Merge branch 'main' into 728-wnl-style-linear-compartment-models-usin…

…g-combined-rxode2

.Rbuildignore

@@ -9,6 +9,7 @@
 ^Meta$
 ^doc$
 .Rdata
+.projectile
 ^\.travis.yml$
 ^\.lintr$
 ^.git.*$

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

@@ -50,13 +50,14 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 7
+          cache-version: 9
           pak-version: stable
           extra-packages: |
             any::rcmdcheck
             nlmixr2/dparser-R
             nlmixr2/lotri
             nlmixr2/rxode2ll
+            nlmixr2/PreciseSums
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -38,12 +38,13 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 6
+          cache-version: 8
           extra-packages: |
             any::pkgdown
             nlmixr2/dparser-R
             nlmixr2/lotri
             nlmixr2/rxode2ll
+            nlmixr2/PreciseSums
             local::.
           needs: website
 

.github/workflows/test-coverage.yaml

@@ -26,12 +26,13 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache-version: 6
+          cache-version: 8
           extra-packages: |
             any::covr
             nlmixr2/dparser-R
             nlmixr2/lotri
             nlmixr2/rxode2ll
+            nlmixr2/PreciseSums
           needs: coverage
 
       - name: Test coverage

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rxode2
-Version: 2.1.3.9000
+Version: 3.0.2
 Title: Facilities for Simulating from ODE-Based Models
 Authors@R: c(
    person("Matthew L.","Fidler", role = c("aut", "cre"), email = "matthew.fidler@gmail.com", comment=c(ORCID="0000-0001-8538-6691")),
@@ -26,6 +26,7 @@ Authors@R: c(
    person("Matt", "Dowle", role="ctb", email="mattjdowle@gmail.com"),
    person("Matteo", "Fasiolo", email = "matteo.fasiolo@gmail.com", role = "ctb"),
    person("Melissa", "Hallow", role = "aut", email = "hallowkm@uga.edu"),
+   person("Michel", "Lang", , "michellang@gmail.com", role = "ctb"),
    person("Morwenn","", role="ctb"),
    person("Nicholas J.", "Higham",role="ctb"),
    person("Omar", "Elashkar", email="omar.i.elashkar@gmail.com", role="ctb"),
@@ -75,22 +76,22 @@ Suggests:
     lifecycle,
     kableExtra
 Imports:
-    PreciseSums (>= 0.3),
+    PreciseSums (>= 0.7),
     Rcpp (>= 0.12.3),
     backports,
     cli (>= 2.0.0),
     checkmate,
     ggplot2 (>= 3.4.0),
     inline,
-    lotri (>= 0.4.0),
+    lotri (>= 1.0.0),
     magrittr,
     memoise,
     methods,
     rex,
     sys,
     tools,
     utils,
-    dparser,
+    dparser (>= 1.3.1-12),
     rxode2ll(>= 2.0.9),
     data.table (>= 1.12.4),
     qs (>= 0.26.3)
@@ -116,14 +117,15 @@ RoxygenNote: 7.3.2
 Biarch: true
 LinkingTo:
     sitmo,
-    PreciseSums (>= 0.3),
+    lotri (>= 1.0.0),
+    PreciseSums (>= 0.7),
     Rcpp,
     RcppArmadillo (>= 0.9.300.2.0),
     BH,
     RcppParallel,
     RcppEigen (>= 0.3.3.9.2),
     StanHeaders (>= 2.21.0.7),
-    dparser
+    dparser (>= 1.3.1-12)
 Encoding: UTF-8
 LazyData: true
 Language: en-US

