Merge pull request #136 from PSIAIMS/renv-config

add renviron
PSIAIMS · Feb 7, 2024 · 8beea59 · 8beea59
2 parents 1be75ae + 091deb9
commit 8beea59
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Showing 7 changed files with 26 additions and 180 deletions.
diff --git a/.Renviron b/.Renviron
@@ -0,0 +1,2 @@
+RENV_CONFIG_AUTO_SNAPSHOT = TRUE
+RENV_CONFIG_SANDBOX_ENABLED = FALSE
diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml
@@ -9,11 +9,13 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install Quarto CLI
-        uses: quarto-dev/quarto-actions/install-quarto@v1
+        uses: quarto-dev/quarto-actions/install-quarto@v2
 
       - name: Install libcurl
         run: |

diff --git a/.github/workflows/pull_request_action.yml b/.github/workflows/pull_request_action.yml
@@ -9,8 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Quarto CLI
         uses: quarto-dev/quarto-actions/setup@v2

diff --git a/R/anova.qmd b/R/anova.qmd
@@ -4,7 +4,7 @@ title: "ANOVA"
 
 ### **Getting Started**
 
-To demonstrate the various types of sums of squares, we'll create a data frame called `df_disease` taken from the SAS documentation (**reference**). For more information/to investigate this data go [here](../data-info/sas_disease.qmd)
+To demonstrate the various types of sums of squares, we'll create a data frame called `df_disease` taken from the SAS documentation. 
 
 ```{r}
 #| echo: false

diff --git a/SAS/anova.qmd b/SAS/anova.qmd
@@ -4,11 +4,12 @@ title: "linear-models"
 
 ### **Getting Started**
 
-To demonstrate the various types of sums of squares, we\'ll create a data frame called `df_disease` taken from the SAS documentation (**reference**). For more information/to investigate this data go [here](../data-info/sas_disease.qmd)
+To demonstrate the various types of sums of squares, we'll create a data frame called `df_disease` taken from the SAS documentation.
 
-### The Model {-}
+### The Model {.unnumbered}
 
 For this example, we're testing for a significant difference in `stem_length` using ANOVA.
+
 ```{r}
 #| eval: false
 proc glm;
@@ -24,8 +25,9 @@ run;
 #knitr::include_graphics("images/linear/sas-f-table.png")
 ```
 
-### Sums of Squares Tables  {-}
-SAS has four types of sums of squares calculations. To get these calculations, the sum of squares option needs to be added (`/ ss1 ss2 ss3 ss4`) to the model statement. 
+### Sums of Squares Tables {.unnumbered}
+
+SAS has four types of sums of squares calculations. To get these calculations, the sum of squares option needs to be added (`/ ss1 ss2 ss3 ss4`) to the model statement.
 
