Merge branch 'main' into vignette-pkncaest

NEWS.md

@@ -19,7 +19,7 @@
   changes in `focei`'s output (`$parHist` is now derived).
 
 * Changed the solving options to match the new steady state options in
-  `rxode2` and how NONMEM implements them.  Also changed the itwres
+  `rxode2` and how NONMEM implements them.  Also changed the iwres
   model to account for the `rxerr.` instead of the `err.` which was
   updated in `rxode2` as well.
 

R/convert.R

@@ -126,7 +126,7 @@ bblDatToMonolix <- function(model, data, table=nlmixr2est::tableControl(), rxCon
          call.=FALSE)
   }
   if (.conv0$hasTinf) {
-    warning("monolix changes infusion times for `tinf` with bioavailability differently than `nlmixr2`, make sure there is no bioavailibilty changes for this infusion in the model",
+    warning("monolix changes infusion times for `tinf` with bioavailability differently than `nlmixr2`, make sure there is no bioavailability changes for this infusion in the model",
             call.=FALSE)
   }
   if (.conv0$hasPhantom) {
@@ -303,7 +303,7 @@ bblDatToNonmem <- function(model, data, table=nlmixr2est::tableControl(),
   .xtra <- paste0(" to convert the data with 'bblDatToNonmem'")
   model <- rxode2::assertRxUi(model, extra=.xtra)
   model <- rxode2::rxUiDecompress(model)
-  .ret <- .bblDatToNonmem (model, data, table, rxControl, 
+  .ret <- .bblDatToNonmem (model, data, table, rxControl,
                            fun="bblDatToNonmem", replaceEvid=5L,
                            replaceOK=FALSE, software="NONMEM", env=env)
   nlmixr2est::nmObjUiSetCompressed(FALSE)
@@ -374,7 +374,7 @@ bblDatToPknca <- function(model, data, table=nlmixr2est::tableControl(),
                           rxControl=rxode2::rxControl(), env=NULL) {
   newData <-
     .bblDatToNonmem(
-      model, data, table, rxControl, 
+      model, data, table, rxControl,
       fun="bblDatToPknca", replaceEvid=5L,
       replaceOK=TRUE, software="pknca", env=env
     )

R/monolixNlmixr2est.R

@@ -237,7 +237,7 @@
     if (!exists("parHistData", .ret$env)) {
       .tmp <- .ret$ui$monolixParHistory
       if (is.null(.tmp)) {
-        .minfo("monolix parameter history needs expoted charts, please export charts")
+        .minfo("monolix parameter history needs exported charts, please export charts")
       } else {
         .tmp$type <- "Unscaled"
         assign("parHistData", .tmp, .ret$env)
@@ -303,7 +303,7 @@
     .tmp <- .ret$ui$monolixParHistory
     assign("message", paste(.msg$message, collapse="\n    "), envir=.ret$env)
     if (is.null(.tmp)) {
-      .minfo("monolix parameter history needs expoted charts, please export charts")
+      .minfo("monolix parameter history needs exported charts, please export charts")
     } else {
       .tmp$type <- "Unscaled"
       assign("parHistData", .tmp, .ret$env)

R/pknca.R

@@ -395,6 +395,7 @@ ini_transform <- function(x, ..., envir = parent.frame()) {
 #' @param ncaResults Already computed NCA results (a PKNCAresults object) to
 #'   bypass automatic calculations.  At least the following parameters must be
 #'   calculated in the NCA: tmax, cmax.dn, cl.last
+#' @param rxControl Control options sent to `rxode2::rxControl()`
 #' @return A list of parameters
 #' @export
 pkncaControl <- function(concu = NA_character_, doseu = NA_character_, timeu = NA_character_,

inst/WORDLIST

@@ -1,32 +1,42 @@
+Babelmixr
 CMD
+CWRES
 Cmax
+CodeFactor
+Codecov
 DV
+ETAs
 ISCALE
 Iaccept
 Isample
 MAPINTER
 Monolix
+Monolix’
 NCA
 NOABORT
 NONMEM
 NONMEM's
+ODEs
 PKNCA
 PKNCAresults
 PreciseSums
 RxODE
 SAEM
 Tmax
 UI
+VPC
+addl
 adm
 advan
 al
 amtu
-api
 babelmixr
 bblDatToMonolix
+bioavailability
 cancelled
 clearanceu
 cmax
+cov
 dn
 doi
 dvu
@@ -36,31 +46,37 @@ evid
 exploratoryAutoStop
 fim
 firstStage
+focei
 foceiFit
 foceiPreProcessData
-https
+ie
+iwres
 ka
-lixoft
 lixoftConnectors
-lixoftconnectors
+lixoftConnectors’
 maxeval
 monolix
 mrgsolve
 nca
 nlmixr
+nlmixr's
 nlmixrDataToMrgsolve
 nlmixrDataToNonmem
 nlmixrDataToRxode
+nlmixrMuDerCov
 nmfe
 nonmem
+objf
 pharmacokinetic
+pknca
 posthoc
 psp
 rxControl
 rxode
 saem
 sigdig
 sigl
+tableControl
 th
 timeu
 tmax
@@ -69,3 +85,5 @@ unitless
 vc
 volumeu
 vp
+vpc
+warfarin

vignettes/articles/running-monlix.Rmd

@@ -32,7 +32,7 @@ To use `Monolix` with nlmixr2, you do not need to change your data or your
 You do need to setup how to run `Monolix`.  If you have setup the
 `lixoftConnectors` package from Monolix, no further setup is needed.
 Instead if you run `Monolix` from the command line for grid processing
-(for example) you can figure out the command to run `Monlix` (it is
+(for example) you can figure out the command to run `Monolix` (it is
 often useful to use the full command path and set it in the options,
 ie `options("babelmixr2.monolix"="monolix")` or use
 `monolixControl(runCommand="monolix")`.  If needed, I prefer the
@@ -107,7 +107,7 @@ fit <- nlmixr(pk.turnover.emax3, nlmixr2data::warfarin, "monolix",
 
 This fit issues an informational tidbit -
 
-- monolix parameter history needs expoted charts, please export charts
+- monolix parameter history needs exported charts, please export charts
 
 This will automatically be generated as well when `lixoftConnectors`
 package is generated and you have a recent version of Monolix.  If you
@@ -171,7 +171,7 @@ v1s
 v2s
 ```
 
-# Notes about Monlix data translation
+# Notes about Monolix data translation
 
 The input dataset expected to be compatible with `rxode2` or
 `nlmixr2`.  This dataset is then converted to Monolix format:
@@ -184,13 +184,13 @@ The input dataset expected to be compatible with `rxode2` or
 
 - `babelmixr2` also creates a macro for each type of dosing:
 
-   - Bolus/infusion uses `depot()` and adds modeled lag time (`Tlag`) or bioavailibilty (`p`) if specified
+   - Bolus/infusion uses `depot()` and adds modeled lag time (`Tlag`) or bioavailability (`p`) if specified
 
    - Modeled rate uses `depot()` with `Tk0=amtDose/rate`. `babelmixr2`
-     also adds modeled lag time (`Tlag`) or bioavailibilty (`p`) if
+     also adds modeled lag time (`Tlag`) or bioavailability (`p`) if
      specified
 
    - Modeled duration uses `depot()` with `Tk0=dur`, also add adds
-     modeled lag time (`Tlag`) or bioavailibilty (`p`) if specified
+     modeled lag time (`Tlag`) or bioavailability (`p`) if specified
      Turning off a compartment uses empty macro