Convert rstan to suggest (#441)

Closes #400

.github/actions/build-src/action.yml

@@ -8,48 +8,27 @@ inputs:
 runs:
   using: "composite"
   steps:
-    
+
     - name: Determine system/package state
       run: |
         sink(".github/meta.txt")
             list(
                 version = version,
-                pkgs = installed.packages()[c("Rcpp", "rstan", "rstantools"), c("Version", "Package")]
+                pkgs = installed.packages()[c("rstan"), c("Version", "Package")]
             )
         sink()
       shell: Rscript {0}
-
-    # The default R/stanmodels.R was updated in v2.2.0 (11Apr2022)
-    # Normally for older versions it would change itself on the fly
-    # when it compiles the stan model
-    # but as we are using cached models we are preventing compilation
-    # and thus need to manually refresh the file
-    - name: Refresh rstantools config files
-      shell: bash
-      run: |
-        echo "inputs.refresh = ${{ inputs.refresh }}"
-        if ${{ inputs.refresh }} ; then
-          Rscript -e "rstantools::rstan_config()"
-        fi
-    
+
     - name: Cache Compiled Stan Code
       id: cache-pkgs
       uses: actions/cache@v3
       with:
-        path: src/*
+        path: local/*
         key: ${{ hashFiles('.github/meta.txt') }}-${{ hashFiles('inst/stan/MMRM.stan') }}
-
-
-    # pkgbuild compares time stamps of *.so object to all header files including
-    # inst/include/stan_meta_header.hpp  so we touch the .so object to push its time
-    # stamp beyond that of the .hpp file
+
     - name: Build if needed
       shell: bash
+      env:
+        RBMI_CACHE_DIR: local
       run: |
-        if [[ ${{ steps.cache-pkgs.outputs.cache-hit == 'true' }} && "${{ runner.os }}" !=  "Windows" ]] ; then
-            echo "No compilation needed!"
-            touch src/*.so
-        else
-            echo "Compilation needed!"
-            Rscript -e "pkgbuild::compile_dll()"
-        fi
+        Rscript -e "pkgload::load_all(); get_stan_model()"

.github/actions/rcmdcheck/action.yml

@@ -1,10 +1,6 @@
 
 name: 'Build src'
 description: 'Build src!'
-inputs:
-  slim:
-    description: 'Should the reduced set of checks be run'
-    default: false
 runs:
   using: "composite"
   steps:
@@ -15,16 +11,12 @@ runs:
       
     - name: Run R CMD check
       env:
+        RBMI_CACHE_DIR: local
         _R_CHECK_CRAN_INCOMING_: false
         _R_CHECK_CRAN_INCOMING_REMOTE_: false
       shell: bash
       run: |
-        echo "inputs.slim = ${{ inputs.slim }}"
-        if ${{ inputs.slim }} ; then
-          R CMD check --no-manual --no-build-vignettes --no-vignettes --ignore-vignettes *.tar.gz
-        else
           R CMD check --no-manual --as-cran *.tar.gz
-        fi
 
     - name: Catch warnings in R CMD check output
       id: catch-errors

.github/workflows/on_biweekly.yaml

@@ -32,6 +32,4 @@ jobs:
 
       - name: Check
         uses: ./.github/actions/rcmdcheck
-        with:
-          slim: true
 

.github/workflows/on_pr_main.yaml

@@ -32,8 +32,6 @@ jobs:
 
       - name: Check
         uses: ./.github/actions/rcmdcheck
-        with:
-          slim: true
 
 
   vignettes:
@@ -53,5 +51,7 @@ jobs:
         uses: ./.github/actions/build-src
 
       - name: Build Vignettes
+        env:
+          RBMI_CACHE_DIR: local
         run: |
           Rscript ./vignettes/build.R

.github/workflows/on_push.yaml

@@ -22,6 +22,8 @@ jobs:
         uses: ./.github/actions/build-src
 
       - name: testthat
+        env:
+          RBMI_CACHE_DIR: local
         run: |
           options(crayon.enabled = TRUE, cli.dynamic = FALSE)
           devtools::test(stop_on_failure = TRUE, reporter = testthat::CheckReporter)

.gitignore

@@ -61,3 +61,4 @@ docs
 
 
 local/
+*.rds

.lintr

@@ -1,4 +1,5 @@
-linters: with_defaults(
+linters: linters_with_defaults(
     line_length_linter(120),
-    object_name_linter = NULL
+    object_name_linter = NULL,
+    indentation_linter(indent = 4L)
     )

.vscode/tasks.json

@@ -18,10 +18,25 @@
             }
         },
         {
-            "label": "R - testthat (FULL)",
+            "label": "rbmi - testthat (local cache)",
+            "problemMatcher": "$testthat",
             "command": "Rscript",
+            "args" : [
+                "-e",
+                "devtools::test()"
+            ],
             "options": {
                 "env": {
+                    "RBMI_CACHE_DIR" : "${workspaceFolder}/local"
+                }
+            },
+        },
+        {
+            "label": "rbmi - testthat (FULL)",
+            "command": "Rscript",
+            "options": {
+                "env": {
+                    "RBMI_CACHE_DIR" : "${workspaceFolder}/local",
                     "R_TEST_FULL" : "TRUE"
                 }
             },
@@ -34,27 +49,7 @@
                 "clear": true,
                 "panel": "dedicated"
             },
-            "problemMatcher": {
-                "owner": "R-testthat",
-                "severity": "error",
-                "fileLocation": [
-                    "relative",
-                    "${workspaceFolder}/tests/testthat"
-                ],
-                "pattern": [
-                    {
-                        "regexp": "^(Failure|Error)\\s\\((.*\\.[Rr]):(\\d+):(\\d+)\\):\\s(.*)",
-                        "file": 2,
-                        "line": 3,
-                        "column": 4,
-                        "message": 5
-                    },
-                    {
-                        "regexp": "^(.*)$",
-                        "message": 1
-                    }
-                ]
-            }
+            "problemMatcher": "$testthat"
         }
     ]
 }

