Merge branch 'main' into vignettes_francois

.Rbuildignore

@@ -26,3 +26,5 @@
 ^local$
 ^README.Rmd$
 ^vignettes/local$
+
+^.lycheeignore$

.github/workflows/check.yaml

@@ -31,9 +31,12 @@ jobs:
         CMDSTAN=/root/.cmdstan
         CMDSTAN_PATH=/root/.cmdstan
         CMDSTANR_NO_VER_CHECK=true
-        JMPOST_CACHE_DIR=${{ github.workspace }}/.cache
-      additional-caches: |
-        ${{ github.workspace }}/.cache
+        NOT_CRAN=TRUE
+        JMPOST_GRAPH_SNAPSHOT=TRUE
+      ### Temporarily removed due to cache bug (#345)
+      #   JMPOST_CACHE_DIR=${{ github.workspace }}/.cache
+      # additional-caches: |
+      #   ${{ github.workspace }}/.cache
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -66,6 +69,10 @@ jobs:
     if: github.event_name == 'pull_request'
     name: Check URLs 🌐
     uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main
+    with:
+      link-checking-method: lychee
+      lychee-additional-args: "" # override the default of excluding private links
+      lychee-fail: true
   version:
     name: Version Check 🏁
     uses: insightsengineering/r.pkg.template/.github/workflows/version.yaml@main

.gitignore

@@ -83,7 +83,11 @@ inst/stanmodels/stan_model
 *.log
 
 
+# Local R environment variables
+.Renviron
+
 
 # Include all gitkeep files
 !.gitkeep
-!**/.gitkeep
+!**/.gitkeep
+

.lycheeignore

@@ -0,0 +1,3 @@
+https://doi.org/10.1002/sim.8756
+https://doi.org/10.1111/bcp.15200
+https://doi.org/10.1002/cpt.1450

DESCRIPTION

@@ -57,15 +57,27 @@ Suggests:
     flexsurv,
     purrr,
     vdiffr,
-    prodlim
+    prodlim,
+    loo
+Additional_repositories: https://stan-dev.r-universe.dev
 Config/testthat/edition: 3
+Config/testthat/parallel: true
 Collate:
     'DataSubject.R'
     'utilities.R'
     'generics.R'
     'DataLongitudinal.R'
     'DataSurvival.R'
     'DataJoint.R'
+    'Grid.R'
+    'GridEven.R'
+    'GridEvent.R'
+    'GridFixed.R'
+    'GridGrouped.R'
+    'GridManual.R'
+    'GridObserved.R'
+    'GridPopulation.R'
+    'GridPrediction.R'
     'constants.R'
     'StanModule.R'
     'Prior.R'
@@ -84,6 +96,10 @@ Collate:
     'LongitudinalQuantities.R'
     'LongitudinalRandomSlope.R'
     'LongitudinalSteinFojo.R'
+    'Promise.R'
+    'QuantityGeneratorPopulation.R'
+    'QuantityGeneratorPrediction.R'
+    'QuantityGeneratorSubject.R'
     'SimGroup.R'
     'SimJointData.R'
     'SimLongitudinal.R'
@@ -98,6 +114,7 @@ Collate:
     'defaults.R'
     'external-exports.R'
     'jmpost-package.R'
+    'link_generics.R'
     'settings.R'
     'zzz.R'
 VignetteBuilder: knitr

