email = "[email protected]", comment=c(ORCID="0000-0001-8538-6691")),
            person("Bill", "Denney", email="[email protected]", role="aut", comment=c(ORCID="0000-0002-5759-428X")),
            person("Nook", "Fulloption", role="ctb", comment="goldfish art"))
@@ -26,7 +26,9 @@ Suggests:
     rmarkdown,
     spelling,
     PopED,
-    units
+    units,
+    vdiffr,
+    dplyr
 Depends:
     R (>= 3.5),
     nlmixr2 (>= 2.0.8)
@@ -41,10 +43,10 @@ Imports:
     qs,
     rex,
     rxode2
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
 LinkingTo:
-    Rcpp, rxode2, RcppArmadillo, RcppEigen, rxode2parse
+    Rcpp, rxode2, RcppArmadillo, RcppEigen
 Language: en-US
 VignetteBuilder: knitr

NAMESPACE

@@ -26,6 +26,7 @@ S3method(nmObjGetControl,nonmem2rx)
 S3method(nmObjGetFoceiControl,monolix)
 S3method(nmObjHandleControlObject,monolixControl)
 S3method(nmObjHandleControlObject,nonmemControl)
+S3method(print,babelmixr2popedScript)
 S3method(print,pkncaEst)
 S3method(rxUiGet,mlxtran)
 S3method(rxUiGet,mlxtranDatafile)
@@ -119,18 +120,28 @@ S3method(rxUiGet,popedCovd)
 S3method(rxUiGet,popedD)
 S3method(rxUiGet,popedFErrorFun)
 S3method(rxUiGet,popedFfFun)
+S3method(rxUiGet,popedFfFunScript)
 S3method(rxUiGet,popedFgFun)
+S3method(rxUiGet,popedFullRxModel)
+S3method(rxUiGet,popedGetEventFun)
 S3method(rxUiGet,popedNotfixedBpop)
 S3method(rxUiGet,popedNotfixedCovd)
 S3method(rxUiGet,popedNotfixedD)
 S3method(rxUiGet,popedNotfixedSigma)
 S3method(rxUiGet,popedParameters)
 S3method(rxUiGet,popedRxmodelBase)
+S3method(rxUiGet,popedScriptBeforeCtl)
 S3method(rxUiGet,popedSettings)
 S3method(rxUiGet,popedSigma)
 export(.minfo)
 export(.popedF)
+export(.popedFree)
 export(.popedRxRunSetup)
+export(.popedSetup)
+export(.popedSolveIdME)
+export(.popedSolveIdME2)
+export(.popedSolveIdN)
+export(.popedSolveIdN2)
 export(.popedW)
 export(as.nlmixr)
 export(as.nlmixr2)
@@ -171,6 +182,7 @@ importFrom(nlmixr2est,nmObjHandleControlObject)
 importFrom(nonmem2rx,as.nonmem2rx)
 importFrom(nonmem2rx,nonmem2rx)
 importFrom(rxode2,.minfo)
+importFrom(rxode2,`model<-`)
 importFrom(rxode2,rxModelVars)
 importFrom(rxode2,rxUiGet)
 importFrom(stats,na.omit)

NEWS.md

@@ -1,3 +1,11 @@
+# babelmixr2 0.1.3
+
+* Changed default NONMEM rounding protection to FALSE
+
+* Added a `run` option to the `monolixControl()` and `nonemControl()`
+  in case you only want to export the modeling files and not run the
+  models.
+
 # babelmixr2 0.1.2
 
 * Handle algebraic `mu` expressions

R/RcppExports.R

@@ -5,6 +5,30 @@ convertDataBack <- function(id, time, amt, ii, evid, cmt, cmtDvid, dvidDvid, lin
     .Call(`_babelmixr2_convertDataBack`, id, time, amt, ii, evid, cmt, cmtDvid, dvidDvid, linNcmt, linKa, neq, replaceEvid, zeroDose2)
 }
 
+popedFree <- function() {
+    .Call(`_babelmixr2_popedFree`)
+}
+
+popedSetup <- function(e, full) {
+    .Call(`_babelmixr2_popedSetup`, e, full)
+}
+
+popedSolveIdN2 <- function(theta, mt, iid, totn) {
+    .Call(`_babelmixr2_popedSolveIdN2`, theta, mt, iid, totn)
+}
+
+popedSolveIdN <- function(theta, mt, iid, totn) {
+    .Call(`_babelmixr2_popedSolveIdN`, theta, mt, iid, totn)
+}
+
+popedSolveIdME <- function(theta, umt, mt, ms, nend, id, totn) {
+    .Call(`_babelmixr2_popedSolveIdME`, theta, umt, mt, ms, nend, id, totn)
+}
+
+popedSolveIdME2 <- function(theta, umt, mt, ms, nend, id, totn) {
+    .Call(`_babelmixr2_popedSolveIdME2`, theta, umt, mt, ms, nend, id, totn)
+}
+
 transDv <- function(inDv, inCmt, cmtTrans, lambda, yj, low, high) {
     .Call(`_babelmixr2_transDv`, inDv, inCmt, cmtTrans, lambda, yj, low, high)
 }

