Issue #362: Reduce dependence on cmdstanr (#424)

* Switch default to rstan rather than cmdstanr * Import BH * Use match.arg as suggested by @jamesmbaazam * Add RcppEigen to Suggests * Change backend to cmdstanr in approximate inference vignette * Use cmdstanr for Laplace test * Remove erroneous output_dir arg * drop backend entirely as an arg * remove cmdstanr using vignettes from cran check * update cmdstan install instructions * update epidist docs * update approx-inference vignette to make it clear we are using cmdstanr and not rstan * switch ebola vignette over to cmdstanr * update test fit returns * update more fit uses in test * fix helper function * bring silence to laplace * fix epidist * get tests passing * fix CRAN check * use fewer cores * drop additional deps * drop duplicate prepping * try and use linking with instead of imports * Update vignettes/epidist.Rmd Co-authored-by: Adam Howes <[email protected]> * Update tests/testthat/test-int-latent_individual.R Co-authored-by: Adam Howes <[email protected]> * Update inst/generate_examples.R Co-authored-by: Adam Howes <[email protected]> --------- Co-authored-by: Sam <[email protected]>
epinowcast · Nov 14, 2024 · 4afb056 · 4afb056
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,4 +14,6 @@
 ^doc$
 ^Meta$
 README.Rmd
-^pkgdown$
+^pkgdown$
+^vignettes/approx-inference\.Rmd$
+^vignettes/ebola\.Rmd$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,7 +31,7 @@ Imports:
     stats,
     cli,
     checkmate,
-    rstan,
+    rstan (>= 2.26.0),
     dplyr
 Suggests:
     bookdown,
@@ -52,6 +52,10 @@ Suggests:
     patchwork,
     cmdstanr,
     priorsense
+LinkingTo: 
+    BH (>= 1.66.0),
+    Rcpp (>= 0.12.0),
+    RcppEigen (>= 0.3.3.3.0)
 Additional_repositories:
     https://stan-dev.r-universe.dev
 Config/Needs/website:

diff --git a/NAMESPACE b/NAMESPACE
@@ -68,3 +68,4 @@ importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(stats,as.formula)
+importFrom(stats,setNames)
diff --git a/R/fit.R → R/epidist.R b/R/fit.R → R/epidist.R
@@ -14,18 +14,15 @@
 #' @param prior One or more `brmsprior` objects created by [brms::set_prior()]
 #' or related functions. These priors are passed to [epidist_prior()] in the
 #' `prior` argument.
-#' @param backend Character string naming the package to use as the backend for
-#' fitting the Stan model. Options are `"rstan"` and `"cmdstanr"` (the default).
-#' This option is passed directly through to `fn`.
 #' @param fn The internal function to be called. By default this is
 #' [brms::brm()] which performs inference for the specified model. Other options
 #' are [brms::make_stancode()] which returns the Stan code for the specified
 #' model, or [brms::make_standata()] which returns the data passed to Stan.
 #' These two later options may be useful for model debugging and extensions.
-#' @param ... Additional arguments passed to method.
+#' @param ... Additional arguments passed to `fn` method.
 #' @family fit
 #' @export
-epidist <- function(data, formula, family, prior, backend, fn, ...) {
+epidist <- function(data, formula, family, prior, fn, ...) {
   UseMethod("epidist")
 }
 
@@ -38,7 +35,7 @@ epidist <- function(data, formula, family, prior, backend, fn, ...) {
 #' @export
 epidist.default <- function(data, formula = mu ~ 1,
                             family = "lognormal", prior = NULL,
-                            backend = "cmdstanr", fn = brms::brm, ...) {
+                            fn = brms::brm, ...) {
   epidist_validate_model(data)
   epidist_family <- epidist_family(data, family)
   epidist_formula <- epidist_formula(
@@ -52,7 +49,7 @@ epidist.default <- function(data, formula = mu ~ 1,
   )
   fit <- fn(
     formula = epidist_formula, family = epidist_family, prior = epidist_prior,
-    stanvars = epidist_stancode, backend = backend, data = data, ...
+    stanvars = epidist_stancode, data = data, ...
   )
   class(fit) <- c(class(fit), "epidist_fit")
   return(fit)

diff --git a/R/utils.R b/R/utils.R
@@ -131,6 +131,7 @@
 #' @param new_names ...
 #' @param old_names ...
 #' @keywords internal
+#' @importFrom stats setNames
 .rename_columns <- function(df, new_names, old_names) {
   are_char <- is.character(new_names) & is.character(old_names)
   valid_new_names <- new_names[are_char]

diff --git a/README.Rmd b/README.Rmd
@@ -76,14 +76,16 @@ remotes::install_github(
 
 </details>
 
-<details><summary>Installing CmdStan</summary>
+<details><summary>Installing CmdStan (optional)</summary>
 
-If you wish to do model fitting, you will need to install [CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also entails having a suitable C++ toolchain setup. We recommend using the [`cmdstanr` package](https://mc-stan.org/cmdstanr/). The Stan team provides instructions in the [_Getting started with
+By default `epidist` uses the `rstan` package for fitting models. If you wish to use the `cmdstanr` package instead, you will need to install [CmdStan](https://mc-stan.org/users/interfaces/cmdstan), which also entails having a suitable C++ toolchain setup. We recommend using the [`cmdstanr` package](https://mc-stan.org/cmdstanr/) to manage CmdStan. The Stan team provides instructions in the [_Getting started with
 `cmdstanr`_](https://mc-stan.org/cmdstanr/articles/cmdstanr.html) vignette, with other details and support at the [package site](https://mc-stan.org/cmdstanr/), but the brief version is:
 
 ```{r, eval = FALSE}
 # if you not yet installed `epidist`, or you installed it without `Suggests` dependencies
-install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
+install.packages(
+  "cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos"))
+)
 # once `cmdstanr` is installed:
 cmdstanr::install_cmdstan()
 ```
@@ -92,12 +94,6 @@ cmdstanr::install_cmdstan()
 
