108 dont run nonmem or monolix just create files

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 +26,8 @@ Suggests:
     rmarkdown,
     spelling,
     PopED,
-    units
+    units,
+    vdiffr
 Depends:
     R (>= 3.5),
     nlmixr2 (>= 2.0.8)

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/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
@@ -92,6 +94,7 @@ 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 +112,7 @@ 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 +201,8 @@ monolixControl <- function(nbSSDoses=7,
                genRxControl=genRxControl,
                useLinearization=useLinearization,
                modelName=modelName,
-               muRefCovAlg=muRefCovAlg)
+               muRefCovAlg=muRefCovAlg,
+               run=run)
   class(.ret) <- "monolixControl"
   .ret
 }

R/monolixNlmixr2est.R

@@ -253,6 +253,10 @@
     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, "")) {

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

@@ -207,6 +207,10 @@
               quote=FALSE)
     .minfo("done")
   }
+  if (!rxode2::rxGetControl(.ui, "run", TRUE)) {
+    .minfo("only exported NONMEM control stream/data")
+    return(invisible())
+  }
   if (is.na(rxode2::rxGetControl(.ui, "runCommand", ""))) {
     .minfo("not running NONMEM")
     return(.ui)
@@ -262,11 +266,11 @@
     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