Make tests runnable on their own

tests/testthat/test-datasets.R

@@ -1,13 +1,15 @@
+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)
   expect_equal(length(unique(df_sarica$subjectID)), 48)
 })
 
 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"))
 

tests/testthat/test-fit-models.R

@@ -1,10 +1,12 @@
-test_that("fit_gam runs as expected", {
+library(testthat)
 
-  sarica <- read_afq_sarica()
+testthat::test_that("fit_gam runs as expected", {
+
+  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",

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",

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"),

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")