 </details>
 
-<!-- <details><summary>Alternative: Docker</summary> -->
-
-<!-- We also provide a [Docker](https://www.docker.com/get-started/) image with [all dependencies installed](https://github.com/orgs/epinowcast/packages/container/package/epidist). You can use this image to run `epidist` without installing dependencies. -->
-
-<!-- </details> -->
-
 ## Resources
 
 <details><summary>Organisation Website</summary>

diff --git a/inst/generate_examples.R b/inst/generate_examples.R
@@ -1,12 +1,4 @@
 source("tests/testthat/setup.R")
-set.seed(1)
-prep_obs <- as_latent_individual(sim_obs)
-fit <- epidist(prep_obs, seed = 1)
+
 saveRDS(fit, "inst/extdata/fit.rds")
-prep_obs_gamma <- as_latent_individual(sim_obs_gamma)
-fit_gamma <- epidist(
-  prep_obs_gamma,
-  family = stats::Gamma(link = "log"),
-  seed = 1
-)
 saveRDS(fit_gamma, "inst/extdata/fit_gamma.rds")
diff --git a/man/epidist.Rd b/man/epidist.Rd
diff --git a/man/epidist.default.Rd b/man/epidist.default.Rd
diff --git a/man/epidist_family.Rd b/man/epidist_family.Rd
diff --git a/man/epidist_family_model.Rd b/man/epidist_family_model.Rd
diff --git a/man/epidist_family_model.default.Rd b/man/epidist_family_model.default.Rd
diff --git a/man/epidist_family_prior.Rd b/man/epidist_family_prior.Rd
diff --git a/man/epidist_family_prior.default.Rd b/man/epidist_family_prior.default.Rd
diff --git a/man/epidist_family_prior.lognormal.Rd b/man/epidist_family_prior.lognormal.Rd
diff --git a/man/epidist_family_reparam.Rd b/man/epidist_family_reparam.Rd
diff --git a/man/epidist_family_reparam.default.Rd b/man/epidist_family_reparam.default.Rd
diff --git a/man/epidist_family_reparam.gamma.Rd b/man/epidist_family_reparam.gamma.Rd
diff --git a/man/epidist_formula.Rd b/man/epidist_formula.Rd
diff --git a/man/epidist_formula_model.default.Rd b/man/epidist_formula_model.default.Rd
diff --git a/man/epidist_model_prior.Rd b/man/epidist_model_prior.Rd
diff --git a/man/epidist_model_prior.default.Rd b/man/epidist_model_prior.default.Rd
diff --git a/man/epidist_stancode.Rd b/man/epidist_stancode.Rd
diff --git a/man/epidist_stancode.default.Rd b/man/epidist_stancode.default.Rd
diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
@@ -0,0 +1,28 @@
+on_ci <- function() {
+  isTRUE(as.logical(Sys.getenv("CI")))
+}
+
+not_on_cran <- function() {
+  identical(Sys.getenv("NOT_CRAN"), "true")
+}
+
+skip_on_local <- function() {
+  if (on_ci()) {
+    return(invisible(TRUE))
+  }
+  testthat::skip("Not on CI")
+}
+
+as_string_formula <- function(formula) {
+  form <- paste(deparse(formula), collapse = " ")
+  form <- gsub("\\s+", " ", form, perl = FALSE)
+  return(form)
+}
+
+extract_normal_parameters_brms <- function(prior) {
+  pattern <- "normal\\(([^,]+), ([^\\)]+)\\)"
+  match <- regmatches(prior, regexec(pattern, prior))
+  mean <- as.numeric(match[[1]][2])
+  sd <- as.numeric(match[[1]][3])
+  return(list(mean = mean, sd = sd))
+}
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -82,3 +82,32 @@ sim_obs_sex <- dplyr::bind_rows(sim_obs_sex_m, sim_obs_sex_f) |>
 
 # Temporary solution for classing time data
 sim_obs_sex <- as_epidist_linelist_time(sim_obs_sex)
+
+prep_obs <- as_latent_individual(sim_obs)
+prep_direct_obs <- as_direct_model(sim_obs)
+prep_obs_gamma <- as_latent_individual(sim_obs_gamma)
+prep_obs_sex <- as_latent_individual(sim_obs_sex)
+
+if (not_on_cran()) {
+  set.seed(1)
+  fit <- epidist(
+    data = prep_obs, seed = 1, chains = 2, cores = 2, silent = 2, refresh = 0,
+    backend = "cmdstanr"
+  )
+  fit_rstan <- epidist(
+    data = prep_obs, seed = 1, chains = 2, cores = 2, silent = 2, refresh = 0
+  )
+
+  fit_gamma <- epidist(
+    data = prep_obs_gamma, family = stats::Gamma(link = "log"),
+    seed = 1, chains = 2, cores = 2, silent = 2, refresh = 0,
+    backend = "cmdstanr"
+  )
+
+  fit_sex <- epidist(
+    data = prep_obs_sex,
+    formula = brms::bf(mu ~ 1 + sex, sigma ~ 1 + sex),
+    seed = 1, silent = 2, refresh = 0,
+    cores = 2, chains = 2, backend = "cmdstanr"
+  )
+}