From d597cf66e22829ce93cb702324fa177f00ea0349 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:25:17 +0000 Subject: [PATCH 01/12] add renviron the auto snapshot will make it so people don't have to worry when adding new packages. the sandbox and pak should make things run a bit faster --- .Renviron | 3 +++ renv.lock | 20 ++++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 .Renviron diff --git a/.Renviron b/.Renviron new file mode 100644 index 00000000..102c8728 --- /dev/null +++ b/.Renviron @@ -0,0 +1,3 @@ +RENV_CONFIG_AUTO_SNAPSHOT = TRUE +RENV_CONFIG_SANDBOX_ENABLED = FALSE +RENV_CONFIG_PAK_ENABLED = TRUE diff --git a/renv.lock b/renv.lock index d8211048..ca65e170 100644 --- a/renv.lock +++ b/renv.lock @@ -2,6 +2,26 @@ "R": { "Version": "4.2.1", "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.16/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.16/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.16/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.16/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.16/books" + }, { "Name": "CRAN", "URL": "https://cran.rstudio.com" From 43405187a4cf83cf1c58e1d8b4e02a388b5f6abe Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:42:22 +0000 Subject: [PATCH 02/12] Update .Renviron --- .Renviron | 1 - 1 file changed, 1 deletion(-) diff --git a/.Renviron b/.Renviron index 102c8728..4b2ea0aa 100644 --- a/.Renviron +++ b/.Renviron @@ -1,3 +1,2 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE -RENV_CONFIG_PAK_ENABLED = TRUE From e5c2e413184f2696e91c37bed959b639265a804b Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:03:47 +0000 Subject: [PATCH 03/12] Remove disease file and try using pak --- .Renviron | 1 + data-info/sas_disease.qmd | 29 ----------------------------- 2 files changed, 1 insertion(+), 29 deletions(-) delete mode 100644 data-info/sas_disease.qmd diff --git a/.Renviron b/.Renviron index 4b2ea0aa..102c8728 100644 --- a/.Renviron +++ b/.Renviron @@ -1,2 +1,3 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE +RENV_CONFIG_PAK_ENABLED = TRUE diff --git a/data-info/sas_disease.qmd b/data-info/sas_disease.qmd deleted file mode 100644 index 0f416de0..00000000 --- a/data-info/sas_disease.qmd +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: "SAS Disease" -server: shiny ---- - -To demonstrate the various types of sums of squares, we'll create a data frame called \`df_disease\` taken from the SAS documentation (\_\_reference\_\_). The summary of the data is shown. - -```{r} -#| echo: false -#| include: false - -library(readr) -library(skimr) -df_disease <- - read_csv( - file = "../data/sas_disease.csv", - col_types = cols(drug = col_factor(), - disease = col_factor(), - y = col_double())) - -``` - -The general summary of the data is as follows - -```{r} -summary(df_disease) - -skim(df_disease) -``` From c3a6ff5d5edf34eb7d383adbd6995bdd3db03d3a Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:08:16 +0000 Subject: [PATCH 04/12] remove data info --- data-info/sas_disease.qmd | 28 ---------------------------- 1 file changed, 28 deletions(-) delete mode 100644 data-info/sas_disease.qmd diff --git a/data-info/sas_disease.qmd b/data-info/sas_disease.qmd deleted file mode 100644 index c91905d3..00000000 --- a/data-info/sas_disease.qmd +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: "SAS Disease" ---- - -To demonstrate the various types of sums of squares, we'll create a data frame called \`df_disease\` taken from the SAS documentation (\_\_reference\_\_). The summary of the data is shown. - -```{r} -#| echo: false -#| include: false - -library(readr) -library(skimr) -df_disease <- - read_csv( - file = "../data/sas_disease.csv", - col_types = cols(drug = col_factor(), - disease = col_factor(), - y = col_double())) - -``` - -The general summary of the data is as follows - -```{r} -summary(df_disease) - -skim(df_disease) -``` From 5e77c5252a1c325de81bd5424af62de5cf80df9a Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:11:41 +0000 Subject: [PATCH 05/12] remove pak --- .Renviron | 1 - 1 file changed, 1 deletion(-) diff --git a/.Renviron b/.Renviron index 102c8728..4b2ea0aa 100644 --- a/.Renviron +++ b/.Renviron @@ -1,3 +1,2 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE -RENV_CONFIG_PAK_ENABLED = TRUE From 72b47658ced01d1610fc7d37171d5e6817f80926 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:15:57 +0000 Subject: [PATCH 06/12] add pak again --- .Renviron | 1 + renv.lock | 145 ++---------------------------------------------------- 2 files changed, 5 insertions(+), 141 deletions(-) diff --git a/.Renviron b/.Renviron index 4b2ea0aa..102c8728 100644 --- a/.Renviron +++ b/.Renviron @@ -1,2 +1,3 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE +RENV_CONFIG_PAK_ENABLED = TRUE diff --git a/renv.lock b/renv.lock index 3dc23a92..d430e18a 100644 --- 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", From 9c645657af0cb3883dedbfde0bc6a8a27de4d4ef Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:22:02 +0000 Subject: [PATCH 07/12] remove pak config --- .Renviron | 1 - 1 file changed, 1 deletion(-) diff --git a/.Renviron b/.Renviron index 102c8728..4b2ea0aa 100644 --- a/.Renviron +++ b/.Renviron @@ -1,3 +1,2 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE -RENV_CONFIG_PAK_ENABLED = TRUE From 5877d11acc407d206f620a6523bab674b209cf06 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:37:41 +0000 Subject: [PATCH 08/12] remove data reference --- R/anova.qmd | 2 +- SAS/anova.qmd | 19 ++++++++++++------- 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/R/anova.qmd b/R/anova.qmd index 4ef8bb78..d7b81792 100644 --- 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 index c08570c7..5863ebf4 100644 --- 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") ``` From 3d67ffe08e295360867c90d90149f3a7197dada8 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:53:26 +0000 Subject: [PATCH 09/12] update to checkout 4 --- .github/workflows/pull_request_action.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pull_request_action.yml b/.github/workflows/pull_request_action.yml index fe69f617..77c2859a 100644 --- 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 From 2eecb46cf65181e93fd26fd2a1f011912c463b94 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 15:59:47 +0000 Subject: [PATCH 10/12] update action versions --- .github/workflows/action.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/action.yml b/.github/workflows/action.yml index 229201cd..7a5beb3f 100644 --- 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: | From 818b5c6351b6b5c37e34cdb63ddfb2080bb94504 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:01:01 +0000 Subject: [PATCH 11/12] try pak now it has a cached packages --- .Renviron | 1 + 1 file changed, 1 insertion(+) diff --git a/.Renviron b/.Renviron index 4b2ea0aa..102c8728 100644 --- a/.Renviron +++ b/.Renviron @@ -1,2 +1,3 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE +RENV_CONFIG_PAK_ENABLED = TRUE From 091deb92aeacea36530870062e79a2b7cc5abbb5 Mon Sep 17 00:00:00 2001 From: statasarus <55274484+statasaurus@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:30:05 +0000 Subject: [PATCH 12/12] removing the pak for now --- .Renviron | 1 - 1 file changed, 1 deletion(-) diff --git a/.Renviron b/.Renviron index 102c8728..4b2ea0aa 100644 --- a/.Renviron +++ b/.Renviron @@ -1,3 +1,2 @@ RENV_CONFIG_AUTO_SNAPSHOT = TRUE RENV_CONFIG_SANDBOX_ENABLED = FALSE -RENV_CONFIG_PAK_ENABLED = TRUE