check_ped

.Rbuildignore

@@ -1,2 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^dev$
+^doc$
+^LICENSE\.md$
+^revdep$
+^cran-comments\.md$

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

@@ -0,0 +1,48 @@
+# 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, development]
+  pull_request:
+    branches: [main, development]
+
+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'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    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

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+revdep/

DESCRIPTION

@@ -1,25 +1,41 @@
 Package: BIGr
-Title: (B)reeding (I)nsight (G)enomics Functions for Polypoid and Diploid Species
-Version: 0.4.2
-Author: Alexander M. Sandercock, Cristiane Taniguti, Josue Chinchilla-Vargas, Shufen Chen, Manoj Sapkota, Meng Lin, Dongyan Zhao, and Breeding Insight Team
+Title: Breeding Insight Genomics Functions for Polypoid and Diploid Species
+Version: 0.5.0
+Author: Alexander M. Sandercock, Cristiane H. Taniguti, Josue
+    Chinchilla-Vargas, Shufen Chen, Manoj Sapkota, Meng Lin, Dongyan Zhao,
+    and Breeding Insight Team
 Maintainer: Alexander M. Sandercock <[email protected]>
-Description: This package contains the functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data.
-License: Apache License 2.0
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Depends: R (>= 4.4.0)
-biocViews:
+Description: Functions developed within Breeding Insight to analyze diploid and polyploid 
+    breeding and genetic data. 'BIGr' provides the ability to filter VCF files, extract SNPs from the DArT MADC file, 
+    and manipulate genotype data for both diploid and polyploid species. It also serves 
+    as the core dependency for the 'BIGapp' Shiny app, which provides a user-friendly interface for performing routine genotype analysis tasks 
+    such as dosage calling, filtering, PCA, GWAS, and Genomic Prediction.
+URL: https://github.com/Breeding-Insight/BIGr
+BugReports: https://github.com/Breeding-Insight/BIGr/issues
+License: Apache License (>= 2)
+Depends: 
+    R (>= 4.4.0)
 Imports: 
+    Biostrings,
     doParallel,
     dplyr,
     foreach,
+    janitor,
+    methods,
+    parallel,
+    pwalign,
     Rdpack (>= 0.7),
     readr (>= 2.1.5),
     reshape2 (>= 1.4.4),
+    stats,
+    tibble,
     tidyr (>= 1.3.1),
-    vcfR (>= 1.15.0),
-    Biostrings,
-    pwalign
-Remotes:
-RdMacros: Rdpack
+    utils,
+    vcfR (>= 1.15.0)
+Suggests:
+  testthat (>= 3.0.0)
+RdMacros: 
+    Rdpack
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2