overall ci and unit tests for expgrowth

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

@@ -71,6 +71,7 @@ jobs:
           needs: check
 
       - name: Install cmdstan
+        if: matrix.config.os == 'ubuntu-latest'
         uses: epinowcast/actions/install-cmdstan@v1
         with:
           cmdstan-version: 'latest'

.github/workflows/check-cmdstan.yaml

@@ -52,13 +52,18 @@ jobs:
 
       - name: Compile model and check syntax
         run: |
-          model <- epinowcast::enw_model()
+          model <- primarycensoreddist::pcd_load_stan_functions(
+            wrap_in_block = TRUE,
+            write_to_file = TRUE,
+            output_file = file.path(tempdir(), "pcd_stan_functions.stan")
+          )
+          model <- cmdstanr::cmdstan_model(model)
           # If the model is not syntactically correct above will fail
           # however it may be correct enougth to compile but still contain
           # soft depreciated syntax and so we check the syntax again below
           # and test the output.
           message <- capture.output(
-            model$check_syntax(pedantic = FALSE),
+            model$check_syntax(pedantic = TRUE),
             type = "message"
           )
           # We can't use TRUE here as pendatic check return lots of false

.github/workflows/pkgdown.yaml

@@ -4,6 +4,10 @@ on:
   push:
     branches: [main]
   workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+
 
 name: pkgdown
 

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, develop]
+    branches: [main]
   pull_request:
-    branches: [main, master, develop]
+    branches: [main]
   workflow_dispatch:
   merge_group:
 

tests/testthat/setup.R

@@ -2,7 +2,9 @@
 options(datatable.print.class = FALSE)
 options(datatable.print.keys = FALSE)
 
-if (on_ci() && Sys.info()["sysname"] == "Linux" && not_on_cran()) {
+if (
+  !on_ci() || (on_ci() && Sys.info()["sysname"] == "Linux" && not_on_cran())
+) {
   library(cmdstanr)
   stan_functions <- pcd_load_stan_functions(
     wrap_in_block = TRUE,
@@ -12,4 +14,5 @@ if (on_ci() && Sys.info()["sysname"] == "Linux" && not_on_cran()) {
   model <- suppressMessages(suppressWarnings(cmdstanr::cmdstan_model(
     file.path(tempdir(), "pcd_stan_functions.stan")
   )))
+  model$expose_functions(global = TRUE)
 }

tests/testthat/test-stan-expgrowth.R

@@ -0,0 +1,67 @@
+skip_on_cran()
+skip_on_os("windows")
+skip_on_os("mac")
+
+test_that("Stan expgrowth_pdf matches R dexpgrowth", {
+  x <- seq(0, 1, by = 0.1)
+  min <- 0
+  max <- 1
+  r <- 0.5
+
+  stan_pdf <- sapply(x, expgrowth_pdf, min, max, r)
+  r_pdf <- dexpgrowth(x, min, max, r)
+
+  expect_equal(stan_pdf, r_pdf, tolerance = 1e-4)
+})
+
+test_that("Stan expgrowth_lpdf matches R dexpgrowth with log = TRUE", {
+  x <- seq(0, 1, by = 0.1)
+  min <- 0
+  max <- 1
+  r <- 0.5
+
+  stan_lpdf <- sapply(x, expgrowth_lpdf, min, max, r)
+  r_lpdf <- dexpgrowth(x, min, max, r, log = TRUE)
+
+  expect_equal(stan_lpdf, r_lpdf, tolerance = 1e-4)
+})
+
+test_that("Stan expgrowth_cdf matches R pexpgrowth", {
+  x <- seq(0, 1, by = 0.1)
+  min <- 0
+  max <- 1
+  r <- 0.5
+
+  stan_cdf <- sapply(x, expgrowth_cdf, min, max, r)
+  r_cdf <- pexpgrowth(x, min, max, r)
+
+  expect_equal(stan_cdf, r_cdf, tolerance = 1e-4)
+})
+
+test_that("Stan expgrowth_lcdf matches R pexpgrowth with log.p = TRUE", {
+  x <- seq(0, 1, by = 0.1)
+  min <- 0
+  max <- 1
+  r <- 0.5
+
+  stan_lcdf <- sapply(x, expgrowth_lcdf, min, max, r)
+  r_lcdf <- pexpgrowth(x, min, max, r, log.p = TRUE)
+
+  expect_equal(stan_lcdf, r_lcdf, tolerance = 1e-6)
+})
+
+test_that("Stan expgrowth_rng matches distribution of R rexpgrowth", {
+  n <- 10000
+  min <- 0
+  max <- 1
+  r <- 0.5
+
+  set.seed(123)
+  stan_samples <- replicate(n, expgrowth_rng(min, max, r))
+  set.seed(123)
+  r_samples <- rexpgrowth(n, min, max, r)
+
+  expect_equal(mean(stan_samples), mean(r_samples), tolerance = 1e-2)
+  expect_equal(sd(stan_samples), sd(r_samples), tolerance = 1e-2)
+  expect_equal(quantile(stan_samples), quantile(r_samples), tolerance = 1e-2)
+})