R/monolixControl.R

@@ -34,6 +34,8 @@
 #'   monolix. See details for function usage.
 #' @param absolutePath Boolean indicating if the absolute path should
 #'   be used for the monolix runs
+#'
+#' @param run Should monolix be run and the results be imported to nlmixr2?  (Default is TRUE)
 #' @inheritParams nonmemControl
 #' @inheritParams nlmixr2est::saemControl
 #' @return A monolix control object
@@ -66,6 +68,7 @@
 #' @importFrom methods is
 #' @importFrom stats na.omit setNames
 #' @importFrom utils assignInMyNamespace read.csv write.csv
+#' @importFrom rxode2 `model<-`
 monolixControl <- function(nbSSDoses=7,
                            useLinearization=FALSE,
                            stiff=FALSE,
@@ -92,6 +95,7 @@ monolixControl <- function(nbSSDoses=7,
                            absolutePath=FALSE,
                            modelName=NULL,
                            muRefCovAlg=TRUE,
+                           run=TRUE,
                            ...) {
   checkmate::assertLogical(stiff, max.len=1, any.missing=FALSE)
   checkmate::assertLogical(exploratoryAutoStop, max.len=1, any.missing=FALSE)
@@ -109,6 +113,7 @@ monolixControl <- function(nbSSDoses=7,
   checkmate::assertNumeric(exploratoryAlpha, lower=0.0, upper=1.0)
   checkmate::assertNumeric(omegaTau, lower=0.0, upper=1.0)
   checkmate::assertNumeric(errorModelTau, lower=0.0, upper=1.0)
+  checkmate::assertLogical(run, len=1, any.missing=FALSE)
 
   if (!is.null(modelName)) {
     checkmate::assertCharacter(modelName, len=1, any.missing=FALSE)
@@ -197,7 +202,8 @@ monolixControl <- function(nbSSDoses=7,
                genRxControl=genRxControl,
                useLinearization=useLinearization,
                modelName=modelName,
-               muRefCovAlg=muRefCovAlg)
+               muRefCovAlg=muRefCovAlg,
+               run=run)
   class(.ret) <- "monolixControl"
   .ret
 }

R/monolixNlmixr2est.R

@@ -137,6 +137,9 @@
   cmd <- rxode2::rxGetControl(ui, "runCommand", "")
   if (is.character(cmd)) {
     cmd <- .monolixRunCommand
+  } else if (is.na(cmd)) {
+    .minfo("run Monolix manually and rerun nlmixr()")
+    return(NULL)
   } else if (!is.function(cmd)) {
     stop("invalid value for monolixControl(runCommand=)",
          call.=FALSE)
@@ -231,7 +234,8 @@
   .mlxtran <- .ui$monolixMlxtranFile
   .runLock <- .ui$monolixRunLock
 
-  if (checkmate::testFileExists(.qs)) {
+  .cmd <- rxode2::rxGetControl(.ui, "runCommand", "")
+if (checkmate::testFileExists(.qs)) {
     .minfo("load saved nlmixr2 object")
     .ret <- qs::qread(.qs)
     if (!exists("parHistData", .ret$env)) {
@@ -253,10 +257,16 @@
     writeLines(text=.hashMd5, con=.hashFile)
     write.csv(.dataDf, file=.csv, na = ".", row.names = FALSE)
     .minfo("done")
+    if (!rxode2::rxGetControl(.ui, "run", TRUE)) {
+      .minfo("only exported Monolix mlxtran, txt model and data")
+      return(invisible())
+    }
     .runLS <- FALSE
-    .cmd <- rxode2::rxGetControl(.ui, "runCommand", "")
     if (!identical(.cmd, "")) {
       .monolixRunner(ui=.ui)
+      if (is.na(.cmd)) {
+        return(invisible())
+      }
     } else {
       if (.hasLixoftConnectors()) {
         .x <- try(lixoftConnectors::loadProject(.mlxtran), silent=TRUE)
@@ -278,6 +288,10 @@
       }
     }
   } else {
+    if (is.na(.cmd)) {
+      .minfo(paste0("leaving alone monolix files because '", .model, "' is present"))
+      return(invisible())
+    }
     .minfo(paste0("assuming monolix is running because '", .model, "' is present"))
   }
   if (!dir.exists(.exportPath)) {

