From 0e3686905393213f306e69d74e33817165456930 Mon Sep 17 00:00:00 2001
From: amyheather <a.heather2@exeter.ac.uk>
Date: Fri, 5 Jul 2024 13:40:04 +0100
Subject: [PATCH] build(env): removed main env, adding knitr and rmarkdown to
 analysis env

---
 DESCRIPTION              |   8 -
 renv.lock                | 358 ---------------------------------------
 reproduction/DESCRIPTION |   4 +-
 3 files changed, 3 insertions(+), 367 deletions(-)
 delete mode 100644 DESCRIPTION
 delete mode 100644 renv.lock

diff --git a/DESCRIPTION b/DESCRIPTION
deleted file mode 100644
index 86e3d44..0000000
--- a/DESCRIPTION
+++ /dev/null
@@ -1,8 +0,0 @@
-Title: quarto_huang_2019
-Depends: 
-    R (>= 3.7)
-Imports:
-    knitr (==1.47),
-    rmarkdown (==2.27),
-    remotes (==2.5.0),
-    tiff (==0.1-12)
diff --git a/renv.lock b/renv.lock
deleted file mode 100644
index 29831f8..0000000
--- a/renv.lock
+++ /dev/null
@@ -1,358 +0,0 @@
-{
-  "R": {
-    "Version": "4.4.1",
-    "Repositories": [
-      {
-        "Name": "CRAN",
-        "URL": "https://cloud.r-project.org"
-      }
-    ]
-  },
-  "Packages": {
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.7.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "fastmap",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "lifecycle",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "8644cc53f43828f19133548195d7e59e"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.1.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
-      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
-    },
-    "cli": {
-      "Package": "cli",
-      "Version": "3.6.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "b21916dd77a27642b447374a5d30ecf3"
-    },
-    "digest": {
-      "Package": "digest",
-      "Version": "0.6.36",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "fd6824ad91ede64151e93af67df6376b"
-    },
-    "evaluate": {
-      "Package": "evaluate",
-      "Version": "0.24.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "a1066cbc05caee9a4bf6d90f194ff4da"
-    },
-    "fastmap": {
-      "Package": "fastmap",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
-    },
-    "fontawesome": {
-      "Package": "fontawesome",
-      "Version": "0.5.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmltools",
-        "rlang"
-      ],
-      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
-    },
-    "fs": {
-      "Package": "fs",
-      "Version": "1.6.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
-    },
-    "glue": {
-      "Package": "glue",
-      "Version": "1.7.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "e0b3a53876554bd45879e596cdb10a52"
-    },
-    "highr": {
-      "Package": "highr",
-      "Version": "0.11",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "xfun"
-      ],
-      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
-    },
-    "htmltools": {
-      "Package": "htmltools",
-      "Version": "0.5.8.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "digest",
-        "fastmap",
-        "grDevices",
-        "rlang",
-        "utils"
-      ],
-      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
-    },
-    "jquerylib": {
-      "Package": "jquerylib",
-      "Version": "0.1.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "htmltools"
-      ],
-      "Hash": "5aab57a3bd297eee1c1d862735972182"
-    },
-    "jsonlite": {
-      "Package": "jsonlite",
-      "Version": "1.8.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "methods"
-      ],
-      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
-    },
-    "knitr": {
-      "Package": "knitr",
-      "Version": "1.47",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "evaluate",
-        "highr",
-        "methods",
-        "tools",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "7c99b2d55584b982717fcc0950378612"
-    },
-    "lifecycle": {
-      "Package": "lifecycle",
-      "Version": "1.0.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "rlang"
-      ],
-      "Hash": "b8552d117e1b808b09a832f589b79035"
-    },
-    "memoise": {
-      "Package": "memoise",
-      "Version": "2.0.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "cachem",
-        "rlang"
-      ],
-      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
-    },
-    "mime": {
-      "Package": "mime",
-      "Version": "0.12",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "tools"
-      ],
-      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
-    },
-    "rappdirs": {
-      "Package": "rappdirs",
-      "Version": "0.3.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
-    },
-    "remotes": {
-      "Package": "remotes",
-      "Version": "2.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "3ee025083e66f18db6cf27b56e23e141"
-    },
-    "renv": {
-      "Package": "renv",
-      "Version": "1.0.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "397b7b2a265bc5a7a06852524dabae20"
-    },
-    "rlang": {
-      "Package": "rlang",
-      "Version": "1.1.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
-    },
-    "rmarkdown": {
-      "Package": "rmarkdown",
-      "Version": "2.27",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bslib",
-        "evaluate",
-        "fontawesome",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "knitr",
-        "methods",
-        "tinytex",
-        "tools",
-        "utils",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
-    },
-    "sass": {
-      "Package": "sass",
-      "Version": "0.4.9",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R6",
-        "fs",
-        "htmltools",
-        "rappdirs",
-        "rlang"
-      ],
-      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
-    },
-    "tiff": {
-      "Package": "tiff",
-      "Version": "0.1-12",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "74b5f7f00e466398fdc0af8889add582"
-    },
-    "tinytex": {
-      "Package": "tinytex",
-      "Version": "0.51",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "xfun"
-      ],
-      "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
-    },
-    "xfun": {
-      "Package": "xfun",
-      "Version": "0.45",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grDevices",
-        "stats",
-        "tools"
-      ],
-      "Hash": "ca59c87fe305b16a9141a5874c3a7889"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "29240487a071f535f5e5d5a323b7afbd"
-    }
-  }
-}
diff --git a/reproduction/DESCRIPTION b/reproduction/DESCRIPTION
index 05834f6..ee1acf9 100644
--- a/reproduction/DESCRIPTION
+++ b/reproduction/DESCRIPTION
@@ -9,4 +9,6 @@ Imports:
     gridExtra,
     plyr,
     shiny,
-    markdown
+    markdown,
+    knitr,
+    rmarkdown