Fix test suite using new function names.

Author: astamm

.gitignore

@@ -5,3 +5,5 @@
 .DS_Store
 .quarto
 docs
+
+/.quarto/

README.Rmd

@@ -59,22 +59,22 @@ sampled from the respective shape, with Gaussian noise added (standard deviation
 function with a maximum scale of 6 and up to dimension 2.
 
 You can use the
-[`two_sample_test()`](https://tdaverse.github.io/inphr/reference/two_sample_test.html)
+[`two_sample_diagram_test()`](https://tdaverse.github.io/inphr/reference/two_sample_diagram_test.html)
 function to perform a two-sample test on these persistence diagrams. For
 example, to test whether the first 5 persistence diagrams from the first set are
 significantly different from the first 5 persistence diagrams from the second
 set, you can run:
 
 ```{r}
-two_sample_test(trefoils1[1:5], trefoils2[1:5], B = 100L)
+two_sample_diagram_test(trefoils1[1:5], trefoils2[1:5], B = 100L)
 ```
 
 To test whether the first 5 persistence diagrams from the first set are
 significantly different from the first 5 persistence diagrams from the third
 set, you can run:
 
 ```{r}
-two_sample_test(trefoils1[1:5], archspirals[1:5], B = 100L)
+two_sample_diagram_test(trefoils1[1:5], archspirals[1:5], B = 100L)
 ```
 
 ## Contributions

inst/tinytest/test-two-sample-diagram-test.R

@@ -0,0 +1,128 @@
+# Test parse_inputs() function
+test_two_sample_diagram_test_inputs <- function() {
+  ps1 <- 0
+  ps2 <- 0
+  expect_error(two_sample_diagram_test(ps1, ps2))
+  ps1 <- trefoils1[1:5]
+  expect_error(two_sample_diagram_test(ps1, ps2))
+  ps2 <- trefoils2[1:5]
+  result <- two_sample_diagram_test(ps1, ps2, B = 10L)
+  expect_true(is.numeric(result))
+
+  ps1 <- c(trefoils1[1:5], trefoils2[1:5])
+  ps2 <- c(5L, 5L) # Sample sizes
+  result <- two_sample_diagram_test(ps1, ps2, B = 10L)
+  expect_true(is.numeric(result))
+
+  D <- phutil::wasserstein_pairwise_distances(
+    ps1,
+    dimension = 0L,
+    p = 2L,
+    ncores = 1L
+  )
+  ps2 <- 0
+  expect_error(two_sample_diagram_test(D, ps2))
+  ps2 <- c(5L, 5L) # Sample sizes
+  result <- two_sample_diagram_test(D, ps2, B = 10L)
+  expect_true(is.numeric(result))
+}
+
+# Test basic functionality
+test_two_sample_diagram_test_basic <- function() {
+  ps1 <- trefoils1[1:5]
+  ps2 <- trefoils2[1:5]
+
+  result <- two_sample_diagram_test(ps1, ps2, B = 10L)
+  expect_true(is.numeric(result))
+  expect_true(result >= 0 && result <= 1)
+}
+
+# Test parameter validation
+test_two_sample_diagram_test_params <- function() {
+  ps1 <- trefoils1[1:5]
+  ps2 <- trefoils2[1:5]
+
+  expect_error(two_sample_diagram_test(ps1, ps2, dimension = -1L))
+  expect_error(two_sample_diagram_test(ps1, ps2, p = 0L))
+  expect_error(two_sample_diagram_test(ps1, ps2, B = 0L))
+  expect_error(two_sample_diagram_test(ps1, ps2, npc = "invalid"))
+}
+
+# Test with distance matrix input
+test_two_sample_diagram_test_dist <- function() {
+  D <- phutil::wasserstein_pairwise_distances(
+    c(trefoils1[1:5], trefoils2[1:5]),
+    dimension = 0L,
+    p = 2L,
+    ncores = 1L
+  )
+  sample_sizes <- c(5L, 5L)
+
+  result <- two_sample_diagram_test(D, sample_sizes, B = 10L)
+  expect_true(is.numeric(result))
+  expect_true(result >= 0 && result <= 1)
+}
+
+# Test verbose output
+test_two_sample_diagram_test_verbose <- function() {
+  ps1 <- trefoils1[1:5]
+  ps2 <- trefoils2[1:5]
+
+  expect_silent(two_sample_diagram_test(ps1, ps2, B = 10L, verbose = FALSE))
+  expect_message(
+    two_sample_diagram_test(ps1, ps2, B = 10L, verbose = TRUE),
+    "Parsing inputs..."
+  )
+  expect_message(
+    two_sample_diagram_test(ps1, ps2, B = 10L, verbose = TRUE),
+    "Setting up the plausibility function..."
+  )
+  expect_message(
+    two_sample_diagram_test(ps1, ps2, B = 10L, verbose = TRUE),
+    "Calculating the p-value..."
+  )
+}
+
+# Test different npc methods
+test_two_sample_diagram_test_npc <- function() {
+  ps1 <- trefoils1[1:5]
+  ps2 <- trefoils2[1:5]
+
+  result_tippett <- two_sample_diagram_test(ps1, ps2, B = 10L, npc = "tippett")
+  result_fisher <- two_sample_diagram_test(ps1, ps2, B = 10L, npc = "fisher")
+
+  expect_true(is.numeric(result_tippett))
+  expect_true(is.numeric(result_fisher))
+}
+
+test_two_sample_diagram_test_bottleneck <- function() {
+  ps1 <- trefoils1[1:5]
+  ps2 <- trefoils2[1:5]
+
+  result <- two_sample_diagram_test(ps1, ps2, p = Inf, B = 10L)
+  expect_true(is.numeric(result))
+  expect_true(result >= 0 && result <= 1)
+}
+
+test_two_sample_diagram_test_seed <- function() {
+  ps1 <- trefoils1[1:5]
+  ps2 <- trefoils2[1:5]
+
+  result <- two_sample_diagram_test(ps1, ps2, p = Inf, B = 10L, seed = 1234)
+  expect_true(is.numeric(result))
+  expect_true(result >= 0 && result <= 1)
+}
+
+# Run all tests
+test_two_sample_diagram_test <- function() {
+  test_two_sample_diagram_test_inputs()
+  test_two_sample_diagram_test_basic()
+  test_two_sample_diagram_test_params()
+  test_two_sample_diagram_test_dist()
+  test_two_sample_diagram_test_verbose()
+  test_two_sample_diagram_test_npc()
+  test_two_sample_diagram_test_bottleneck()
+  test_two_sample_diagram_test_seed()
+}
+
+test_two_sample_diagram_test()