From eda4bdc3e075170e2cf6c39f5b6f378585bdd85f Mon Sep 17 00:00:00 2001
From: Stuart Wheater <stuart.wheater@arjuna.com>
Date: Mon, 3 Nov 2025 00:14:29 +0000
Subject: [PATCH] Initial 'mdPatternDS' tests

---
 man/mdPatternDS.Rd                    | 54 +++++++++++++++++++++++++++
 tests/testthat/test-arg-mdPatternDS.R | 41 ++++++++++++++++++++
 tests/testthat/test-smk-mdPatternDS.R | 37 ++++++++++++++++++
 3 files changed, 132 insertions(+)
 create mode 100644 man/mdPatternDS.Rd
 create mode 100644 tests/testthat/test-arg-mdPatternDS.R
 create mode 100644 tests/testthat/test-smk-mdPatternDS.R

diff --git a/man/mdPatternDS.Rd b/man/mdPatternDS.Rd
new file mode 100644
index 00000000..1084565e
--- /dev/null
+++ b/man/mdPatternDS.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mdPatternDS.R
+\name{mdPatternDS}
+\alias{mdPatternDS}
+\title{Missing data pattern with disclosure control}
+\usage{
+mdPatternDS(x)
+}
+\arguments{
+\item{x}{a character string specifying the name of a data frame or matrix
+containing the data to analyze for missing patterns.}
+}
+\value{
+A list containing:
+\item{pattern}{The missing data pattern matrix with disclosure control applied}
+\item{valid}{Logical indicating if all patterns meet disclosure requirements}
+\item{message}{A message describing the validity status}
+}
+\description{
+This function is a serverside aggregate function that computes the 
+missing data pattern using mice::md.pattern and applies disclosure control to
+prevent revealing small cell counts.
+}
+\details{
+This function calls the mice::md.pattern function to generate a matrix
+showing the missing data patterns in the input data. To ensure disclosure control,
+any pattern counts that are below the threshold (nfilter.tab, default=3) are
+suppressed.
+
+\strong{Suppression Method:}
+
+When a pattern count is below threshold:
+- Row name is changed to "suppressed(<N>)" where N is the threshold
+- All pattern values in that row are set to NA
+- Summary row is also set to NA (prevents back-calculation)
+
+\strong{Output Matrix Structure:}
+
+- Rows represent different missing data patterns (plus a summary row at the bottom)
+- Row names contain pattern counts (or "suppressed(<N>)" for invalid patterns)
+- Columns show 1 if variable is observed, 0 if missing
+- Last column shows total number of missing values per pattern
+- Last row shows total number of missing values per variable
+
+\strong{Note for Pooling:}
+
+When this function is called from ds.mdPattern with type='combine', suppressed
+patterns are excluded from pooling to prevent disclosure through subtraction.
+This means pooled counts may underestimate the true total when patterns are
+suppressed in some studies.
+}
+\author{
+Xavier Escribà montagut for DataSHIELD Development Team
+}
diff --git a/tests/testthat/test-arg-mdPatternDS.R b/tests/testthat/test-arg-mdPatternDS.R
new file mode 100644
index 00000000..f6b4f941
--- /dev/null
+++ b/tests/testthat/test-arg-mdPatternDS.R
@@ -0,0 +1,41 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2025 ProPASS Consortium. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("mdPatternDS::arg::setup")
+
+#
+# Tests
+#
+
+context("mdPatternDS::arg::x NULL")
+test_that("mdPatternDS x NULL", {
+    x <- NULL
+
+    expect_error(mdPatternDS(x), "The input object must be of type 'data.frame' or 'matrix'. Current type: NULL")
+})
+
+context("mdPatternDS::arg::x not valid variable")
+test_that("mdPatternDS x not variable", {
+    x <- "not a variable"
+
+    expect_error(mdPatternDS(x), "Object 'not a variable' does not exist on the server")
+})
+
+#
+# Done
+#
+
+context("mdPatternDS::arg::shutdown")
+
+context("mdPatternDS::arg::done")
diff --git a/tests/testthat/test-smk-mdPatternDS.R b/tests/testthat/test-smk-mdPatternDS.R
new file mode 100644
index 00000000..33e65055
--- /dev/null
+++ b/tests/testthat/test-smk-mdPatternDS.R
@@ -0,0 +1,37 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2025 ProPASS Consortium. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("mdPatternDS::smk::setup")
+
+#
+# Tests
+#
+
+context("mdPatternDS::smk::sample data.frame")
+test_that("mdPatternDS: sample data.frame", {
+    x_val <- data.frame(v1 = c(0.0, 1.0, 2.0, 3.0, 4.0), v2 = c(4.0, 3.0, 2.0, 1.0, 0.0))
+    x     <- "x_val"
+
+    res <- mdPatternDS(x)
+
+    expect_length(res, 3)
+})
+
+#
+# Done
+#
+
+context("mdPatternDS::smk::shutdown")
+
+context("mdPatternDS::smk::done")