DESCRIPTION

@@ -33,28 +33,17 @@ Suggests:
     lubridate,
     purrr,
     ggplot2,
+    rstan (>= 2.26.0),
     R.rsp
-Biarch: true
 Config/testthat/edition: 3
 Imports:
     mmrm,
     pkgload,
     Matrix,
+    tools,
     methods,
-    Rcpp (>= 0.12.0),
-    RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
-    rstantools (>= 2.1.1),
     R6,
     assertthat
-LinkingTo: 
-    BH (>= 1.66.0),
-    Rcpp (>= 0.12.0),
-    RcppEigen (>= 0.3.3.3.0),
-    RcppParallel (>= 5.0.1),
-    rstan (>= 2.26.0),
-    StanHeaders (>= 2.26.0)
-SystemRequirements: GNU make
 Depends: 
     R (>= 3.4.0)
 License: Apache License (>= 2)

NAMESPACE

@@ -75,13 +75,9 @@ export(strategy_MAR)
 export(validate)
 export(validate_analyse_pars)
 import(R6)
-import(Rcpp)
 import(methods)
 importFrom(assertthat,assert_that)
 importFrom(mmrm,VarCorr)
-importFrom(rstan,extract)
-importFrom(rstan,sampling)
-importFrom(rstan,summary)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)
 importFrom(stats,binomial)
@@ -107,4 +103,3 @@ importFrom(stats,var)
 importFrom(stats,vcov)
 importFrom(utils,capture.output)
 importFrom(utils,relist)
-useDynLib(rbmi, .registration = TRUE)

R/mcmc.R

@@ -4,7 +4,7 @@
 #' @description
 #' `fit_mcmc()` fits the base imputation model using a Bayesian approach.
 #' This is done through a MCMC method that is implemented in `stan`
-#' and is run by using the function [rstan::sampling()].
+#' and is run by using the function `rstan::sampling()`.
 #' The function returns the draws from the posterior distribution of the model parameters
 #' and the `stanfit` object. Additionally it performs multiple diagnostics checks of the chain
 #' and returns warnings in case of any detected issues.
@@ -45,10 +45,7 @@
 #' - `fit`: a `stanfit` object.
 #'
 #'
-#' @import Rcpp
 #' @import methods
-#' @importFrom rstan sampling
-#' @useDynLib rbmi, .registration = TRUE
 fit_mcmc <- function(
     designmat,
     outcome,
@@ -95,7 +92,7 @@ fit_mcmc <- function(
     )
 
     sampling_args <- list(
-        object = stanmodels$MMRM,
+        object = get_stan_model(),
         data = stan_data,
         pars = c("beta", "Sigma"),
         chains = 1,
@@ -116,7 +113,7 @@ fit_mcmc <- function(
     sampling_args$seed <- sample.int(.Machine$integer.max, 1)
 
     stan_fit <- record({
-        do.call(sampling, sampling_args)
+        do.call(rstan::sampling, sampling_args)
     })
 
     if (!is.null(stan_fit$errors)) {
@@ -218,8 +215,8 @@ split_dim <- function(a, n) {
 #' @description
 #' Extract draws from a `stanfit` object and convert them into lists.
 #'
-#' The function [rstan::extract()] returns the draws for a given parameter as an array. This function
-#' calls [rstan::extract()] to extract the draws from a `stanfit` object
+#' The function `rstan::extract()` returns the draws for a given parameter as an array. This function
+#' calls `rstan::extract()` to extract the draws from a `stanfit` object
 #' and then convert the arrays into lists.
 #'
 #' @param stan_fit A `stanfit` object.
@@ -233,10 +230,9 @@ split_dim <- function(a, n) {
 #'   of the list is a list with length equal to 1 if `same_cov = TRUE` or equal to the
 #'   number of groups if `same_cov = FALSE`.
 #'
-#' @importFrom rstan extract
 extract_draws <- function(stan_fit) {
 
-    pars <- extract(stan_fit, pars = c("beta", "Sigma"))
+    pars <- rstan::extract(stan_fit, pars = c("beta", "Sigma"))
     names(pars) <- c("beta", "sigma")
 
     ##################### from array to list
@@ -261,7 +257,6 @@ extract_draws <- function(stan_fit) {
 #' @return
 #' A named vector containing the ESS for each parameter of the model.
 #'
-#' @importFrom rstan summary
 get_ESS <- function(stan_fit) {
     return(rstan::summary(stan_fit, pars = c("beta", "Sigma"))$summary[, "n_eff"])
 }
@@ -316,7 +311,7 @@ check_ESS <- function(stan_fit, n_draws, threshold_lowESS = 0.4) {
 #' 2. The Bayesian Fraction of Missing Information (BFMI) is sufficiently low.
 #' 3. The number of iterations that saturated the max treedepth is zero.
 #'
-#' Please see [rstan::check_hmc_diagnostics()] for details.
+#' Please see `rstan::check_hmc_diagnostics()` for details.
 #'
 #' @param stan_fit A `stanfit` object.
 #'