Merge branch 'main' into 588-matexp-fortran

.Rbuildignore

@@ -21,6 +21,9 @@ testthat/.*\.(so|dll)$
 BinaryFiles$
 rxode2.*\.(zip|pdf)$
 ^/?inst/Install-windows.md
+^/?inst/residualErrors.csv$
+^/?inst/syntax-functions.csv$
+^/?inst/reserved-keywords.csv$
 ^/?.Rhistory
 ^/?R/.Rhistory
 ^/?src/.Rhistory
@@ -128,12 +131,10 @@ authors.md
 ^cran-comments\.md$
 ^authors\.md$
 tests/testthat/test-lincmt-parse.R
-^/?po/.*$
 ^/?build/buildRxODE.R$
 ^/?build/depends.R$
 ^/?build/dual.R$
 ^/?build/refresh.R$
 ^/?build/sensitivites.R$
-
 ^CRAN-SUBMISSION$
 ^revdep$

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

@@ -50,7 +50,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 2
+          cache-version: 5
           pak-version: stable
           extra-packages: |
             any::rcmdcheck

.github/workflows/pkgdown.yaml

@@ -24,6 +24,8 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       _R_CHECK_FORCE_SUGGESTS_: false
+    permissions:
+      contents: write
 
     steps:
       - uses: actions/checkout@v3
@@ -32,13 +34,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 2
+          cache-version: 4
           extra-packages: |
             any::pkgdown
             nlmixr2/dparser-R

.github/workflows/test-coverage.yaml

@@ -26,7 +26,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 2
+          cache-version: 4
           extra-packages: |
             any::covr
             nlmixr2/dparser-R

.gitignore

@@ -46,3 +46,4 @@ docs/
 *.gcda
 revdep/
 /src/sbuf.c
+docs

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rxode2
-Version: 2.0.14
+Version: 2.0.14.9000
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler",
@@ -69,7 +69,8 @@ Suggests:
     devtools,
     patchwork,
     nlmixr2data,
-    lifecycle
+    lifecycle,
+    kableExtra
 Imports:
     PreciseSums (>= 0.3),
     Rcpp (>= 0.12.3),
@@ -88,8 +89,8 @@ Imports:
     utils,
     rxode2ll(>= 2.0.9),
     rxode2et (>= 2.0.9),
-    rxode2parse (>= 2.0.12),
-    rxode2random (>= 2.0.9),
+    rxode2parse (> 2.0.16),
+    rxode2random (> 2.0.11),
     data.table (>= 1.12.4),
     qs
 Description: Facilities for running simulations from ordinary
@@ -108,7 +109,8 @@ BugReports: https://github.com/nlmixr2/rxode2/issues/
 NeedsCompilation: yes
 VignetteBuilder: knitr
 License: GPL (>= 3)
-URL: https://nlmixr2.github.io/rxode2/, https://github.com/nlmixr2/rxode2/
+URL: https://nlmixr2.github.io/rxode2/,
+    https://github.com/nlmixr2/rxode2/
 RoxygenNote: 7.2.3
 Biarch: true
 LinkingTo:

