Merge pull request #160 from nlmixr2/159-sslag-options

159 sslag options
nlmixr2 · Aug 27, 2023 · f9c6be3 · f9c6be3
2 parents 3d114f0 + 08709e7
commit f9c6be3
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Showing 4 changed files with 43 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -37,7 +37,7 @@ Imports:
     dparser,
     lotri,
     Rcpp,
-    rxode2 (>= 2.0.12),
+    rxode2 (> 2.0.13),
     magrittr,
     cli,
     tools,

diff --git a/R/buildParser.R b/R/buildParser.R
@@ -103,9 +103,25 @@
       covsInterpolation <- "nocb"
       .minfo("using nocb interpolation like NONMEM, specify directly to change")
     }
+    if (missing(addlKeepsCov)) {
+      .minfo("using addlKeepsCov=TRUE like NONMEM, specify directly to change")
+      addlKeepsCov <- TRUE
+    }
+    if (missing(addlDropSs)) {
+      .minfo("using addlDropSs=TRUE like NONMEM, specify directly to change")
+      addlDropSs <- TRUE
+    }
+    if (missing(ssAtDoseTime)) {
+      .minfo("using ssAtDoseTime=TRUE like NONMEM, specify directly to change")
+      ssAtDoseTime <- TRUE
+    }
     if (missing(safeZero)) {
       .minfo("using safeZero=FALSE since NONMEM does not use protection by default")
-      safeZero=TRUE
+      safeZero <- TRUE
+    }
+    if (missing(ss2cancelAllPending)) {
+      .minfo("using ss2cancelAllPending=FALSE since NONMEM does not cancel pending doses with SS=2")
+      ss2cancelAllPending <- FALSE
     }
     if (!missing(nStud)) {
       if (missing(dfSub)) {

diff --git a/R/rxSolve.R b/R/rxSolve.R
@@ -36,14 +36,32 @@ rxSolve.nonmem2rx <- function(object, params = NULL, events = NULL,
         rate2 = TRUE, dur2 = TRUE), resample = NULL, resampleID = TRUE, 
     maxwhile = 1e+05, atolSens = 1e-08, rtolSens = 1e-06, ssAtolSens = 1e-08, 
     ssRtolSens = 1e-06, simVariability = NA, nLlikAlloc = NULL, 
-    useStdPow = FALSE) {
+    useStdPow = FALSE, naTimeHandle = c("ignore", "warn", "error"), 
+    addlKeepsCov = FALSE, addlDropSs = TRUE, ssAtDoseTime = TRUE, 
+    ss2cancelAllPending = FALSE) {
     if (missing(covsInterpolation)) {
         covsInterpolation <- "nocb"
         .minfo("using nocb interpolation like NONMEM, specify directly to change")
     }
+    if (missing(addlKeepsCov)) {
+        .minfo("using addlKeepsCov=TRUE like NONMEM, specify directly to change")
+        addlKeepsCov <- TRUE
+    }
+    if (missing(addlDropSs)) {
+        .minfo("using addlDropSs=TRUE like NONMEM, specify directly to change")
+        addlDropSs <- TRUE
+    }
+    if (missing(ssAtDoseTime)) {
+        .minfo("using ssAtDoseTime=TRUE like NONMEM, specify directly to change")
+        ssAtDoseTime <- TRUE
+    }
     if (missing(safeZero)) {
         .minfo("using safeZero=FALSE since NONMEM does not use protection by default")
-        safeZero = TRUE
+        safeZero <- TRUE
+    }
+    if (missing(ss2cancelAllPending)) {
+        .minfo("using ss2cancelAllPending=FALSE since NONMEM does not cancel pending doses with SS=2")
+        ss2cancelAllPending <- FALSE
     }
     if (!missing(nStud)) {
         if (missing(dfSub)) {
@@ -128,5 +146,7 @@ rxSolve.nonmem2rx <- function(object, params = NULL, events = NULL,
         resampleID = resampleID, maxwhile = maxwhile, atolSens = atolSens, 
         rtolSens = rtolSens, ssAtolSens = ssAtolSens, ssRtolSens = ssRtolSens, 
         simVariability = simVariability, nLlikAlloc = nLlikAlloc, 
-        useStdPow = useStdPow)
+        useStdPow = useStdPow, naTimeHandle = naTimeHandle, addlKeepsCov = addlKeepsCov, 
+        addlDropSs = addlDropSs, ssAtDoseTime = ssAtDoseTime, 
+        ss2cancelAllPending = ss2cancelAllPending)
 }
diff --git a/R/validate.R b/R/validate.R
@@ -118,7 +118,7 @@
       }
       if (!is.null(.rx$predDf)) {
         for (.v in .rx$predDf$var) {
-          .params[[paste0("err.", .v)]] <- 0
+          .params[[paste0("rxerr.", .v)]] <- 0
         }
       }
       .wid <- which(tolower(names(.params)) == "id")
@@ -236,7 +236,7 @@
                           }, double(1), USE.NAMES = TRUE))
       if (!is.null(.rx$predDf)) {
         .params <- c(.params, setNames(rep(0, length(.rx$predDf$cond)),
-                                           paste0("err.", .rx$predDf$var)))
+                                           paste0("rxerr.", .rx$predDf$var)))
       }
       .minfo("solving pred problem")
       .predSolve <- try(rxSolve(.model, .params, .nonmemData, returnType = "tibble",