From 0478b9c425d668d6ef0aa0e860f8e4eac8ee78a0 Mon Sep 17 00:00:00 2001
From: Chris Sobczak <chris@sobczak.family>
Date: Fri, 10 Jul 2026 16:31:33 -0700
Subject: get going and create test for simulate_data

---
 DESCRIPTION                         |  6 ++++++
 NAMESPACE                           |  2 ++
 R/simulate_data.R                   | 16 ++++++----------
 man/simulate_data.Rd                |  5 ++---
 tests/testthat.R                    | 12 ++++++++++++
 tests/testthat/test-simulate_data.R |  4 ++++
 6 files changed, 32 insertions(+), 13 deletions(-)
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test-simulate_data.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 34d6b7b..2e67bd8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,3 +8,9 @@ License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 8.0.0
+Imports: 
+    MASS,
+    stats
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
index 5045b57..59ce237 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,3 +2,5 @@
 
 export(simulate_data)
 importFrom(MASS,mvrnorm)
+importFrom(stats,rchisq)
+importFrom(stats,runif)
diff --git a/R/simulate_data.R b/R/simulate_data.R
index 2338805..297b76f 100644
--- a/R/simulate_data.R
+++ b/R/simulate_data.R
@@ -15,11 +15,12 @@
 #' @return A list with X, S and a vector identifying the contaminated rows.
 #'
 #' @examples
-#' X_obj <- generate_data(n = 10, p = 10)
+#' X_obj <- simulate_data(n = 10, p = 10)
 #' X <- X_obj$X
 #' S_true <- X_obj$S
 #'
 #' @importFrom MASS mvrnorm
+#' @importFrom stats rchisq runif
 #'
 #' @export
 simulate_data <- function(
@@ -28,8 +29,7 @@ simulate_data <- function(
 	rho = 0.8,
 	contamination = 0,
 	block_fraction = 0.5,
-	t_df = Inf,
-	exact_contamination = FALSE
+	t_df = Inf
 ){
 	if(any(
 		rho < 0,
@@ -56,7 +56,7 @@ simulate_data <- function(
 	# Regular clean observations
 	Z <- MASS::mvrnorm(n = n, mu = numeric(p), Sigma = Sigma)
 	if(is.finite(t_df)){
-		w <- rchisq(n, df = t_df)
+		w <- stats::rchisq(n, df = t_df)
 		X <- Z / sqrt(w / t_df)
 	}else{
 		X <- Z
@@ -65,15 +65,11 @@ simulate_data <- function(
 	# Contamination - by row
 	outlier_rows <- integer(0)
 	if(contamination > 0){
-		if(exact_contamination){
-			outlier_rows <- sample.int(n, ceiling(contamination * n))
-		}else{
-			outlier_rows <- which(runif(n) < contamination)
-		}
+		outlier_rows <- which(stats::runif(n) < contamination)
 
 		if(length(outlier_rows) > 0){
 			X[outlier_rows, ] <- matrix(
-				rchisq(length(outlier_rows) * p, df = 1),
+				stats::rchisq(length(outlier_rows) * p, df = 1),
 				nrow = length(outlier_rows),
 				ncol = p
 			)
diff --git a/man/simulate_data.Rd b/man/simulate_data.Rd
index b362518..09ae881 100644
--- a/man/simulate_data.Rd
+++ b/man/simulate_data.Rd
@@ -10,8 +10,7 @@ simulate_data(
   rho = 0.8,
   contamination = 0,
   block_fraction = 0.5,
-  t_df = Inf,
-  exact_contamination = FALSE
+  t_df = Inf
 )
 }
 \arguments{
@@ -37,7 +36,7 @@ with the intention of evaluating the performance
 of covariance or correlation matrix estimators.
 }
 \examples{
-X_obj <- generate_data(n = 10, p = 10)
+X_obj <- simulate_data(n = 10, p = 10)
 X <- X_obj$X
 S_true <- X_obj$S
 
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..7b29596
--- /dev/null
+++ b/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(RSC.analysis)
+
+test_check("RSC.analysis")
diff --git a/tests/testthat/test-simulate_data.R b/tests/testthat/test-simulate_data.R
new file mode 100644
index 0000000..9d0cba3
--- /dev/null
+++ b/tests/testthat/test-simulate_data.R
@@ -0,0 +1,4 @@
+test_that("Returns a true sparse correlation matrix", {
+	X_obj <- simulate_data(n = 10, p = 10, rho = 0)
+	expect_equal(X_obj$S, diag(nrow = 10))
+})
-- 
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