Cmdstanr option

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

@@ -36,9 +36,18 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          dependencies: NA
+          extra-packages: |
+            rcmdcheck
+            stan-dev/cmdstanr
+            testthat
+
+      - name: Install cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          upload-snapshots: true
+          upload-snapshots: true

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

@@ -47,13 +47,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install cmdstan Linux system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev || true
-          sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
-          sudo apt-get install -y libpng-dev || true
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -65,8 +58,20 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          dependencies: NA
+          extra-packages: |
+            dplyr
+            rmarkdown
+            rcmdcheck
+            stan-dev/cmdstanr
+            testthat
+
+      - name: Install cmdstan
+        if: runner.os != 'Windows'
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/lint-only-changed-files.yaml

@@ -21,11 +21,12 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          dependencies: NA
           extra-packages: |
+            stan-dev/cmdstanr
             any::gh
             any::lintr
             any::purrr
-          needs: check
 
       - name: Add lintr options
         run: |
@@ -44,4 +45,4 @@ jobs:
           lintr::lint_package(exclusions = exclusions_list)
         shell: Rscript {0}
         env:
-          LINTR_ERROR_ON_LINT: true
+          LINTR_ERROR_ON_LINT: true

.github/workflows/synthetic-validation.yaml

@@ -24,7 +24,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          dependencies: NA
           extra-packages: |
+            here
             dplyr
             tidyr
             scoringutils
@@ -48,4 +50,4 @@ jobs:
         with:
           name: fits
           retention-days: 5
-          path: synthetic.rds
+          path: synthetic.rds

.github/workflows/test-coverage.yaml

@@ -26,9 +26,18 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
-          needs: coverage
+          dependencies: NA
+          extra-packages: |
+            covr
+            stan-dev/cmdstanr
+            testthat
+
+      - name: Install cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
+        shell: Rscript {0}
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
-        shell: Rscript {0}
+        shell: Rscript {0}

.gitignore

@@ -40,3 +40,8 @@ vignettes/results
 
 # unused figures
 man/figures/*.png
+
+# exclude compiled stan files
+inst/stan/*
+!inst/stan/*/
+!inst/stan/*.stan

DESCRIPTION

@@ -109,6 +109,7 @@ Imports:
     lubridate,
     methods,
     patchwork,
+    posterior,
     progressr,
     purrr,
     R.utils (>= 2.0.0),
@@ -122,6 +123,7 @@ Imports:
     truncnorm,
     utils
 Suggests:
+    cmdstanr,
     covr,
     dplyr,
     here,
@@ -143,13 +145,15 @@ LinkingTo:
     RcppParallel (>= 5.0.1),
     rstan (>= 2.26.0),
     StanHeaders (>= 2.26.0)
+Additional_repositories:
+    https://mc-stan.org/r-packages/
 Biarch: true
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 NeedsCompilation: yes
 SystemRequirements: GNU make
        C++17

NAMESPACE

@@ -46,6 +46,7 @@ export(estimates_by_report_date)
 export(expose_stan_fns)
 export(extract_CrIs)
 export(extract_inits)
+export(extract_samples)
 export(extract_stan_param)
 export(fix_dist)
 export(forecast_infections)
@@ -66,6 +67,7 @@ export(make_conf)
 export(map_prob_change)
 export(obs_opts)
 export(opts_list)
+export(package_model)
 export(plot_estimates)
 export(plot_summary)
 export(regional_epinow)
@@ -91,6 +93,8 @@ export(setup_target_folder)
 export(simulate_infections)
 export(simulate_secondary)
 export(stan_opts)
+export(stan_sampling_opts)
+export(stan_vb_opts)
 export(summarise_key_measures)
 export(summarise_results)
 export(trunc_opts)
@@ -133,6 +137,7 @@ importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
 importFrom(data.table,setDTthreads)
 importFrom(data.table,setcolorder)
+importFrom(data.table,setkey)
 importFrom(data.table,setnames)
 importFrom(data.table,setorder)
 importFrom(data.table,setorderv)
@@ -184,6 +189,7 @@ importFrom(lifecycle,deprecate_warn)
 importFrom(lubridate,days)
 importFrom(lubridate,wday)
 importFrom(patchwork,plot_layout)
+importFrom(posterior,mcse_mean)
 importFrom(progressr,progressor)
 importFrom(progressr,with_progress)
 importFrom(purrr,compact)

