Merge pull request with unit testing etc

pull request #4 from TheOafidian/feature/unit-testing

.Rbuildignore

@@ -1,2 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.github$
+^codecov\.yml$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,65 @@
+# 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
+on:
+  push:
+    branches: [main, master, feature/unit-testing]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+
+          - {os: windows-latest, r: 'release'}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
+
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          # dada2 needs atleast R3.6
+          # - {os: ubuntu-latest,   r: 'oldrel-4'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,46 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.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, feature/unit-testing]
+  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@v3
+
+      - 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(Sys.getenv("RUNNER_TEMP"), "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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,21 +1,36 @@
-Package: tidyamplicons
 Type: Package
+Package: tidyamplicons
 Title: Functions to Manipulate and Visualize Amplicon Abundance Data
 Version: 0.2.2
-Authors@R: c(person("Stijn", "Wittouck", email = "stijn.wittouck@uantwerpen.be", role = c("aut", "cre"))) 
-Description: A toolkit for processing and visualizing amplicon abundance data, based on the tidyverse framework. 
+Authors@R: 
+    person("Stijn", "Wittouck", , "stijn.wittouck@uantwerpen.be", role = c("aut", "cre"))
+Description: A toolkit for processing and visualizing amplicon abundance
+    data, based on the tidyverse framework.
 License: GPL-3
-Encoding: UTF-8
-LazyData: true
+Depends: R (>= 3.6.0)
 Imports:
-    ggplot2,
-    tidyr,
     dplyr,
+    ggplot2,
+    magrittr,
+    purrr,
+    readr,
+    rlang (>= 0.4.11),
     stringr,
+    tibble,
+    tidyr,
     vegan
 Suggests: 
+    covr,
+    vdiffr,
+    dada2,
     knitr,
+    phyloseq,
     rmarkdown,
-    phyloseq
-VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+    roxygen2,
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.3
+Config/testthat/edition: 3

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
+export(":=")
+export(.data)
 export(abundances)
 export(abundances_matrix)
 export(add_alphas)
@@ -28,6 +31,8 @@ export(aggregate_samples)
 export(aggregate_taxa)
 export(as_abundances)
 export(as_abundances_matrix)
+export(as_label)
+export(as_name)
 export(as_phyloseq)
 export(as_tidyamplicons)
 export(bar_plot)
@@ -36,7 +41,10 @@ export(change_id_samples)
 export(change_id_taxa)
 export(classify_taxa)
 export(codifab_plot)
+export(create_test_ta)
 export(create_tidyamplicons)
+export(enquo)
+export(enquos)
 export(everything)
 export(filter_abundances)
 export(filter_samples)
@@ -65,6 +73,7 @@ export(process_taxon_selection)
 export(rank_names)
 export(rarefy)
 export(read_tidyamplicons)
+export(remove_empty_samples)
 export(report_numbers)
 export(reset_ids)
 export(sample_plot)
@@ -86,3 +95,13 @@ import(ggplot2)
 import(stringr)
 import(tidyr)
 import(vegan)
+importFrom(magrittr,"%>%")
+importFrom(readr,read_csv)
+importFrom(readr,write_csv)
+importFrom(rlang,":=")
+importFrom(rlang,.data)
+importFrom(rlang,as_label)
+importFrom(rlang,as_name)
+importFrom(rlang,enquo)
+importFrom(rlang,enquos)
+importFrom(tibble,tibble)

R/adders_samples.R

@@ -31,7 +31,7 @@
 #' # Initiate sample tibble
 #' sample <- c("sample1", "sample2")
 #' environment <- c("food fermentation", "human stool")
-#' sample_tibble <- tibble(sample, environment)
+#' sample_tibble <- tibble::tibble(sample, environment)
 #'
 #' # Add sample tibble to tidyamplicons object
 #' data <- data %>%
@@ -40,7 +40,7 @@
 #' @export
 add_sample_tibble <- function(ta, sample_tibble) {
 
-  modify_at(ta, "samples", left_join, sample_tibble)
+  purrr::modify_at(ta, "samples", left_join, sample_tibble)
 
 }
 
@@ -137,7 +137,6 @@ add_lib_size <- function(ta, step = "current") {
 #' # Add total abundance
 #' data <- data %>%
 #'  add_diversity_measures()
-#'
 #' @export
 add_alphas <- function(ta) {
 
@@ -175,7 +174,7 @@ add_diversity_measures <- function(ta) {
 
   ta %>%
     add_alphas %>%
-    modify_at(
+    purrr::modify_at(
       "samples", rename, div_observed = observed,
       div_inv_simpson = inverse_simpson
     )
@@ -258,11 +257,11 @@ add_sample_clustered <- function(ta) {
 #' @examples
 #' # Initiate abundance matrix
 #' x <- matrix(
-#'  c(1500, 1300, 280, 356),
-#'  ncol = 2
+#'  c(1500, 1300, 280, 356, 456, 678),
+#'  ncol = 3
 #' )
 #' rownames(x) <- c("taxon1", "taxon2")
-#' colnames(x) <- c("sample1", "sample2")
+#' colnames(x) <- c("sample1", "sample2", "sample3")
 #'
 #' # Convert to tidyamplicons object
 #' data <- create_tidyamplicons(x,
@@ -396,7 +395,7 @@ add_spike_ratio <- function(ta, spike_taxon) {
 #'
 #' # Add total abundance
 #' data <- data %>%
-#'  add_cluster(n_clusters = 5)
+#'  add_cluster(n_clusters = 2)
 #'
 # Adds a variable "cluster" to the samples table
 # To do: merge with add_sample_clustered somehow