From e778bfc10f67d948d0a71abc7c5570b6d69643ef Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Thu, 12 Dec 2024 22:11:30 -0800
Subject: [PATCH 1/3] Make this test runnable on its own

---
 tests/testthat/test-fit-models.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-fit-models.R b/tests/testthat/test-fit-models.R
index b7ad585..3768462 100644
--- a/tests/testthat/test-fit-models.R
+++ b/tests/testthat/test-fit-models.R
@@ -1,4 +1,7 @@
-test_that("fit_gam runs as expected", {
+library(testthat)
+library(tractable)
+
+testthat::test_that("fit_gam runs as expected", {
 
   sarica <- read_afq_sarica()
   sarica$group <- factor(sarica$class)

From ef625ed1ad6b5a032d0cf2ce08c3b341fa30e076 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Thu, 12 Dec 2024 22:22:02 -0800
Subject: [PATCH 2/3] Be explicit about where the function is coming from

---
 tests/testthat/test-fit-models.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-fit-models.R b/tests/testthat/test-fit-models.R
index 3768462..7874d28 100644
--- a/tests/testthat/test-fit-models.R
+++ b/tests/testthat/test-fit-models.R
@@ -1,13 +1,12 @@
 library(testthat)
-library(tractable)
 
 testthat::test_that("fit_gam runs as expected", {
 
-  sarica <- read_afq_sarica()
+  sarica <- tractable::read_afq_sarica()
   sarica$group <- factor(sarica$class)
   sarica$subjectID <- unclass(factor(sarica$subjectID))
 
-  selected <- select_bundle(
+  selected <- tractable::select_bundle(
     df_afq = sarica,
     tract = "Right Corticospinal",
     dwi_metric = "fa",

From 4b329492e62aa56f9bfa1d34b819674c17d9e6e2 Mon Sep 17 00:00:00 2001
From: Ariel Rokem <arokem@gmail.com>
Date: Thu, 12 Dec 2024 22:25:32 -0800
Subject: [PATCH 3/3] Generalize to all test files

---
 tests/testthat/test-datasets.R | 8 +++++---
 tests/testthat/test-gam.R      | 6 ++++--
 tests/testthat/test-select.r   | 8 +++++---
 tests/testthat/test-shuffle.R  | 2 ++
 4 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-datasets.R b/tests/testthat/test-datasets.R
index 42399dc..302e36e 100644
--- a/tests/testthat/test-datasets.R
+++ b/tests/testthat/test-datasets.R
@@ -1,5 +1,7 @@
+library(testthat)
+
 test_that("read_afq_sarica loads the sarica dataset", {
-  df_sarica <- read_afq_sarica()
+  df_sarica <- tractable::read_afq_sarica()
 
   expect_equal(nrow(df_sarica), 96000)
   expect_equal(ncol(df_sarica), 8)
@@ -7,7 +9,7 @@ test_that("read_afq_sarica loads the sarica dataset", {
 })
 
 test_that("read_afq_weston_havens loads the WH dataset", {
-  df_hbn <- read_afq_weston_havens()
+  df_hbn <- tractable::read_afq_weston_havens()
 
   expect_equal(nrow(df_hbn), 154000)
   expect_equal(ncol(df_hbn), 8)
@@ -24,7 +26,7 @@ test_that("read_afq_hbn loads the HBN dataset", {
 
 test_that("read_afq_files returns an unsupervised dataset when pheno_csv is NULL", {
   nodes_url <- "https://github.com/yeatmanlab/Sarica_2017/raw/gh-pages/data/nodes.csv"
-  df <- read_afq_files(nodes_csv   = nodes_url,
+  df <- tractable::read_afq_files(nodes_csv   = nodes_url,
                        dwi_metrics = c("fa", "md"),
                        pheno_cols  = c("age", "class", "gender"))
 
diff --git a/tests/testthat/test-gam.R b/tests/testthat/test-gam.R
index 4216233..572c593 100644
--- a/tests/testthat/test-gam.R
+++ b/tests/testthat/test-gam.R
@@ -1,9 +1,11 @@
+library(testthat)
+
 test_that("tractable_single_bundle runs as expected", {
- sarica <- read_afq_sarica()
+ sarica <- tractable::read_afq_sarica()
  sarica$group <- factor(sarica$class)
  sarica$subjectID <- unclass(factor(sarica$subjectID))
  gam_fit <- expect_no_error(
-    tractable_single_bundle(df_afq = sarica,
+   tractable::tractable_single_bundle(df_afq = sarica,
                          tract = "Right Corticospinal",
                          participant_id = "subjectID",
                          group_by = "group",
diff --git a/tests/testthat/test-select.r b/tests/testthat/test-select.r
index ad2e0ab..86ffc16 100644
--- a/tests/testthat/test-select.r
+++ b/tests/testthat/test-select.r
@@ -1,10 +1,12 @@
+library(testthat)
+
 test_that("select_bundle runs as expected", {
- sarica <- read_afq_sarica()
+ sarica <- tractable::read_afq_sarica()
  sarica$group <- factor(sarica$class)
  sarica$subjectID <- unclass(factor(sarica$subjectID))
 
  selected <- expect_no_error(
-    select_bundle(df_afq = sarica,
+    tractable::select_bundle(df_afq = sarica,
                   tract = "Right Corticospinal",
                   dwi_metric = "fa",
                   covariates = c("age", "group"),
@@ -19,7 +21,7 @@ expect_identical(tract_names, c("Right Corticospinal"))
 expect_identical(length(colnames(df_tract)), as.integer(6))
 
  selected <- expect_no_error(
-    select_bundle(df_afq = sarica,
+    tractable::select_bundle(df_afq = sarica,
                   tract = "all",
                   dwi_metric = "fa",
                   covariates = c("age", "group"),
diff --git a/tests/testthat/test-shuffle.R b/tests/testthat/test-shuffle.R
index 170c6df..1cdefad 100644
--- a/tests/testthat/test-shuffle.R
+++ b/tests/testthat/test-shuffle.R
@@ -1,3 +1,5 @@
+library(testthat)
+
 test_that("shuffle_df shuffles an afq dataframe", {
   df_afq <- read.csv("afq_12_rows.csv")