NAMESPACE

@@ -1,12 +1,29 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.CmdStanMCMC,JointModelSamples)
+S3method(as.QuantityCollapser,GridEven)
+S3method(as.QuantityCollapser,GridEvent)
+S3method(as.QuantityCollapser,GridFixed)
+S3method(as.QuantityCollapser,GridGrouped)
+S3method(as.QuantityCollapser,GridManual)
+S3method(as.QuantityCollapser,GridObserved)
+S3method(as.QuantityCollapser,GridPopulation)
+S3method(as.QuantityCollapser,GridPrediction)
+S3method(as.QuantityGenerator,GridEven)
+S3method(as.QuantityGenerator,GridEvent)
+S3method(as.QuantityGenerator,GridFixed)
+S3method(as.QuantityGenerator,GridGrouped)
+S3method(as.QuantityGenerator,GridManual)
+S3method(as.QuantityGenerator,GridObserved)
+S3method(as.QuantityGenerator,GridPopulation)
+S3method(as.QuantityGenerator,GridPrediction)
 S3method(as.StanModule,JointModel)
 S3method(as.StanModule,Link)
 S3method(as.StanModule,LinkComponent)
 S3method(as.StanModule,Parameter)
 S3method(as.StanModule,ParameterList)
 S3method(as.StanModule,Prior)
+S3method(as.StanModule,PromiseLinkComponent)
 S3method(as.character,JointModel)
 S3method(as.character,Parameter)
 S3method(as.character,Prior)
@@ -21,48 +38,73 @@ S3method(as.list,DataJoint)
 S3method(as.list,DataLongitudinal)
 S3method(as.list,DataSubject)
 S3method(as.list,DataSurvival)
+S3method(as.list,GridEven)
+S3method(as.list,GridEvent)
+S3method(as.list,GridFixed)
+S3method(as.list,GridGrouped)
+S3method(as.list,GridManual)
+S3method(as.list,GridObserved)
+S3method(as.list,GridPopulation)
+S3method(as.list,GridPrediction)
 S3method(as.list,Link)
 S3method(as.list,LinkComponent)
 S3method(as.list,ParameterList)
 S3method(as.list,StanModel)
 S3method(as.list,StanModule)
+S3method(as_formula,DataSurvival)
+S3method(as_formula,default)
 S3method(as_print_string,DataLongitudinal)
 S3method(as_print_string,DataSubject)
 S3method(as_print_string,DataSurvival)
 S3method(as_print_string,JointModelSamples)
 S3method(as_print_string,Link)
 S3method(as_print_string,LinkComponent)
 S3method(as_print_string,LongitudinalModel)
-S3method(as_print_string,LongitudinalQuantities)
 S3method(as_print_string,ParameterList)
 S3method(as_print_string,Quantities)
 S3method(as_print_string,StanModel)
 S3method(as_print_string,StanModule)
 S3method(as_print_string,SurvivalModel)
-S3method(as_print_string,SurvivalQuantities)
 S3method(as_stan_list,DataJoint)
 S3method(as_stan_list,DataLongitudinal)
 S3method(as_stan_list,DataSubject)
 S3method(as_stan_list,DataSurvival)
 S3method(as_stan_list,Parameter)
 S3method(as_stan_list,ParameterList)
 S3method(as_stan_list,Prior)
+S3method(as_stan_list,QuantityGeneratorPopulation)
+S3method(as_stan_list,QuantityGeneratorPrediction)
+S3method(as_stan_list,QuantityGeneratorSubject)
 S3method(as_stan_list,default)
 S3method(autoplot,LongitudinalQuantities)
 S3method(autoplot,SurvivalQuantities)
 S3method(brierScore,SurvivalQuantities)
+S3method(coalesceGridTime,GridFixed)
+S3method(coalesceGridTime,GridGrouped)
+S3method(coalesceGridTime,GridPopulation)
+S3method(coalesceGridTime,GridPrediction)
+S3method(coalesceGridTime,default)
 S3method(compileStanModel,JointModel)
 S3method(dim,Quantities)
+S3method(enableGQ,JointModel)
+S3method(enableGQ,LongitudinalGSF)
+S3method(enableGQ,LongitudinalRandomSlope)
+S3method(enableGQ,LongitudinalSteinFojo)
+S3method(enableGQ,default)
 S3method(enableLink,LongitudinalGSF)
 S3method(enableLink,LongitudinalRandomSlope)
 S3method(enableLink,LongitudinalSteinFojo)
+S3method(enableLink,default)
 S3method(extractVariableNames,DataSubject)
 S3method(extractVariableNames,DataSurvival)
 S3method(generateQuantities,JointModelSamples)
 S3method(getParameters,Link)
 S3method(getParameters,LinkComponent)
 S3method(getParameters,StanModel)
 S3method(getParameters,default)
+S3method(getPredictionNames,LongitudinalGSF)
+S3method(getPredictionNames,LongitudinalRandomSlope)
+S3method(getPredictionNames,LongitudinalSteinFojo)
 S3method(initialValues,JointModel)