R/nonmemControl.R

@@ -27,15 +27,16 @@
 #' @param tol NONMEM tolerance for ODE solving advan
 #' @param atol NONMEM absolute tolerance for ODE solving
 #' @param sstol NONMEM tolerance for steady state ODE solving
-#' @param ssatol NONMEM absolute tolerance for steady state ODE solving
+#' @param ssatol NONMEM absolute tolerance for steady state ODE
+#'   solving
 #' @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 outputExtension Extension to use for the NONMEM output
 #'   listing
-#' @param runCommand Command to run NONMEM (typically the path to "nmfe75") or a
-#'   function.  See the details for more information.
+#' @param runCommand Command to run NONMEM (typically the path to
+#'   "nmfe75") or a function.  See the details for more information.
 #' @param iniSigDig How many significant digits are printed in $THETA
 #'   and $OMEGA when the estimate is zero.  Also controls the zero
 #'   protection numbers
@@ -45,14 +46,15 @@
 #'   simulations
 #' @param mapiter the number of map iterations for IMP method
 #' @param niter number of iterations in NONMEM estimation methods
-#' @param isample Isample argument for NONMEM  ITS estimation method
+#' @param isample Isample argument for NONMEM ITS estimation method
 #' @param iaccept Iaccept for NONMEM ITS estimation methods
 #' @param iscaleMin parameter for IMP NONMEM method (ISCALE_MIN)
 #' @param iscaleMax parameter for IMP NONMEM method (ISCALE_MAX)
 #' @param df degrees of freedom for IMP method
 #' @param seed is the seed for NONMEM methods
 #' @param mapinter is the MAPINTER parameter for the IMP method
-#' @param  addProp,sumProd,optExpression,calcTables,compress,ci,sigdigTable
+#' @param
+#'   addProp,sumProd,optExpression,calcTables,compress,ci,sigdigTable
 #'   Passed to \code{nlmixr2est::foceiControl}
 #' @param readRounding Try to read NONMEM output when NONMEM
 #'   terminated due to rounding errors
@@ -62,6 +64,9 @@
 #' @param modelName Model name used to generate the NONMEM output.  If
 #'   `NULL` try to infer from the model name (could be `x` if not
 #'   clear).  Otherwise use this character for outputs.
+#' @param run Should NONMEM be run (and the files imported to
+#'   nlmixr2); default is TRUE, but FALSE will simply create the
+#'   NONMEM control stream and data file.
 #' @param ... optional \code{genRxControl} argument controlling
 #'   automatic \code{rxControl} generation.
 #'
@@ -93,7 +98,7 @@ nonmemControl <- function(est=c("focei", "imp", "its", "posthoc"),
                           outputExtension=getOption("babelmixr2.nmOutputExtension", ".lst"),
                           runCommand=getOption("babelmixr2.nonmem", ""),
                           iniSigDig=5,
-                          protectZeros=TRUE,
+                          protectZeros=FALSE,
                           muRef=TRUE,
                           addProp = c("combined2", "combined1"),
                           rxControl=NULL,
@@ -117,6 +122,7 @@ nonmemControl <- function(est=c("focei", "imp", "its", "posthoc"),
                           noabort=TRUE,
                           modelName=NULL,
                           muRefCovAlg=TRUE,
+                          run=TRUE,
                           ...) {
   # nonmem manual slides suggest tol=6, sigl=6 sigdig=2
   checkmate::assertIntegerish(maxeval, lower=100, len=1, any.missing=FALSE)
@@ -142,6 +148,7 @@ nonmemControl <- function(est=c("focei", "imp", "its", "posthoc"),
   checkmate::assertIntegerish(seed, lower=1, len=1, any.missing=FALSE)
   checkmate::assertIntegerish(mapiter, len=1, any.missing=FALSE)
   checkmate::assertLogical(muRefCovAlg, any.missing=FALSE, len=1)
+  checkmate::assertLogical(run, any.missing=FALSE, len=1)
   if (!is.null(modelName)) {
     checkmate::assertCharacter(modelName, len=1, any.missing=FALSE)
   }
@@ -240,7 +247,8 @@ nonmemControl <- function(est=c("focei", "imp", "its", "posthoc"),
                seed=seed,
                mapiter=mapiter,
                modelName=modelName,
-               muRefCovAlg=muRefCovAlg
+               muRefCovAlg=muRefCovAlg,
+               run=run
                )
   class(.ret) <- "nonmemControl"
   .ret

R/nonmemNlmixr2est.R

@@ -207,9 +207,11 @@
               quote=FALSE)
     .minfo("done")
   }
-  if (is.na(rxode2::rxGetControl(.ui, "runCommand", ""))) {
-    .minfo("not running NONMEM")
-    return(.ui)
+  .cmd <- rxode2::rxGetControl(.ui, "runCommand", "")
+  if (!rxode2::rxGetControl(.ui, "run", TRUE) ||
+        is.na(.cmd)) {
+    .minfo("only exported NONMEM control stream/data")
+    return(invisible(.ui))
   }
   if (!file.exists(file.path(.exportPath, .ui$nonmemXml))) {
     print(file.path(.exportPath, .ui$nonmemXml))
@@ -262,11 +264,11 @@
     assign("message", paste(.msg$message, collapse="\n    "), envir=.ret$env)
     qs::qsave(.ret, .qs)
   }
-  return(.ret)
+  .ret
 }
 
 #' Run NONMEM using either the user-specified command or function
-#' 
+#'
 #' @param ui The nlmixr2 UI object for running
 #' @param monolix are we actually running monolix
 #' @return NULL