add tests

.Rbuildignore

@@ -7,3 +7,5 @@
 ^docs$
 ^pkgdown$
 ^man-roxygen$
+^CODE_OF_CONDUCT\.md$
+^codecov\.yml$

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at Athanasia Mo Mowinckel. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -26,5 +26,7 @@ URL: https://github.com/capro-uio/neuromat, http://www.capro.dev/neuromat/
 BugReports: https://github.com/capro-uio/neuromat/issues
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3

R/qdec.R

@@ -153,9 +153,12 @@ plot.qdec <- function(x,
   if(!inherits(x, "qdec")){
     stop("Input `x` must be a qdec object", call. = FALSE)
   }
-  x <- x[, !names(x) %in% attr(x, "vars")]
+  if(ncol(x) < 2 | nrow(x) < 2){
+    stop("qdec must have at least 2 rows and 2 columns", call. = FALSE)
+  }
+  x <- x[, !names(x) %in% attr(x, "vars"), drop = FALSE]
   x <- as.matrix(x)
-  x <- x[dim(x)[1]:1, ]
+  x <- x[dim(x)[1]:1, , drop = FALSE]
   heatmap(x, scale = "none",
           Rowv = NA, Colv = NA,
           col = col,

R/utils.R

@@ -5,7 +5,6 @@
 #'
 #' @return scaled vector
 #' @export
-#' @keywords internal
 #' @examples
 #' scale_vec(1:20)
 scale_vec <- function(x, ...) {
@@ -16,10 +15,24 @@ scale_vec <- function(x, ...) {
   as.numeric(scale(x, ...))
 }
 
-scale_num_data <- function(data, formula){
+#' Scale numeric variables in a data frame
+#'
+#' @param data data.frame
+#' @param vars variables selected
+#'
+#' @return
+scale_num_data <- function(data, vars){
+  if(!inherits(data, "data.frame")){
+    stop("Input `data` must be a data.frame", call. = FALSE)
+  }
+  if(!is.null(vars) && !all(vars %in% names(data))){
+    stop("Input `vars` must be a subset of the column names of `data`", call. = FALSE)
+  }
+
+  data <- data[ ,vars, drop = FALSE]
   # scale continuous variables
   cl <- sapply(data, class)
-  dataz <- data[,which(cl %in% "numeric")]
+  dataz <- data[,which(cl %in% "numeric"), drop = FALSE]
   dataz <- apply(dataz, 2, scale_vec)
   dataz <- as.data.frame(dataz, check.names = FALSE)
   names(dataz) <- paste0(names(dataz), "z")

README.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/capro-uio/neuromat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/capro-uio/neuromat/actions/workflows/R-CMD-check.yaml)
 [![CRAN status](https://www.r-pkg.org/badges/version/neuromat)](https://CRAN.R-project.org/package=neuromat)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test coverage](https://codecov.io/gh/capro-uio/neuromat/branch/main/graph/badge.svg)](https://app.codecov.io/gh/capro-uio/neuromat?branch=main)
 <!-- badges: end -->
 
 Running vertex-wise linear mixed effects models in [Freesurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) requires a specific file format. 

README.md

@@ -10,6 +10,8 @@
 status](https://www.r-pkg.org/badges/version/neuromat)](https://CRAN.R-project.org/package=neuromat)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test
+coverage](https://codecov.io/gh/capro-uio/neuromat/branch/main/graph/badge.svg)](https://app.codecov.io/gh/capro-uio/neuromat?branch=main)
 <!-- badges: end -->
 
 Running vertex-wise linear mixed effects models in
@@ -31,8 +33,6 @@ install.packages('neuromat',
 
 ## Example
 
-Add child document from vignette
-
 ``` r
 library(neuromat)
 cars <- mtcars

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

test.csv

@@ -0,0 +1,33 @@
+"cyl4","cyl6","cyl8","gearz"
+0,1,0,0.42355418561047
+0,1,0,0.42355418561047
+1,0,0,0.42355418561047
+0,1,0,-0.931819208343033
+0,0,1,-0.931819208343033
+0,1,0,-0.931819208343033
+0,0,1,-0.931819208343033
+1,0,0,0.42355418561047
+1,0,0,0.42355418561047
+0,1,0,0.42355418561047
+0,1,0,0.42355418561047
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+1,0,0,0.42355418561047
+1,0,0,0.42355418561047
+1,0,0,0.42355418561047
+1,0,0,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+0,0,1,-0.931819208343033
+1,0,0,0.42355418561047
+1,0,0,1.77892757956397
+1,0,0,1.77892757956397
+0,0,1,1.77892757956397
+0,1,0,1.77892757956397
+0,0,1,1.77892757956397
+1,0,0,0.42355418561047

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(neuromat)
+
+test_check("neuromat")

tests/testthat/_snaps/qdec.md

@@ -0,0 +1,20 @@
+# make_fs_qdec works
+
+    Code
+      make_fs_qdec(cars, ~ -1 + cyl + gear, path = "test.csv")
+    Output
+      # A data frame: 32 x 4
+          cyl4  cyl6  cyl8  gearz
+       * <dbl> <dbl> <dbl>  <dbl>
+       1     0     1     0  0.424
+       2     0     1     0  0.424
+       3     1     0     0  0.424
+       4     0     1     0 -0.932
+       5     0     0     1 -0.932
+       6     0     1     0 -0.932
+       7     0     0     1 -0.932
+       8     1     0     0  0.424
+       9     1     0     0  0.424
+      10     0     1     0  0.424
+      # i 22 more rows
+