From 47d723e9ba887170c2d2c7eb18311a21bd2a6a08 Mon Sep 17 00:00:00 2001
From: Nate <97904561+promicrobial@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:47:47 -0400
Subject: [PATCH 1/2] Update R.gitignore

Added patterns for tools commonly used in the R ecosystem (renv, Quarto).
---
 R.gitignore | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/R.gitignore b/R.gitignore
index e75435c1..02d1ba66 100644
--- a/R.gitignore
+++ b/R.gitignore
@@ -47,3 +47,19 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+
+# renv dependency management
+renv/
+.renvignore
+!renv/activate.R
+
+# Quarto 
+.quarto/
+/_site/
+/_book/
+/_output/
+*_files/
+/_extensions/
+/_*.local
+
+/_freeze/

From cac2c8c1feaa0e2bd8581c36fe15ad73aaa7e6e0 Mon Sep 17 00:00:00 2001
From: Nate <97904561+promicrobial@users.noreply.github.com>
Date: Mon, 16 Jun 2025 19:58:45 -0400
Subject: [PATCH 2/2] Update R.gitignore

Made _freeze directory exclusion optional
---
 R.gitignore | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/R.gitignore b/R.gitignore
index 02d1ba66..2b8127e3 100644
--- a/R.gitignore
+++ b/R.gitignore
@@ -20,6 +20,7 @@
 
 # RStudio files
 .Rproj.user/
+.Rbuildignore
 
 # produced vignettes
 vignettes/*.html
@@ -28,7 +29,7 @@ vignettes/*.pdf
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
-# knitr and R markdown default cache directories
+# Quarto, knitr and R markdown default cache directories
 *_cache/
 /cache/
 
@@ -62,4 +63,6 @@ renv/
 /_extensions/
 /_*.local
 
-/_freeze/
+# **Optional**
+# Depends on if you need others to reproduce your computational environment (https://quarto.org/docs/projects/code-execution.html#using-freeze)
+#/_freeze/