NAMESPACE

@@ -24,6 +24,7 @@ S3method(.DollarNames,rxUi)
 S3method(as.function,rxModelVars)
 S3method(as.function,rxUi)
 S3method(as.function,rxode2)
+S3method(as.function,rxode2tos)
 S3method(as.ini,call)
 S3method(as.ini,character)
 S3method(as.ini,data.frame)
@@ -33,31 +34,44 @@ S3method(as.ini,matrix)
 S3method(as.model,call)
 S3method(as.model,character)
 S3method(as.model,default)
+S3method(as.model,list)
 S3method(as.rxUi,"function")
 S3method(as.rxUi,default)
 S3method(as.rxUi,rxModelVars)
 S3method(as.rxUi,rxUi)
 S3method(as.rxUi,rxode2)
+S3method(as.rxUi,rxode2tos)
+S3method(binomProbs,default)
 S3method(coef,rxode2)
 S3method(confint,rxSolve)
 S3method(dimnames,rxSolve)
 S3method(format,boundInits)
 S3method(format,boundParams)
 S3method(format,rxSolveSimType)
+S3method(getBaseIniSimModel,default)
 S3method(getBaseSimModel,default)
+S3method(getBaseSymengineModel,default)
 S3method(ini,default)
 S3method(ini,rxUi)
+S3method(meanProbs,default)
 S3method(model,"function")
 S3method(model,default)
 S3method(model,rxModelVars)
 S3method(model,rxUi)
 S3method(model,rxode2)
+S3method(modelExtract,"function")
+S3method(modelExtract,default)
+S3method(modelExtract,rxModelVars)
+S3method(modelExtract,rxUi)
+S3method(modelExtract,rxode2)
 S3method(plot,rxSolve)
 S3method(plot,rxSolveConfint1)
 S3method(plot,rxSolveConfint2)
+S3method(predict,"function")
 S3method(predict,rxEt)
 S3method(predict,rxParams)
 S3method(predict,rxSolve)
+S3method(predict,rxUi)
 S3method(predict,rxode2)
 S3method(print,boundInits)
 S3method(print,boundParams)
@@ -104,6 +118,7 @@ S3method(rxSolve,default)
 S3method(rxSolve,nlmixr2FitCore)
 S3method(rxSolve,nlmixr2FitData)
 S3method(rxSolve,rxUi)
+S3method(rxSolve,rxode2tos)
 S3method(rxTrans,character)
 S3method(rxTrans,default)
 S3method(rxUiGet,allCovs)
@@ -131,10 +146,13 @@ S3method(rxUiGet,multipleEndpoint)
 S3method(rxUiGet,mvFromExpression)
 S3method(rxUiGet,omega)
 S3method(rxUiGet,paramsLine)
+S3method(rxUiGet,simulationIniModel)
 S3method(rxUiGet,simulationModel)
 S3method(rxUiGet,simulationSigma)
 S3method(rxUiGet,state)
 S3method(rxUiGet,stateDf)
+S3method(rxUiGet,symengineModelNoPrune)
+S3method(rxUiGet,symengineModelPrune)
 S3method(rxUiGet,theta)
 S3method(rxUiGet,thetaLhs)
 S3method(rxUiGet,thetaLower)
@@ -180,11 +198,13 @@ export(.handleSingleErrTypeNormOrTFoceiBase)
 export(.iniHandleFixOrUnfix)
 export(.iniHandleLine)
 export(.malert)
+export(.matchesLangTemplate)
 export(.minfo)
 export(.modelHandleModelLines)
 export(.msuccess)
 export(.mwarn)
 export(.quoteCallInfoLines)
+export(.rxDocTable)
 export(.rxFromSE)
 export(.rxGetHiBoundaryPred1AndIni)
 export(.rxGetLambdaFromPred1AndIni)
@@ -227,6 +247,7 @@ export(assertRxUiPrediction)
 export(assertRxUiRandomOnIdOnly)
 export(assertRxUiSingleEndpoint)
 export(assertRxUiTransformNormal)
+export(binomProbs)
 export(cvPost)
 export(erf)
 export(et)
@@ -252,7 +273,9 @@ export(genShinyApp.template)
 export(geom_amt)
 export(geom_cens)
 export(geom_line)
+export(getBaseIniSimModel)
 export(getBaseSimModel)
+export(getBaseSymengineModel)
 export(getRxThreads)
 export(ggplot)
 export(guide_none)
@@ -282,7 +305,9 @@ export(logit)
 export(logitNormInfo)
 export(lotri)
 export(lowergamma)
+export(meanProbs)
 export(model)
+export(modelExtract)
 export(odeMethodToInt)
 export(phi)
 export(probit)
@@ -378,6 +403,7 @@ export(rxSeedEng)
 export(rxSetControl)
 export(rxSetCovariateNamesForPiping)
 export(rxSetIni0)
+export(rxSetPipingAuto)
 export(rxSetProd)
 export(rxSetProgressBar)
 export(rxSetSeed)