Initial commit with updated testthat files

Author: annemarie-sharp

DESCRIPTION

@@ -29,11 +29,12 @@ Imports:
     ggplot2,
     kableExtra
 Suggests: 
-    BiocStyle, 
+    BiocStyle,
     knitr,
     rmarkdown,
     broom,
-    jtools
+    jtools,
+    testthat (>= 3.0.0)
 Remotes:
     waldronlab/BugSigDBStats,
     waldronlab/bugsigdbr
@@ -43,3 +44,4 @@ VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 Encoding: UTF-8
 URL: https://waldronlab.io/bugSigSimple
+Config/testthat/edition: 3

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(bugSigSimple)
+
+test_check("bugSigSimple")

tests/testthat/test-MPA.TAX.LEVELS.R

@@ -0,0 +1,11 @@
+#Function file: simple.R
+
+
+test_that("MPA.TAX.LEVELS contains correct taxonomic level abbreviations", {
+  expected <- c("k", "p", "c", "o", "f", "g", "s", "t")
+  names(expected) <- c("kingdom", "phylum", "class", "order",
+                       "family", "genus", "species", "strain")
+  
+  expect_equal(MPA.TAX.LEVELS, expected)
+})
+

tests/testthat/test-countBug.R

@@ -0,0 +1,16 @@
+#Function file: montecarlo.R
+
+
+test_that(".countBug returns max frequency of most common taxon", {
+  relevant.sigs <- list(
+    sig1 = c("Bacteroides", "Escherichia"),
+    sig2 = c("Bacteroides", "Bifidobacterium")
+  )
+  
+  set.seed(123)
+  result <- .countBug(relevant.sigs, c(2, 2))
+  
+  expect_type(result, "integer")
+  expect_true(result >= 1)
+  expect_true(result <= 4)  # Max possible count
+})

tests/testthat/test-createStudyTable.R

@@ -0,0 +1,6 @@
+#Function file: describe_curation.R
+
+bsdb <- bugsigdbr::importBugSigDB()
+test_that("createStudyTable creates a table of all studies currently in data.frame", {
+  expect_s3_class(createStudyTable(bsdb[1:10,]), "data.frame")
+})

tests/testthat/test-createTaxonTable.R

@@ -0,0 +1,6 @@
+#Function file: describe_curation.R
+
+bsdb <- bugsigdbr::importBugSigDB()
+test_that("createTaxonTable creates a table of most frequent taxa in a data.frame", {
+  expect_s3_class(createTaxonTable(bsdb[1:10,]), "data.frame")
+})

tests/testthat/test-frequencySigs.R

@@ -0,0 +1,18 @@
+#Function file: montecarlo.R
+
+
+# Mock .getTip function since it's not in global environment
+.getTip <- function(x) x
+
+test_that("frequencySigs identifies the most frequently occuring taxa", {
+  test_sigs <- list(
+    "UP_sig1" = c("Bacteroides", "Escherichia"),
+    "UP_sig2" = c("Bacteroides", "Bifidobacterium")
+  )
+  
+  result <- frequencySigs(test_sigs, n = 2)
+  
+  expect_s3_class(result, "table")
+  expect_equal(length(result), 2)
+  expect_equal(names(result)[1], "Bacteroides")
+})

tests/testthat/test-getCriticalN.R

@@ -0,0 +1,16 @@
+#Function file: montecarlo.R
+
+
+test_that("getCriticalN returns 95th percentile threshold", {
+  relevant.sigs <- list(
+    sig1 = c("Bacteroides", "Escherichia"),
+    sig2 = c("Bacteroides", "Bifidobacterium")
+  )
+  
+  set.seed(123)
+  result <- getCriticalN(relevant.sigs, c(2, 2), nsim = 100)
+  
+  expect_type(result, "double")
+  expect_true(result >= 1)
+  expect_true(result <= 4)
+})

tests/testthat/test-getMostFrequentTaxa.R

@@ -0,0 +1,33 @@
+#Function file: simple.R
+
+
+test_that("getMostFrequentTaxa returns the most frequently occurring taxa in a table of signatures", {
+  # Create test data
+  test_data <- data.frame(
+    PMID = c("123", "456", "789"),
+    `Abundance in Group 1` = c("increased", "decreased", "increased"),
+    check.names = FALSE
+  )
+  
+  # Mock bugsigdbr::getSignatures to return test taxa
+  mock_signatures <- list(
+    "123" = c("k__Bacteria|g__Blautia", "k__Bacteria|g__Bacteroides"),
+    "456" = c("k__Bacteria|g__Blautia", "k__Bacteria|g__Lactobacillus"), 
+    "789" = c("k__Bacteria|g__Blautia")
+  )
+  
+  with_mocked_bindings(
+    getSignatures = function(...) mock_signatures,
+    .package = "bugsigdbr",
+    {
+      result <- getMostFrequentTaxa(test_data, n = 5)
+      
+      # Basic checks
+      expect_true(is.table(result))
+      expect_true(length(result) <= 5)
+      expect_equal(as.numeric(result[1]), 3)  # Blautia appears 3 times
+      expect_equal(names(result[1]), "k__Bacteria|g__Blautia")  # Check name
+      expect_true(all(diff(result) <= 0))  # Sorted descending
+    }
+  )
+})

tests/testthat/test-getTip.R

@@ -0,0 +1,19 @@
+#Function file: simple.R
+
+
+# Firstly, test when there are multiple levels
+test_that(".getTip returns the last part of the string", {
+  s <- "k__Bacteria|p__Firmicutes|g__Lactobacillus"
+  
+  result <- .getTip(s)
+
+  expect_equal(result, "g__Lactobacillus")
+})
+
+
+# Secondly, test when there is only one level
+test_that(".getTip works when string has only one level", {
+  s <- "k__Bacteria"
+  result <- .getTip(s)
+  expect_equal(result, "k__Bacteria")
+})