Merge remote-tracking branch 'origin/main'

R/dataImport.R

@@ -172,10 +172,16 @@
   if (length(.w) != 1L) return(data) # no observationtype in the dataset
   if (is.null(ui$predDf)) return(data[, -.w]) # single endpoint; no need to define
   # multiple endpoint
+  .dvid <- unique(data$rxMDvid)
+  .dvid <- .dvid[!is.na(.dvid)]
+  .dvid <- .dvid[!(.dvid %in% seq_along(ui$predDf$cond))]
   for (.i in seq_along(ui$predDf$cond)) {
     # only overwrite non-dosing events (ie make sure the cmt is NA)
     data$cmt[which(is.na(data$cmt) & data$rxMDvid == .i)] <- ui$predDf$var[.i]
   }
+  for(.i in .dvid) {
+    data <- data[-which(is.na(data$cmt) & data$rxMDvid == .i), ]
+  }
   data[, -.w]
 }
 

R/equation.R

@@ -258,6 +258,29 @@ mlxTxt <- function(file, retFile=FALSE) {
     .lines <- file
     .dirn <- getwd()
   } else {
+    if (requireNamespace("lixoftConnectors", quietly = TRUE)) {
+      if (!checkmate::testCharacter(file, min.chars = 5, len=1)) {
+        .pre <- substr(file, 1, 4)
+      }
+      if (.pre == "lib:") {
+        if (is.na(.monolix2rx$lixoftConnectors)) {
+          x <- try(lixoftConnectors::initializeLixoftConnectors(software = "monolix", force=TRUE), silent=TRUE)
+          if (inherits(x, "try-error")) {
+            warning("lixoftConnectors cannot be initialized",
+                    call.=FALSE)
+            .monolix2rx$lixoftConnectors <- FALSE
+          } else {
+            .monolix2rx$lixoftConnectors <- TRUE
+          }
+        }
+        if (.monolix2rx$lixoftConnectors) {
+          .ret <- try(lixoftConnectors::getLibraryModelContent(, print=FALSE), silent=TRUE)
+          if (!inherits(.ret, "try-error")) {
+            return(as.character(.ret))
+          }
+        }
+      }
+    }
     .f <- .mlxtranLib(file)
     if (checkmate::testFileExists(.f, "r")) {
       .lines <- suppressWarnings(readLines(.f))

R/monolix2rx.R

@@ -1,4 +1,5 @@
 .monolix2rx <- new.env(parent=emptyenv())
+.monolix2rx$lixoftConnectors <- NA
 #' Output the information
 #'
 #' @param text character vector of the text to echo

R/rxUiGet.R

@@ -12,6 +12,8 @@ rxUiGet.monolixModelIwres <- function(x, ...) {
     if (length(.ui$predDf$cond) == 1) {
       .ret <- suppressMessages(rxode2::model(.ui, iwres <- (DV-rx_pred_)/sqrt(rx_r_),
                                              append=sim, auto=FALSE))
+      .ret <- suppressMessages(rxode2::model(.ret, ires <- DV-rx_pred_,
+                                             append=sim, auto=FALSE))
     } else {
       .ret <- suppressMessages(rxode2::as.rxUi(.ui))
       .lstExpr <- .ret$lstExpr
@@ -20,7 +22,8 @@ rxUiGet.monolixModelIwres <- function(x, ...) {
               identical(.lstExpr[[.l]][[1]], quote(`cmt`))) .l <- .l - 1
       .lstOut <- c(list(quote(`{`)),
                    lapply(seq_len(.l), function(i) .lstExpr[[i]]),
-                   list(quote(iwres <- (DV-rx_pred_)/sqrt(rx_r_))),
+                   list(quote(iwres <- (DV-rx_pred_)/sqrt(rx_r_)),
+                        quote(ires <- DV-rx_pred_)),
                    lapply(seq(.l+1, length(.lstExpr)), function(i) .lstExpr[[i]]))
       .lstOut <- as.call(list(quote(`model`), as.call(.lstOut)))
       rxode2::model(.ret) <- .lstOut