R/create.R

@@ -630,8 +630,14 @@ create_initial_conditions <- function(data) {
 #'
 #' @param data A list of stan data as created by [create_stan_data()]
 #'
-#' @param init Initial conditions passed to `{rstan}`. Defaults to "random" but
-#' can also be a function (as supplied by [create_initial_conditions()]).
+#' @param init Initial conditions passed to `{rstan}`. Defaults to "random"
+#' (initial values randomly drawn between -2 and 2) but can also be a
+#' function (as supplied by [create_initial_conditions()]).
+#'
+#' @param model Character, name of the model for which arguments are
+#' to be created.
+#' @param fixed_param Logical, defaults to `FALSE`. Should arguments be
+#' created to sample from fixed parameters (used by simulation functions).
 #'
 #' @param verbose Logical, defaults to `FALSE`. Should verbose progress
 #' messages be returned.
@@ -650,7 +656,28 @@ create_initial_conditions <- function(data) {
 create_stan_args <- function(stan = stan_opts(),
                              data = NULL,
                              init = "random",
+                             model = "estimate_infections",
+                             fixed_param = FALSE,
                              verbose = FALSE) {
+  if (fixed_param) {
+    if (stan$backend == "rstan") {
+      stan$algorithm <- "Fixed_param"
+    } else if (stan$backend == "cmdstanr") {
+      stan$fixed_param <- TRUE
+      stan$adapt_delta <- NULL
+      stan$max_treedepth <- NULL
+    }
+  }
+  ## generate stan model
+  if (is.null(stan$object)) {
+    stan$object <- stan_model(stan$backend, model)
+    stan$backend <- NULL
+  }
+  # cmdstanr doesn't have an init = "random" argument
+  if (is.character(init) && init == "random" &&
+      inherits(stan$object, "CmdStanModel")) {
+    init <- 2
+  }
   # set up shared default arguments
   args <- list(
     data = data,

R/dist.R

@@ -199,6 +199,7 @@
 #' @return A stan fit of an interval censored distribution
 #' @author Sam Abbott
 #' @export
+#' @inheritParams stan_opts
 #' @examples
 #' \donttest{
 #' # integer adjusted exponential model
@@ -221,7 +222,8 @@
 #' )
 #' }
 dist_fit <- function(values = NULL, samples = 1000, cores = 1,
-                     chains = 2, dist = "exp", verbose = FALSE) {
+                     chains = 2, dist = "exp", verbose = FALSE,
+                     backend = "rstan") {
   if (samples < 1000) {
     samples <- 1000
     warning(sprintf("%s %s", "`samples` must be at least 1000.",
@@ -244,7 +246,7 @@
     par_sigma = numeric(0)
   )
 
-  model <- stanmodels$dist_fit
+  model <- stan_model(backend, "dist_fit")
 
   if (dist == "exp") {
     data$dist <- 0
@@ -268,16 +270,21 @@
   }
 
   # fit model
-  fit <- rstan::sampling(
-    model,
-    data = data,
-    iter = samples + 1000,
-    warmup = 1000,
-    control = list(adapt_delta = adapt_delta),
-    chains = chains,
-    cores = cores,
-    refresh = ifelse(verbose, 50, 0)
+  args <- create_stan_args(
+    stan = stan_opts(
+      model,
+      samples = samples,
+      warmup = 1000,
+      control = list(adapt_delta = adapt_delta),
+      chains = chains,
+      cores = cores,
+      backend = backend
+    ),
+    data = data, verbose = verbose, model = "dist_fit"
   )
+
+  fit <- fit_model(args, id = "dist_fit")
+
   return(fit)
 }
 
@@ -533,11 +540,11 @@
 
     out <- list()
     if (dist == "lognormal") {
-      out$mean_samples <- sample(rstan::extract(fit)$mu, samples)
-      out$sd_samples <- sample(rstan::extract(fit)$sigma, samples)
+      out$mean_samples <- sample(extract(fit)$mu, samples)
+      out$sd_samples <- sample(extract(fit)$sigma, samples)
     } else if (dist == "gamma") {
-      alpha_samples <- sample(rstan::extract(fit)$alpha, samples)
-      beta_samples <- sample(rstan::extract(fit)$beta, samples)
+      alpha_samples <- sample(extract(fit)$alpha, samples)
+      beta_samples <- sample(extract(fit)$beta, samples)
       out$mean_samples <- alpha_samples / beta_samples
       out$sd_samples <- sqrt(alpha_samples) / beta_samples
     }