From 8a2864b6ff0762d206dfeb7b91e30195529090a6 Mon Sep 17 00:00:00 2001
From: stephematician <stephematician@gmail.com>
Date: Fri, 5 Apr 2024 08:39:51 +1100
Subject: [PATCH 1/2] Fixes #633

use any() in test for trivial minpuc
---
 R/quickpred.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/quickpred.R b/R/quickpred.R
index 569cf13e..f785d31e 100644
--- a/R/quickpred.R
+++ b/R/quickpred.R
@@ -106,7 +106,7 @@ quickpred <- function(data, mincor = 0.1, minpuc = 0, include = "",
   predictorMatrix[maxc > mincor] <- 1
 
   # exclude predictors with a percentage usable cases below minpuc
-  if (minpuc != 0) {
+  if (any(minpuc != 0)) {
     p <- md.pairs(data)
     puc <- p$mr / (p$mr + p$mm)
     predictorMatrix[puc < minpuc] <- 0

From 72bb81d101bafc9bdefba14d7b928b8a120f3f20 Mon Sep 17 00:00:00 2001
From: stephematician <stephematician@gmail.com>
Date: Fri, 5 Apr 2024 08:41:11 +1100
Subject: [PATCH 2/2] Add basic tests for quickpred

Tests for acceptable arguments
Tests for output format
---
 tests/testthat/test-quickpred.R | 64 +++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 tests/testthat/test-quickpred.R

diff --git a/tests/testthat/test-quickpred.R b/tests/testthat/test-quickpred.R
new file mode 100644
index 00000000..ca96549a
--- /dev/null
+++ b/tests/testthat/test-quickpred.R
@@ -0,0 +1,64 @@
+context("quickpred")
+
+test_that("returns square binary matrix", {
+
+    predictorMatrix <- quickpred(nhanes)
+
+    expect_is(predictorMatrix, 'matrix')
+    expect_equal(nrow(predictorMatrix), ncol(predictorMatrix))
+    expect_in(predictorMatrix, c(0, 1))
+
+})
+
+test_that("mincor supports scalar, vector, matrix", {
+
+    n_col <- ncol(nhanes)
+    expect_in(quickpred(nhanes, mincor=0), c(0, 1))
+    expect_in(quickpred(nhanes, mincor=1), 0)
+    expect_in(quickpred(nhanes, mincor=rep(0.1, n_col)), c(0, 1))
+    expect_in(
+        quickpred(nhanes, mincor=matrix(rep(0.1, n_col*n_col), ncol=n_col)),
+        c(0, 1)
+    )
+
+})
+
+test_that("minpuc supports scalar, vector, matrix", {
+
+    n_col <- ncol(nhanes)
+    expect_in(quickpred(nhanes, minpuc=0), c(0, 1))
+    expect_in(quickpred(nhanes, minpuc=rep(0.1, n_col)), c(0, 1))
+    expect_in(
+        quickpred(nhanes, minpuc=matrix(rep(0.1, n_col*n_col), ncol=n_col)),
+        c(0, 1)
+    )
+
+})
+
+test_that("include one or more variables", {
+
+    result_include_bmi <- quickpred(nhanes, include="bmi")
+    has_missing <- apply(is.na(nhanes), 2, any)
+    not_bmi <- setdiff(names(nhanes)[has_missing], "bmi")
+    expect_in(result_include_bmi[not_bmi, "bmi"], 1)
+
+    expect_in(quickpred(nhanes, include=names(nhanes)), c(0, 1))
+
+    n_col <- ncol(nhanes)
+    result_include_all <- quickpred(nhanes, include=names(nhanes))
+    expect_in(
+        result_include_all[has_missing, ] - (1 - diag(n_col)[has_missing,]),
+        0
+    )
+
+})
+
+test_that("exclude one or more variables", {
+
+    result_exclude_age <- quickpred(nhanes, exclude="age")
+    expect_in(result_exclude_age[, "age"], 0)
+
+    result_exclude_all <- quickpred(nhanes, exclude=names(nhanes))
+    expect_in(result_exclude_all, 0)
+
+})