R/validate.R

@@ -88,7 +88,6 @@
     return(.ret)
   }
 }
-
 #' Validate the imported model
 #'
 #' @param ui rxode2 ui that is used to validate the model
@@ -125,7 +124,8 @@
                                        atol=.tol, rtol=.tol,
                                        ssAtol=100, ssRtol=100, omega=NULL,
                                        addDosing = FALSE))
-    .ipredSolve <- .subsetMonolix(.ui, .ipredSolve, "iwres")
+
+    .ipredSolve <- .subsetMonolix(.ui, .ipredSolve, c("iwres", "ires"))
     .minfo("done")
     .minfo("solving pred problem")
     .predSolve <- try(rxode2::rxSolve(.model, .pop, .data, returnType = "data.frame",
@@ -138,7 +138,19 @@
                                       ssAtol=100, ssRtol=100, omega=NULL,
                                       addDosing = FALSE))
     .predSolve <- .subsetMonolix(.ui, .predSolve)
-    .both <- merge(.predSolve, .ipredSolve)
+    .nPredSolve <- length(.predSolve[, 1])
+    .nIpredSolve <- length(.ipredSolve[, 1])
+    if (.nPredSolve == .nIpredSolve &&
+          all(.ipredSolve$id == .predSolve$id) &&
+          all(.ipredSolve$time == .predSolve$time) &&
+          all(.ipredSolve$cmt == .predSolve$cmt)) {
+      .both <- .ipredSolve
+      .both$pred <-.predSolve$pred
+      .nBoth <- length(.both[, 1])
+    } else {
+      .minfo("ipred and pred rxode2 solves do not match for id, time and cmt")
+      return(invisible())
+    }
     .monolix <- ui$predIpredData
     names(.monolix) <- vapply(names(.monolix),
                               function(n) {
@@ -148,6 +160,11 @@
                                 }
                                 n
                               }, character(1), USE.NAMES = FALSE)
+    .nMonolix <- length(.monolix[, 1])
+    if (.nMonolix != .nBoth) {
+      .minfo("monolix and rxode2 solves have different number of rows")
+      return(invisible())
+    }
     .both <- merge(.monolix, .both)
     .ci0 <- .ci <- ci
     .sigdig <- sigdig

README.Rmd

@@ -122,42 +122,26 @@ try(monolix2rx("lib:notThere.txt"))
 ```
 
 In newer versions of Monolix, the model library was turned into a
-binary database that is accessed by the GUI.  To me there are
-advantages of this:
+binary database that is accessed by the GUI and `lixoftConnectors`.
+If you have `lixoftConnectors` on your system and it can successfully
+load the model with `lixoftConnectors::getLibraryModelContent()` then
+`monolix2rx` will also load the model correctly (and will use this
+version over the text files when both are setup)
 
-- A binary database would be much faster in loading models
+This means you will need to import models into `rxode2` you need to:
 
-- With a model library, you don't have to put common model files all
-  over the place (saving space on your system)
+- For a model built from the model library you will need:
 
-- It would make their hard work on the excellent model library harder
-  to take and put into another system (They have at least 31,558
-  models).
+  - have a path to the text file Monolix Library and setup the
+    `monolix2rx.library` with
+    `options(monolix2rx.library="~/src/monolix/library/")`
 
-  - While this now allows a complete import of the Monolix library, I
-    believe our `nlmixr2lib` should only be built from imported from a
-    open-source library or be created on its own (as we are doing in
-    `nlmixr2lib`).
+  - have `lixoftConnectors` installed and connected to a newer (and
+    licensed) version of Monolix that can get the model library
+    content by `lixoftConnectors::getLibraryModelContent()`
 
-  - Please do not request direct translations of models
-    from Monolix to our library `nlmixr2lib`; these requests will be
-    rejected.
-
-If you want the model library as text files, you may be able to reach
-out to Lixoft and ask if they will provide them to you (or point to
-the last version that used these text files.)
-
-My biggest concern with this a approach is submitting Monolix models
-from the model library to regulatory bodies.  For the regulators to be
-able to truly see the models they have to have a working copy
-Monolix. If they do not, the model is a black box.
-
-For that reason, I believe best practice when submitting to a
-regulatory body is to make the model available by making some change
-to the model and saving it to a final location. That way the
-regulators can see the model.
-
-This approach also allows the model to be translated to `rxode2`.
+  - or without these options, you will need to save the model to a
+    text file outside of the model library so you can import the model.
 
 # Note on testing
 

README.md

@@ -39,7 +39,6 @@ theophylline is included in `monolix2rx` and can be imported below:
 
