Merge pull request #70 from poissonconsulting/b-conditional-suggests

Skip tests if suggested packages aren't installed, remove dependency on aods3 package.

DESCRIPTION

@@ -28,7 +28,6 @@ Imports:
     lifecycle,
     stats
 Suggests: 
-    aods3,
     covr,
     hms,
     ggplot2,

cran-comments.md

@@ -20,6 +20,16 @@ New maintainer:
   Nicole Hill <[email protected]>
 Old maintainer(s):
   Joe Thorley <[email protected]>
+
+## CRAN Issues
+
+Fixed the following error by conditionally skipping tests that rely on packages listed in suggests, if those packages are not installed.
+After review, also decided to remove the dependency to the 'aods3' package.
+
+══ Failed tests ════════════════════════════════════════════════════════════════
+── Error ('test-log-lik.R:184:3'): beta_binom log_lik ──────────────────────────
+<packageNotFoundError/error/condition>
+Error in `loadNamespace(x)`: there is no package called 'aods3'
 
 ## revdepcheck results
 

tests/testthat/_snaps/log-lik.md

@@ -0,0 +1,21 @@
+# beta_binom log_lik
+
+    Code
+      log_lik_beta_binom(x = samples, size = 50, prob = 0.2, theta = 1.1)
+    Output
+        [1] -4.976366 -2.395701 -1.375050 -3.917547 -1.375050 -4.314925 -4.409988
+        [8] -3.218659 -4.045703 -1.375050 -4.409988 -1.375050 -3.685783 -1.375050
+       [15] -1.375050 -2.395701 -1.375050 -1.375050 -4.845012 -1.375050 -2.395701
+       [22] -4.631547 -2.787926 -1.375050 -1.375050 -1.375050 -3.983622 -3.769878
+       [29] -1.375050 -1.375050 -1.375050 -3.769878 -3.035763 -3.769878 -3.364624
+       [36] -3.486792 -5.021646 -1.375050 -2.395701 -1.375050 -1.375050 -1.375050
+       [43] -3.218659 -1.375050 -3.592380 -4.045703 -1.375050 -1.375050 -1.375050
+       [50] -2.787926 -5.269883 -4.976366 -2.395701 -1.375050 -5.326411 -1.375050
+       [57] -1.375050 -4.716959 -1.375050 -3.218659 -1.375050 -3.685783 -5.521217
+       [64] -1.375050 -1.375050 -1.375050 -3.486792 -3.364624 -1.375050 -2.395701
+       [71] -1.375050 -4.265252 -1.375050 -2.395701 -1.375050 -2.395701 -3.592380
+       [78] -3.486792 -1.375050 -3.769878 -2.395701 -4.045703 -1.375050 -3.035763
+       [85] -2.395701 -3.218659 -1.375050 -2.787926 -1.375050 -3.035763 -1.375050
+       [92] -1.375050 -1.375050 -1.375050 -4.265252 -1.375050 -2.395701 -3.364624
+       [99] -3.035763 -1.375050
+

tests/testthat/test-dev.R

@@ -242,6 +242,7 @@ test_that("gamma_pois log_lik", {
 })
 
 test_that("gamma_pois deviance", {
+  skip_if_not_installed("MASS")
   samples <- ran_gamma_pois(10000, 3, 0.5)
   mod <- MASS::glm.nb(samples ~ 1)
   deviance <- sum(dev_gamma_pois(samples, exp(coef(mod)[1]), theta = 1 / mod$theta))

tests/testthat/test-log-lik.R

@@ -178,21 +178,18 @@ test_that("beta_binom vectorized", {
 })
 
 test_that("beta_binom log_lik", {
-  samples2 <- ran_beta_binom(100, size = 50, prob = 0.1, theta = 1)
-  data <- data.frame(
-    samples2 = samples2,
-    mod_prob2 = 50 - samples2
+  withr::with_seed(
+    101,
+    samples <- ran_beta_binom(100, size = 50, prob = 0.1, theta = 1)
   )
-  mod2 <- aods3::aodml(cbind(samples2, mod_prob2) ~ 1,
-    data = data,
-    family = "bb", method = "Nelder-Mead"
+  expect_snapshot(
+    log_lik_beta_binom(
+      x = samples,
+      size = 50,
+      prob = 0.2,
+      theta = 1.1
+    )
   )
-  est_prob <- ilogit(mod2$b)
-  est_theta <- 2 / (1 / mod2$phi - 1)
-  expect_equal(mod2$logL, sum(log_lik_beta_binom(samples2,
-    size = 50,
-    prob = est_prob, theta = est_theta
-  )))
 })
 
 test_that("skewnorm missing values", {

tests/testthat/test-numericise.R

@@ -92,6 +92,7 @@ test_that("numericise.data.frame", {
 })
 
 test_that("numericise.hms", {
+  skip_if_not_installed("hms")
   x <- structure(10.9, class = c("hms", "difftime"), units = "secs")
   expect_identical(numericise(x), 10.9)
 })