From 3f474b2ebe880843f386180b6fa7cb0a52d79051 Mon Sep 17 00:00:00 2001
From: Maria Valdez Cabrera <laniakea@Laniakea-2.local>
Date: Wed, 4 Sep 2024 15:15:16 -0700
Subject: [PATCH 1/2] Adding documents to generate Webpage through pkgdown

---
 .Rbuildignore                  |   2 ++
 .github/.DS_Store              | Bin 0 -> 6148 bytes
 .github/workflows/pkgdown.yaml |  48 +++++++++++++++++++++++++++++++++
 DESCRIPTION                    |   1 +
 _pkgdown.yml                   |   4 +++
 5 files changed, 55 insertions(+)
 create mode 100644 .Rbuildignore
 create mode 100644 .github/.DS_Store
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 _pkgdown.yml

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..a295580
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,2 @@
+^_pkgdown\.yml$
+^pkgdown$
diff --git a/.github/.DS_Store b/.github/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..bb82970c471b54b066e241b3d57161d93069e8fb
GIT binary patch
literal 6148
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z(X*HtL=TEEsfZ?3*e8ZC>1dZW&a;>qH0dDp%=jHUv#>7|p=U?C)ZrjJgWNI$%)lZ8
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aTF@@3gXmez459^vF9MndZkT~zW#9wAt4*5#

literal 0
HcmV?d00001

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..a7276e8
--- /dev/null
+++ b/.github/workflows/pkgdown.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, 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 }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
index 78934ef..f357b2e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -6,6 +6,7 @@ Authors@R: as.person(c(
     "Amy Willis [aut]"
   ))
 Description: tinyvamp estimates the model described in Clausen & Willis, 2022. Notably, our model allows relative abundances to lie on the boundary of the simplex. We present a stable algorithm for computing parameter estimates, asymptotically valid procedures for inference in this nonstandard problem, and examples of the utility of the method. Our approach can be used to select or compare experimental protocols, design experiments with appropriate control data, analyze mixed-specimen samples, and remove across-sample contamination.
+URL: https://github.com/statdivlab/tinyvamp, https://statdivlab.github.io/tinyvamp/
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..2e4ad3a
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: https://mariaavc.github.io/tinyvamp/
+template:
+  bootstrap: 5
+

From 0bf5bc62abd2058f5aa273bba60c967ec5099afd Mon Sep 17 00:00:00 2001
From: Maria Valdez Cabrera <laniakea@Laniakea-2.local>
Date: Wed, 4 Sep 2024 16:11:46 -0700
Subject: [PATCH 2/2] Changing the URL from my personal page to StatDivLab

---
 _pkgdown.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2e4ad3a..87f2ac8 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: https://mariaavc.github.io/tinyvamp/
+url: https://statdivlab.github.io/tinyvamp/
 template:
   bootstrap: 5