 ```{r}
 #| eval: false
@@ -36,22 +38,25 @@ run;
 ```
 
 #### Type I
+
 ```{r, echo=FALSE, fig.align='center', out.width="75%"}
 knitr::include_graphics("../images/linear/sas-ss-type-1.png")
 ```
 
+#### Type II {.unnumbered}
 
-#### Type II {-}
 ```{r, echo=FALSE, fig.align='center', out.width="75%"}
 knitr::include_graphics("../images/linear/sas-ss-type-2.png")
 ```
 
-#### Type III {-}
+#### Type III {.unnumbered}
+
 ```{r, echo=FALSE, fig.align='center', out.width="75%"}
 knitr::include_graphics("../images/linear/sas-ss-type-3.png")
 ```
 
-#### Type IV {-}
+#### Type IV {.unnumbered}
+
 ```{r, echo=FALSE, fig.align='center', out.width="75%"}
 knitr::include_graphics("../images/linear/sas-ss-type-4.png")
 ```
diff --git a/data-info/sas_disease.qmd b/data-info/sas_disease.qmd
diff --git a/renv.lock b/renv.lock
@@ -844,18 +844,6 @@
       ],
       "Hash": "51e70d990c320e677d0728c4584a6ed5"
     },
-    "fontawesome": {
-      "Package": "fontawesome",
-      "Version": "0.4.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmltools",
-        "rlang"
-      ],
-      "Hash": "c5a628c2570aa86a96cc6ef739d8bfda"
-    },
     "forcats": {
       "Package": "forcats",
       "Version": "0.5.2",
@@ -1271,21 +1259,6 @@
       ],
       "Hash": "b677ee5954471eaa974c0d099a343a1a"
     },
-    "httpuv": {
-      "Package": "httpuv",
-      "Version": "1.6.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "Rcpp",
-        "later",
-        "promises",
-        "utils"
-      ],
-      "Hash": "08e611aee165b27f8ff18770285fb535"
-    },
     "httr": {
       "Package": "httr",
       "Version": "1.4.4",
@@ -1402,17 +1375,6 @@
       ],
       "Hash": "3d5108641f47470611a32d0bdf357a72"
     },
-    "later": {
-      "Package": "later",
-      "Version": "1.3.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Rcpp",
-        "rlang"
-      ],
-      "Hash": "7e7b457d7766bc47f2a5f21cc2984f8e"
-    },
     "lattice": {
       "Package": "lattice",
       "Version": "0.20-45",
@@ -1825,7 +1787,7 @@
     },
     "procs": {
       "Package": "procs",
-      "Version": "1.0.4",
+      "Version": "1.0.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -1838,7 +1800,7 @@
         "tibble",
         "utils"
       ],
-      "Hash": "66ee432fe5a2474eb70a410b3e18ca24"
+      "Hash": "6c3aeb7d6b9c4e0eecf3e70287e780e4"
     },
     "progress": {
       "Package": "progress",
@@ -1853,21 +1815,6 @@
       ],
       "Hash": "14dc9f7a3c91ebb14ec5bb9208a07061"
     },
-    "promises": {
-      "Package": "promises",
-      "Version": "1.2.0.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R6",
-        "Rcpp",
-        "later",
-        "magrittr",
-        "rlang",
-        "stats"
-      ],
-      "Hash": "4ab2c43adb4d4699cf3690acd378d75d"
-    },
     "ps": {
       "Package": "ps",
       "Version": "1.7.2",
@@ -2063,22 +2010,6 @@
       ],
       "Hash": "516e0139c940b699e0ec000cca4b44d5"
     },
-    "repr": {
-      "Package": "repr",
-      "Version": "1.1.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "grDevices",
-        "htmltools",
-        "jsonlite",
-        "pillar",
-        "utils"
-      ],
-      "Hash": "ab67841ce609df761bc69764c2be0db6"
-    },
     "reprex": {
       "Package": "reprex",
       "Version": "2.0.2",
@@ -2252,74 +2183,6 @@
       ],
       "Hash": "3838071b66e0c566d55cc26bd6e27bf4"
     },
-    "shiny": {
-      "Package": "shiny",
-      "Version": "1.7.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "bslib",
-        "cachem",
-        "commonmark",
-        "crayon",
-        "ellipsis",
-        "fastmap",
-        "fontawesome",
-        "glue",
-        "grDevices",
-        "htmltools",
-        "httpuv",
-        "jsonlite",
-        "later",
-        "lifecycle",
-        "methods",
-        "mime",
-        "promises",
-        "rlang",
-        "sourcetools",
-        "tools",
-        "utils",
-        "withr",
-        "xtable"
-      ],
-      "Hash": "c2eae3d8c670fa9dfa35a12066f4a1d5"
-    },
-    "skimr": {
-      "Package": "skimr",
-      "Version": "2.1.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "dplyr",
-        "knitr",
-        "magrittr",
-        "pillar",
-        "purrr",
-        "repr",
-        "rlang",
-        "stats",
-        "stringr",
-        "tibble",
-        "tidyr",
-        "tidyselect",
-        "vctrs"
-      ],
-      "Hash": "8f138ff2c8fbea9e0a523f6c399c0386"
-    },
-    "sourcetools": {
-      "Package": "sourcetools",
-      "Version": "0.1.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "947e4e02a79effa5d512473e10f41797"
-    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.7.12",
@@ -2767,10 +2630,10 @@
     },
     "zip": {
       "Package": "zip",
-      "Version": "2.3.0",
+      "Version": "2.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "d98c94dacb7e0efcf83b0a133a705504"
+      "Hash": "fcc4bd8e6da2d2011eb64a5e5cc685ab"
     },
     "zoo": {
       "Package": "zoo",
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		RENV_CONFIG_AUTO_SNAPSHOT = TRUE
		RENV_CONFIG_SANDBOX_ENABLED = FALSE