Merge pull request #56 from aberHRML/devel

v2.6.3

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

@@ -1,12 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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, devel]
   pull_request:
     branches: [main, master]
-  schedule:
-    - cron: '0 0 * * *'
 
 name: R-CMD-check
 
@@ -33,37 +31,19 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt install libnetcdf-dev libgit2-dev
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.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@v2
+
+      - 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/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,31 @@
+# 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@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::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}

.gitignore

@@ -7,3 +7,4 @@ doc
 Meta
 /doc/
 /Meta/
+docs

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: binneR
 Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
-Version: 2.6.2
+Version: 2.6.3
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
-Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
+Description: A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) metabolome fingerprinting data. The methodology for this approach is outlined in Finch et al. (2022) <doi:10.1007/s11306-022-01923-6>.
 biocViews: MassSpectrometry, Metabolomics
-URL: https://aberHRML.github.io/binneR/
+URL: https://aberhrml.github.io/binneR/
 BugReports: https://github.com/aberHRML/binneR/issues
 Depends: R (>= 3.5)
 Imports: 
@@ -26,7 +26,7 @@ Imports:
     furrr
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Collate: allGenerics.R allClasses.R binneRlyse.R
     binParameters.R spectralBinning-method.R 
     show-method.R get.R calc.R readFiles.R
@@ -44,3 +44,4 @@ Suggests:
     testthat,
     gifski
 VignetteBuilder: knitr
+Remotes: bioc::mzR

NEWS.md

@@ -1,3 +1,9 @@
+# binneR 2.6.3
+
+* Fix the calculation of quartiles in [`binneR::plotTIC`](https://aberhrml.github.io/binneR/reference/plotTIC.html).  
+
+* Added the DOI of the methodology article (https://doi.org/10.1007/s11306-022-01923-6) to the package DESCRIPTION and README. 
+
 # binneR 2.6.2
 
 * Improved themes of all plotting functions.

R/plot.R

@@ -385,8 +385,8 @@ setMethod('plotTIC',signature = 'Binalysis',
 						TICmedian <- TICdat %>%
 							group_by(Mode) %>%
 							summarise(Median = median(TIC),
-												Q1 = Median - IQR(TIC),
-												Q3 = Median + IQR(TIC),
+												Q1 = Median - IQR(TIC) / 2,
+												Q3 = Median + IQR(TIC) / 2,
 												LowerOut = Q1 - IQR(TIC) * 1.5,
 												UpperOut = Q3 + IQR(TIC) * 1.5)
 

README.md

@@ -2,7 +2,7 @@
 
 <!-- badges: start -->
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![R-CMD-check](https://github.com/aberHRML/binneR/workflows/R-CMD-check/badge.svg)](https://github.com/aberHRML/binneR/actions)
+[![R-CMD-check](https://github.com/aberHRML/binneR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/aberHRML/binneR/actions/workflows/R-CMD-check.yaml)
 [![Coverage status](https://codecov.io/gh/aberHRML/binneR/branch/master/graph/badge.svg)](https://codecov.io/github/aberHRML/binneR?branch=master)
 [![CRAN](https://www.r-pkg.org/badges/version/binneR)](https://cran.r-project.org/web/packages/binneR/index.html)
 ![downloads](https://cranlogs.r-pkg.org/badges/binneR)
@@ -11,15 +11,20 @@
 
 > **Spectral Processing for High Resolution Flow Infusion Mass Spectrometry**
 
-A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) data.
-Includes tools for generating intensity matrices from converted raw data file formats such as `.mzML` and `.mzXML`, plotting chromatograms and total ion counts.
+A spectral binning approach for flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) metabolome fingerprinting data.
+The package includes an integrated workflow for generating spectrally binned intensity matrices from converted raw data file formats such as `.mzML` and `.mzXML`. 
+There are also tools for plotting chromatograms, spectra and total ion counts.
+
+The methodology is outlined in the article:
+
+[Finch, J.P., Wilson, T., Lyons, L., Phillips, H., Beckmann, M. and Draper, J., 2022. Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data. *Metabolomics*, 18(8), pp.1-9.](https://doi.org/10.1007/s11306-022-01923-6)
 
 ### Installation
 
 To download and install this development version run:
 
 ``` r
-remotes::install_github('aberHRML/binneR',build_vignettes = TRUE)
+remotes::install_github('aberHRML/binneR')
 ```
 
 ### Learn more

_pkgdown.yml

@@ -1 +1,4 @@
-destination: docs
+url: http://aberhrml.github.io/binneR/
+template:
+  bootstrap: 5
+