 ``` r
 library(monolix2rx)
-#> Loading required namespace: rxode2
 # First load in the model; in this case the theo model
 # This is modified from the Monolix demos by saving the model
 # file as a text file (hence you can access without model library).
@@ -60,14 +59,6 @@ rx <- monolix2rx(mlxtranFile)
 #> ℹ imported monolix ETAS (_SAEM) imported to rxode2 compatible data ($etaData)
 #> ℹ imported monolix pred/ipred data to compare ($predIpredData)
 #> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-#> In file included from /usr/share/R/include/R.h:71,
-#>                  from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2parse.h:33,
-#>                  from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2/include/rxode2.h:9,
-#>                  from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2_model_shared.h:3,
-#>                  from rx_3eaac9dbb7c8e82fd82febcc413da174_.c:117:
-#> /usr/share/R/include/R_ext/Complex.h:80:6: warning: ISO C99 doesn’t support unnamed structs/unions [-Wpedantic]
-#>    80 |     };
-#>       |      ^
 #> ℹ solving ipred problem
 #> ℹ done
 #> ℹ solving pred problem
@@ -99,6 +90,8 @@ rx
 #>  ── Model (Normalized Syntax): ── 
 #> function() {
 #>     description <- "The administration is extravascular with a first order absorption (rate constant ka).\nThe PK model has one compartment (volume V) and a linear elimination (clearance Cl).\nThis has been modified so that it will run without the model library"
+#>     dfObs <- 120
+#>     dfSub <- 12
 #>     thetaMat <- lotri({
 #>         ka_pop + V_pop + Cl_pop ~ c(0.09785, 0.00082606, 0.00041937, 
 #>             -4.2833e-05, -6.7957e-06, 1.1318e-05)
@@ -271,14 +264,6 @@ to `rxode2`:
 ``` r
 monolix2rx("lib:bolus_1cpt_TlagVCl.txt")
 #> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
-#> In file included from /usr/share/R/include/R.h:71,
-#>                  from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2parse.h:33,
-#>                  from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2/include/rxode2.h:9,
-#>                  from /home/matt/R/x86_64-pc-linux-gnu-library/4.4/rxode2parse/include/rxode2_model_shared.h:3,
-#>                  from rx_006529352ac819b40b322c71010f90c5_.c:117:
-#> /usr/share/R/include/R_ext/Complex.h:80:6: warning: ISO C99 doesn’t support unnamed structs/unions [-Wpedantic]
-#>    80 |     };
-#>       |      ^
 #> ℹ cannot find individual parameter estimates
 #>  ── rxode2-based free-form 1-cmt ODE model ────────────────────────────────────── 
 #> 
@@ -313,41 +298,27 @@ try(monolix2rx("lib:notThere.txt"))
 ```
 
 In newer versions of Monolix, the model library was turned into a binary
-database that is accessed by the GUI. To me there are advantages of
-this:
+database that is accessed by the GUI and `lixoftConnectors`. If you have
+`lixoftConnectors` on your system and it can successfully load the model
+with `lixoftConnectors::getLibraryModelContent()` then `monolix2rx` will
+also load the model correctly (and will use this version over the text
+files when both are setup)
 
-  - A binary database would be much faster in loading models
+This means you will need to import models into `rxode2` you need to:
 
-  - With a model library, you don’t have to put common model files all
-    over the place (saving space on your system)
-
-  - It would make their hard work on the excellent model library harder
-    to take and put into another system (They have at least 31,558
-    models).
+  - For a model built from the model library you will need:
 
-      - While this now allows a complete import of the Monolix library,
-        I believe our `nlmixr2lib` should only be built from imported
-        from a open-source library or be created on its own (as we are
-        doing in `nlmixr2lib`).
+      - have a path to the text file Monolix Library and setup the
+        `monolix2rx.library` with
+        `options(monolix2rx.library="~/src/monolix/library/")`
 
-      - Please do not request direct translations of models from Monolix
-        to our library `nlmixr2lib`; these requests will be rejected.
-
-If you want the model library as text files, you may be able to reach
-out to Lixoft and ask if they will provide them to you (or point to the
-last version that used these text files.)
-
-My biggest concern with this a approach is submitting Monolix models
-from the model library to regulatory bodies. For the regulators to be
-able to truly see the models they have to have a working copy Monolix.
-If they do not, the model is a black box.
-
-For that reason, I believe best practice when submitting to a regulatory
-body is to make the model available by making some change to the model
-and saving it to a final location. That way the regulators can see the
-model.
-
-This approach also allows the model to be translated to `rxode2`.
+      - have `lixoftConnectors` installed and connected to a newer (and
+        licensed) version of Monolix that can get the model library
+        content by `lixoftConnectors::getLibraryModelContent()`
+
+      - or without these options, you will need to save the model to a
+        text file outside of the model library so you can import the
+        model.
 
 # Note on testing