remove tools and simplify coverage reporting

Author: soodoku

.Rbuildignore

@@ -24,4 +24,3 @@
 ^\.RData$
 ^\.Ruserdata$
 ^Makefile$
-^tools$

Makefile

@@ -0,0 +1,35 @@
+.PHONY: help check test coverage doc build install clean
+
+help:
+	@echo "Available commands:"
+	@echo "  make check    - Run R CMD check"
+	@echo "  make test     - Run tests"
+	@echo "  make coverage - Check code coverage"
+	@echo "  make doc      - Generate documentation"
+	@echo "  make build    - Build package"
+	@echo "  make install  - Install package locally"
+	@echo "  make clean    - Clean build artifacts"
+
+check:
+	R CMD check .
+
+test:
+	Rscript -e "devtools::test()"
+
+coverage:
+	@echo "Running code coverage analysis..."
+	Rscript -e "cov <- covr::package_coverage(quiet = FALSE); print(cov); cat('Coverage: ', covr::percent_coverage(cov), '%\n')"
+
+doc:
+	Rscript -e "devtools::document()"
+
+build:
+	R CMD build .
+
+install:
+	Rscript -e "devtools::install()"
+
+clean:
+	rm -f *.tar.gz
+	rm -rf guess.Rcheck
+	rm -f .Rhistory

NEWS.md

@@ -12,8 +12,8 @@
 * **Documentation improvements**: Enhanced validation function documentation with proper `@importFrom` declarations
 
 ## Development Workflow Improvements
-* **Local code coverage**: Replaced Codecov.io with local coverage reporting
-  - Added `tools/check_coverage.R` for local coverage analysis
+* **Local code coverage**: Replaced Codecov.io with simple local coverage reporting
+  - Added `make coverage` command for quick coverage analysis
   - Created `Makefile` for common development tasks
   - Removed external Codecov dependency and badge
 * **Fixed CRAN URL**: Updated to canonical CRAN package URL format

README.md

@@ -55,7 +55,8 @@ make doc
 Or run coverage directly in R:
 ```r
 # Check code coverage
-source("tools/check_coverage.R")
+cov <- covr::package_coverage()
+print(cov)
 ```
 
 ### Key Functions

tests/testthat/test-lca-adj.R

@@ -0,0 +1,57 @@
+context("Test LCA Adjustment Function")
+
+test_that("lca_adj works with basic data", {
+  # Create test data with DK responses 
+  pre_test <- data.frame(
+    item1 = c(1, 0, 0, 1, "d", 1, 0, "d"),
+    item2 = c(1, 0, 1, "d", 0, "d", 1, 0)
+  )
+  pst_test <- data.frame(
+    item1 = c(1, 1, 0, "d", 1, 0, "d", 1),
+    item2 = c(1, 0, 1, 0, "d", 1, "d", 0)
+  )
+  
+  # Test basic functionality
+  result <- lca_adj(pre_test, pst_test)
+  
+  # Check structure
+  expect_type(result, "list")
+  expect_named(result, c("pre", "pst"))
+  
+  # Check that something was returned (basic smoke test)
+  expect_true(!is.null(result$pre))
+  expect_true(!is.null(result$pst))
+})
+
+test_that("lca_adj handles NA values", {
+  # Create test data with NAs and DK
+  pre_test <- data.frame(
+    item1 = c(1, 0, NA, 1, "d", 0, 1, "d"),
+    item2 = c(1, NA, 1, "d", 0, "d", 1, 0)
+  )
+  pst_test <- data.frame(
+    item1 = c(1, 1, 0, "d", NA, 1, "d", 0),
+    item2 = c(NA, 0, 1, 0, "d", 0, "d", 1)
+  )
+  
+  # Should produce a warning about NA conversion
+  expect_warning(
+    result <- lca_adj(pre_test, pst_test),
+    "NAs will be converted to 0"
+  )
+  
+  # Check that function still works
+  expect_type(result, "list")
+  expect_named(result, c("pre", "pst"))
+})
+
+test_that("lca_adj validates basic inputs", {
+  # Test with NULL inputs (should error)
+  expect_error(lca_adj(NULL, NULL))
+  
+  # Test basic functionality doesn't crash
+  pre_test <- data.frame(item1 = c(1, 0, "d", 1, 0))
+  pst_test <- data.frame(item1 = c(1, "d", 1, 0, 1))
+  
+  expect_no_error(result <- lca_adj(pre_test, pst_test))
+})