Update tests

microbiome · Jan 7, 2025 · e4cd2d9 · e4cd2d9
1 parent 9d48076
commit e4cd2d9
Show file tree

Hide file tree

Showing 4 changed files with 21 additions and 17 deletions.
diff --git a/tests/testthat/test-0diversity.R b/tests/testthat/test-0diversity.R
@@ -9,7 +9,7 @@ test_that("diversity estimates", {
     indices <- c("coverage", "fisher", "gini_simpson", "faith",
                  "inverse_simpson", "log_modulo_skewness",
                  "shannon")
-    tse_idx <- .estimate_diversity(tse, index = indices, threshold = 0.473)
+    tse_idx <- addAlpha(tse, index = indices, threshold = 0.473)
 
     # Checks that the type of output is the same as the type of input.
     expect_true(typeof(tse_idx) == typeof(tse))
@@ -43,7 +43,7 @@ test_that("diversity estimates", {
 
     # Tests that 'quantile' and 'nclasses' are working
     expect_equal(unname(round(colData(
-        .estimate_diversity(
+        addAlpha(
             tse, index="log_modulo_skewness", quantile=0.855,nclasses=32)
         )$log_modulo_skewness, 6)), c(1.814770, 1.756495, 1.842704))
 
@@ -121,16 +121,16 @@ test_that("diversity estimates", {
     data(GlobalPatterns, package="mia")
     data(esophagus, package="mia")
     tse <- mergeSEs(GlobalPatterns, esophagus,  join = "full", assay.type = "counts")
-    expect_error(.estimate_diversity(tse, index = c("shannon", "faith"), 
+    expect_error(addAlpha(tse, index = c("shannon", "faith"), 
                                      tree.name = "phylo.1", assay.type="counts"))
-    expect_error(.estimate_diversity(tse, index = c("faith"), 
+    expect_error(addAlpha(tse, index = c("faith"), 
                                    tree.name = "test"))
-    expect_error(.estimate_diversity(tse, index = c("shannon", "faith"), 
+    expect_error(addAlpha(tse, index = c("shannon", "faith"), 
                                    tree.name = TRUE))
-    expect_error(.estimate_diversity(tse, index = c("shannon", "faith"), 
+    expect_error(addAlpha(tse, index = c("shannon", "faith"), 
                                    tree.name = 1))
 
-    expect_error(.estimate_diversity(tse, index = c("shannon", "faith"), 
+    expect_error(addAlpha(tse, index = c("shannon", "faith"), 
                                    tree.name = c("phylo", "phylo.1")))
 
     # Test Faith with picante packages results (version 1.8.2)

diff --git a/tests/testthat/test-5dominance.R b/tests/testthat/test-5dominance.R
@@ -11,7 +11,10 @@ test_that(".estimate_dominance", {
 
         #.estimate_dominance
         #Calculates all indices.
-        tse_idx <- .estimate_dominance(tse)
+        indices <- c(
+            "absolute", "dbp", "core_abundance", "gini", "dmn", "relative",
+            "simpson_lambda")
+        tse_idx <- addAlpha(tse, index = indices)
 
         #Checks that the type of output is the same as the type of input.
         expect_true(typeof(tse_idx) == typeof(tse))
@@ -22,8 +25,7 @@ test_that(".estimate_dominance", {
         #in the input vector.
         expect_named(
             colData(tse_idx),
-            c("absolute", "dbp", "core_abundance", "gini", "dmn", "relative",
-            "simpson_lambda"))
+            indices)
 
         #.calc_core_dominance
         #Rounded because, without it gave an error (average difference was

diff --git a/tests/testthat/test-5evenness.R b/tests/testthat/test-5evenness.R
@@ -8,14 +8,15 @@ test_that(".estimate_evenness", {
         # colData.
         # Check that the order of indices is right / the same as the order
         # in the input vector.
-	    tse_idx <- .estimate_evenness(tse)
+        indices <- c("camargo", "pielou", "simpson_evenness", "evar", "bulla")
+	    tse_idx <- addAlpha(tse, index = indices)
 
         # Check that the type of output is the same as the type of input.
         expect_true(typeof(tse_idx) == typeof(tse))
 
         expect_named(
             colData(tse_idx),
-            c("camargo", "pielou", "simpson_evenness", "evar", "bulla"))
+            indices)
 
         mat <- assay(tse_idx,"counts")
 

diff --git a/tests/testthat/test-5richness.R b/tests/testthat/test-5richness.R
@@ -5,8 +5,9 @@ test_that(".estimate_richness", {
 
     skip_if_not(requireNamespace("vegan", quietly = TRUE))
     data(esophagus, package="mia")
-
-    tse <- .estimate_richness(esophagus, detection = 1)
+
+    indices <- c("ace", "chao1", "hill", "observed")
+    tse <- addAlpha(esophagus, index = indices, detection = 1)
     cd <- colData(tse)    
     expect_equal(unname(round(cd$observed, 0)), c(15, 24, 16))
     # These are unaffected by detection parameter
@@ -17,7 +18,7 @@ test_that(".estimate_richness", {
     test_internal_.estimate_richness <- function(tse){
 
         # Calculate all indices.
-        tse_idx <- .estimate_richness(tse)
+        tse_idx <- addAlpha(tse, index = indices)
 
         # Check that the type of output is the same as the type of input.
         expect_true(typeof(tse_idx) == typeof(tse))
@@ -31,10 +32,10 @@ test_that(".estimate_richness", {
             c("ace", "ace_se", "chao1", "chao1_se", "hill", "observed"))
 
         # Delete colData
-	colData(tse_idx) <- NULL
+	    colData(tse_idx) <- NULL
 
         # Calculate all indices with specified names
-        tse_idx <- .estimate_richness(tse,
+        tse_idx <- addAlpha(tse,
 	    index = c("observed", "chao1", "ace", "hill"),
 	    name = c("Observed", "Chao1", "ACE", "Hill")
 	    )