 S3method(initialValues,Link)
 S3method(initialValues,LinkComponent)
@@ -71,19 +113,32 @@ S3method(initialValues,ParameterList)
 S3method(initialValues,Prior)
 S3method(initialValues,StanModel)
 S3method(length,Link)
+S3method(length,QuantityCollapser)
 S3method(linkDSLD,LongitudinalGSF)
-S3method(linkDSLD,LongitudinalModel)
 S3method(linkDSLD,LongitudinalRandomSlope)
 S3method(linkDSLD,LongitudinalSteinFojo)
+S3method(linkDSLD,PromiseLongitudinalModel)
+S3method(linkDSLD,default)
+S3method(linkGrowth,LongitudinalGSF)
+S3method(linkGrowth,LongitudinalRandomSlope)
+S3method(linkGrowth,LongitudinalSteinFojo)
+S3method(linkGrowth,PromiseLongitudinalModel)
+S3method(linkGrowth,default)
 S3method(linkIdentity,LongitudinalGSF)
-S3method(linkIdentity,LongitudinalModel)
 S3method(linkIdentity,LongitudinalRandomSlope)
 S3method(linkIdentity,LongitudinalSteinFojo)
+S3method(linkIdentity,PromiseLongitudinalModel)
+S3method(linkIdentity,default)
 S3method(linkTTG,LongitudinalGSF)
-S3method(linkTTG,LongitudinalModel)
 S3method(linkTTG,LongitudinalSteinFojo)
+S3method(linkTTG,PromiseLongitudinalModel)
+S3method(linkTTG,default)
+S3method(names,LinkComponent)
 S3method(names,Parameter)
 S3method(names,ParameterList)
+S3method(resolvePromise,Link)
+S3method(resolvePromise,PromiseLinkComponent)
+S3method(resolvePromise,default)
 S3method(sampleObservations,SimLongitudinalGSF)
 S3method(sampleObservations,SimLongitudinalRandomSlope)
 S3method(sampleObservations,SimLongitudinalSteinFojo)
@@ -105,6 +160,14 @@ export(DataJoint)
 export(DataLongitudinal)
 export(DataSubject)
 export(DataSurvival)
+export(GridEven)
+export(GridEvent)
+export(GridFixed)
+export(GridGrouped)
+export(GridManual)
+export(GridObserved)
+export(GridPopulation)
+export(GridPrediction)
 export(JointModel)
 export(Link)
 export(LinkComponent)
@@ -116,6 +179,8 @@ export(LongitudinalSteinFojo)
 export(Parameter)
 export(ParameterList)
 export(Prior)
+export(PromiseLinkComponent)
+export(PromiseLongitudinalModel)
 export(STAN_BLOCKS)
 export(SimGroup)
 export(SimJointData)
@@ -136,24 +201,29 @@ export(SurvivalModel)
 export(SurvivalQuantities)
 export(SurvivalWeibullPH)
 export(as.CmdStanMCMC)
+export(as.QuantityCollapser)
+export(as.QuantityGenerator)
+export(as_formula)
 export(as_stan_list)
 export(autoplot)
 export(brierScore)
 export(compileStanModel)
+export(enableGQ)
 export(enableLink)
 export(generateQuantities)
+export(getParameters)
+export(getPredictionNames)
 export(initialValues)
 export(linkDSLD)
+export(linkGrowth)
 export(linkIdentity)
+export(linkNone)
 export(linkTTG)
-export(link_dsld)
-export(link_identity)
-export(link_none)
-export(link_ttg)
 export(merge)
 export(prior_beta)
 export(prior_cauchy)
 export(prior_gamma)
+export(prior_init_only)
 export(prior_invgamma)
 export(prior_logistic)
 export(prior_loglogistic)
@@ -162,6 +232,7 @@ export(prior_normal)
 export(prior_std_normal)
 export(prior_student_t)
 export(prior_uniform)
+export(resolvePromise)
 export(sampleObservations)
 export(sampleStanModel)
 export(sampleSubjects)
@@ -181,6 +252,9 @@ exportClasses(LongitudinalSteinFojo)
 exportClasses(Parameter)
 exportClasses(ParameterList)
 exportClasses(Prior)
+exportClasses(Promise)
+exportClasses(PromiseLinkComponent)
+exportClasses(PromiseLongitudinalModel)
 exportClasses(SimGroup)
 exportClasses(SimJointData)
 exportClasses(SimLongitudinal)
@@ -204,7 +278,12 @@ importFrom(Rdpack,reprompt)
 importFrom(ggplot2,autoplot)
 importFrom(ggplot2.utils,geom_km)
 importFrom(glue,as_glue)
+importFrom(stats,.checkMFClasses)
 importFrom(stats,acf)
+importFrom(stats,as.formula)
+importFrom(stats,delete.response)
+importFrom(stats,model.frame)
+importFrom(stats,model.matrix)
 importFrom(stats,rbeta)
 importFrom(stats,rcauchy)
 importFrom(stats,rgamma)
@@ -213,5 +292,7 @@ importFrom(stats,rlogis)
 importFrom(stats,rnorm)
 importFrom(stats,rt)
 importFrom(stats,runif)
+importFrom(stats,terms)
 importFrom(survival,Surv)
+importFrom(survival,coxph)
 importFrom(tibble,add_case)