From 3d6b1c4a2dc6e99b31c4f8d1c478254b71eaf881 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Fri, 18 Apr 2025 09:59:53 -0400
Subject: [PATCH] minor fix

---
 tests/README.md                  |  1 +
 tests/testthat/test_colocboost.R | 15 ++++-----------
 tests/testthat/test_inference.R  |  8 ++++----
 3 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/tests/README.md b/tests/README.md
index 54c6810..4758617 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -28,6 +28,7 @@ This repository contains a comprehensive testing framework for the [colocboost](
 - `testthat/`: Directory containing test files
   - `test_package.R`: Tests for basic package functionality
   - `test_colocboost.R`: Tests for the main colocalization functions
+  - `test_inference.R`: Tests for the post inference functions
   - `test_utils.R`: Tests for utility functions
   - `test_model.R`: Tests for model fitting and prediction functions
 - `.github/workflows/`: GitHub Actions workflow configurations
diff --git a/tests/testthat/test_colocboost.R b/tests/testthat/test_colocboost.R
index e8360bd..e7e7c25 100644
--- a/tests/testthat/test_colocboost.R
+++ b/tests/testthat/test_colocboost.R
@@ -43,7 +43,6 @@ test_data <- generate_test_data()
 
 # Basic test for colocboost functionality with individual data
 test_that("colocboost runs with individual data", {
-  skip_on_cran()
   
   # Convert Y to list
   Y_list <- list(test_data$Y[,1], test_data$Y[,2])
@@ -71,7 +70,6 @@ test_that("colocboost runs with individual data", {
 
 # Test with summary statistics
 test_that("colocboost runs with summary statistics", {
-  skip_on_cran()
   
   # Generate summary statistics from the individual data
   X <- test_data$X
@@ -120,7 +118,6 @@ test_that("colocboost runs with summary statistics", {
 
 # Test focal outcome functionality
 test_that("colocboost handles focal outcome correctly", {
-  skip_on_cran()
   
   # Convert Y to list
   Y_list <- list(test_data$Y[,1], test_data$Y[,2])
@@ -145,7 +142,6 @@ test_that("colocboost handles focal outcome correctly", {
 
 # Test get_cos_summary functionality
 test_that("get_cos_summary returns expected structure", {
-  skip_on_cran()
   
   # Convert Y to list
   Y_list <- list(test_data$Y[,1], test_data$Y[,2])
@@ -180,7 +176,6 @@ test_that("get_cos_summary returns expected structure", {
 
 # Test colocboost_plot functionality (basic call should not error)
 test_that("colocboost_plot runs without error", {
-  skip_on_cran()
   
   # Convert Y to list
   Y_list <- list(test_data$Y[,1], test_data$Y[,2])
@@ -199,9 +194,8 @@ test_that("colocboost_plot runs without error", {
   expect_error(suppressWarnings(colocboost_plot(result)), NA)
 })
 
-# Test get_strong_colocalization functionality
-test_that("get_strong_colocalization maintains colocboost structure", {
-  skip_on_cran()
+# Test get_robust_colocalization functionality
+test_that("get_robust_colocalization maintains colocboost structure", {
   
   # Convert Y to list
   Y_list <- list(test_data$Y[,1], test_data$Y[,2])
@@ -216,7 +210,7 @@ test_that("get_strong_colocalization maintains colocboost structure", {
   )
   
   # Run get_strong_colocalization
-  strong_result <- get_strong_colocalization(
+  strong_result <- get_robust_colocalization(
     result, 
     cos_npc_cutoff = 0.2,  # Lower threshold for testing
     npc_outcome_cutoff = 0.1  # Lower threshold for testing
@@ -231,8 +225,7 @@ test_that("get_strong_colocalization maintains colocboost structure", {
 
 # Test error handling with malformed input
 test_that("colocboost handles missing/invalid inputs appropriately", {
-  skip_on_cran()
-  
+
   # Test missing both individual data and summary stats
   expect_warning(colocboost(), "Error: No individual data")
   
diff --git a/tests/testthat/test_inference.R b/tests/testthat/test_inference.R
index 72bb0f1..863456a 100644
--- a/tests/testthat/test_inference.R
+++ b/tests/testthat/test_inference.R
@@ -82,17 +82,17 @@ test_that("get_cos_summary handles different parameters", {
 })
 
 # Test for get_strong_colocalization
-test_that("get_strong_colocalization filters results correctly", {
+test_that("get_robust_colocalization filters results correctly", {
 
   # Generate a test colocboost results
   cb_res <- generate_test_result()
   
   # Basic call
-  expect_error(get_strong_colocalization(cb_res), NA)
+  expect_error(get_robust_colocalization(cb_res), NA)
   
   # With stricter thresholds
-  expect_error(get_strong_colocalization(cb_res, cos_npc_cutoff = 0.8), NA)
+  expect_error(get_robust_colocalization(cb_res, cos_npc_cutoff = 0.8), NA)
   
   # With p-value threshold
-  expect_error(get_strong_colocalization(cb_res, pvalue_cutoff = 0.05), NA)
+  expect_error(get_robust_colocalization(cb_res, pvalue_cutoff = 0.05), NA)
 })
\ No newline at end of file