NAMESPACE

@@ -27,6 +27,7 @@ S3method("ini<-",default)
 S3method("model<-",default)
 S3method("rxode2<-","function")
 S3method("rxode2<-",default)
+S3method("units<-",rxEvid)
 S3method(.DollarNames,rxEt)
 S3method(.DollarNames,rxSolve)
 S3method(.DollarNames,rxUi)
@@ -157,6 +158,46 @@ S3method(rxSolve,rxUi)
 S3method(rxSolve,rxode2tos)
 S3method(rxTrans,character)
 S3method(rxTrans,default)
+S3method(rxUdfUi,default)
+S3method(rxUdfUi,linMod)
+S3method(rxUdfUi,linMod0)
+S3method(rxUdfUi,linModA)
+S3method(rxUdfUi,linModA0)
+S3method(rxUdfUi,linModB)
+S3method(rxUdfUi,linModB0)
+S3method(rxUdfUi,linModD)
+S3method(rxUdfUi,linModD0)
+S3method(rxUdfUi,linModM)
+S3method(rxUdfUi,linModM0)
+S3method(rxUdfUi,ribeta)
+S3method(rxUdfUi,ribinom)
+S3method(rxUdfUi,ricauchy)
+S3method(rxUdfUi,richisq)
+S3method(rxUdfUi,riexp)
+S3method(rxUdfUi,rif)
+S3method(rxUdfUi,rigamma)
+S3method(rxUdfUi,rigeom)
+S3method(rxUdfUi,rinorm)
+S3method(rxUdfUi,ripois)
+S3method(rxUdfUi,rit)
+S3method(rxUdfUi,riunif)
+S3method(rxUdfUi,riweibull)
+S3method(rxUdfUi,rxbeta)
+S3method(rxUdfUi,rxbinom)
+S3method(rxUdfUi,rxcauchy)
+S3method(rxUdfUi,rxchisq)
+S3method(rxUdfUi,rxexp)
+S3method(rxUdfUi,rxf)
+S3method(rxUdfUi,rxgamma)
+S3method(rxUdfUi,rxgeom)
+S3method(rxUdfUi,rxnorm)
+S3method(rxUdfUi,rxpois)
+S3method(rxUdfUi,rxt)
+S3method(rxUdfUi,rxunif)
+S3method(rxUdfUi,rxweibull)
+S3method(rxUiDeparse,default)
+S3method(rxUiDeparse,lotriFix)
+S3method(rxUiDeparse,rxControl)
 S3method(rxUiGet,allCovs)
 S3method(rxUiGet,cmtLines)
 S3method(rxUiGet,covLhs)
@@ -169,6 +210,8 @@ S3method(rxUiGet,funPrint)
 S3method(rxUiGet,funTxt)
 S3method(rxUiGet,ini)
 S3method(rxUiGet,iniFun)
+S3method(rxUiGet,interpLines)
+S3method(rxUiGet,levels)
 S3method(rxUiGet,lhsCov)
 S3method(rxUiGet,lhsEta)
 S3method(rxUiGet,lhsTheta)
@@ -182,13 +225,14 @@ S3method(rxUiGet,muRefTable)
 S3method(rxUiGet,multipleEndpoint)
 S3method(rxUiGet,mvFromExpression)
 S3method(rxUiGet,omega)
-S3method(rxUiGet,params)
 S3method(rxUiGet,paramsLine)
+S3method(rxUiGet,props)
 S3method(rxUiGet,simulationIniModel)
 S3method(rxUiGet,simulationModel)
 S3method(rxUiGet,simulationSigma)
 S3method(rxUiGet,state)
 S3method(rxUiGet,stateDf)
+S3method(rxUiGet,statePropDf)
 S3method(rxUiGet,symengineModelNoPrune)
 S3method(rxUiGet,symengineModelPrune)
 S3method(rxUiGet,theta)
@@ -262,6 +306,7 @@ export(.pipeRx)
 export(.pipeSigma)
 export(.pipeThetaMat)
 export(.quoteCallInfoLines)
+export(.rxBlankIni)
 export(.rxC)
 export(.rxDocTable)
 export(.rxFromSE)
@@ -281,10 +326,12 @@ export(.rxSEeqUsr)
 export(.rxSens)
 export(.rxToSE)
 export(.rxTransInfo)
+export(.rxTransform)
 export(.rxWithOptions)
 export(.rxWithSink)
 export(.rxWithSinkBoth)
 export(.rxWithWd)
+export(.rxode2ptrs)
 export(.s3register)
 export(.solComp2)
 export(.solComp3)
@@ -312,6 +359,7 @@ export(assertCompartmentExists)
 export(assertCompartmentName)
 export(assertCompartmentNew)
 export(assertExists)
+export(assertIniDf)
 export(assertParameterValue)
 export(assertRxLinCmt)
 export(assertRxUi)
@@ -324,10 +372,13 @@ export(assertRxUiPrediction)
 export(assertRxUiRandomOnIdOnly)
 export(assertRxUiSingleEndpoint)
 export(assertRxUiTransformNormal)
+export(assertRxUnbounded)
 export(assertVariableExists)
 export(assertVariableName)
 export(assertVariableNew)
 export(binomProbs)
+export(boxCox)
+export(boxCoxInv)
 export(cvPost)
 export(dfWishart)
 export(erf)
@@ -369,6 +420,15 @@ export(label_both)
 export(label_context)
 export(label_value)
 export(label_wrap_gen)
+export(linMod)
+export(linMod0)
+export(linModA0)
+export(linModB)
+export(linModB0)
+export(linModD)
+export(linModD0)
+export(linModM)
+export(linModM0)
 export(llikBeta)
 export(llikBinom)
 export(llikCauchy)
@@ -450,6 +510,8 @@ export(rxIndLinState)
 export(rxIndLinStrategy)
 export(rxInit)
 export(rxInits)
+export(rxIntToBase)
+export(rxIntToLetter)
 export(rxInv)
 export(rxIs)
 export(rxIsCurrent)
@@ -520,8 +582,18 @@ export(rxTheme)
 export(rxTick)
 export(rxToSE)
 export(rxTrans)
+export(rxUdfUi)
+export(rxUdfUiData)
+export(rxUdfUiEst)
+export(rxUdfUiIniDf)
+export(rxUdfUiIniLhs)
+export(rxUdfUiMv)
+export(rxUdfUiNum)
+export(rxUdfUiParsing)
+export(rxUdfUiReset)
 export(rxUiCompress)
 export(rxUiDecompress)
+export(rxUiDeparse)
 export(rxUiGet)
 export(rxUnload)
 export(rxUnloadAll)
@@ -571,14 +643,19 @@ export(stat_cens)
 export(swapMatListWithCube)
 export(testCompartmentExists)
 export(testExists)
+export(testIniDf)
 export(testRxLinCmt)
+export(testRxUnbounded)
 export(testVariableExists)
 export(toTrialDuration)
 export(uppergamma)
 export(waiver)
+export(warnRxBounded)
 export(write.template.server)
 export(write.template.ui)
 export(xlab)
+export(yeoJohnson)
+export(yeoJohnsonInv)
 export(ylab)
 export(zeroRe)
 import(data.table)