From eeb281284593c7b31375e5909cd6374c8cec1573 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 11 Sep 2024 13:00:21 -0400 Subject: [PATCH 1/6] Add headers --- 06-setting-up.Rmd | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/06-setting-up.Rmd b/06-setting-up.Rmd index 42c675b5..79f6410e 100644 --- a/06-setting-up.Rmd +++ b/06-setting-up.Rmd @@ -8,3 +8,19 @@ ottrpal::set_knitr_image_path() ```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA/edit#slide=id.g21a84b32106_0_13") ``` + + + +## Understand general principles of project organization + +## Understand why project organization is key to reproducible analyses. + +## Create and use the following tools: + +### RProject + +### ProjectTemplate + +### R Markdown files + +### Navigate file paths From de30e0a75b7f20e4ead53564fc2d7670983760ac Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 11 Sep 2024 13:21:43 -0400 Subject: [PATCH 2/6] Revising outline --- 06-setting-up.Rmd | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/06-setting-up.Rmd b/06-setting-up.Rmd index 79f6410e..cbba7e2f 100644 --- a/06-setting-up.Rmd +++ b/06-setting-up.Rmd @@ -11,16 +11,20 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_ +## Understand why project organization is key to reproducible analyses + ## Understand general principles of project organization -## Understand why project organization is key to reproducible analyses. +## Navigate file paths + +## Handy R Tools -## Create and use the following tools: +### here package -### RProject +### RProj files ### ProjectTemplate ### R Markdown files -### Navigate file paths +### Quarto files From dca28f4efae0380417b6b3d863444c059d963aca Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 11 Sep 2024 13:22:21 -0400 Subject: [PATCH 3/6] Add the chapter back in bookdown --- _bookdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_bookdown.yml b/_bookdown.yml index 91d34822..ab4a42c5 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -8,7 +8,7 @@ rmd_files: ["index.Rmd", "03-components.Rmd", "04-rstudio-tour.Rmd", "05-rmarkdown.Rmd", - #"06-setting-up.Rmd", + "06-setting-up.Rmd", "07-code.Rmd", "08-github-workflow.Rmd", "09-software-versions.Rmd", From 34f0d662d993014e04c3479237381d8d0d8cf944 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 11 Sep 2024 13:34:39 -0400 Subject: [PATCH 4/6] Link dump --- 06-setting-up.Rmd | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/06-setting-up.Rmd b/06-setting-up.Rmd index cbba7e2f..e754452f 100644 --- a/06-setting-up.Rmd +++ b/06-setting-up.Rmd @@ -13,18 +13,54 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_ ## Understand why project organization is key to reproducible analyses +```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} +ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA/edit#slide=id.g2fea8805c08_0_1121") +``` + ## Understand general principles of project organization +```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} +ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA/edit#slide=id.g2fea8805c08_0_421") +``` + +```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} +ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA/edit#slide=id.g2fea8805c08_0_426") +``` + +```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} +ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA/edit#slide=id.g2fea8805c08_0_442") +``` + +https://github.com/jhudsl/reproducible-r-example + ## Navigate file paths +```{r, fig.align='center', out.width="100%", echo = FALSE, fig.alt= "Major point!! example image"} +ottrpal::include_slide("https://docs.google.com/presentation/d/1MNHf8JpolaEP_vQ_kB-1xRBF9wo3haCArRu117hBoHA/edit#slide=id.g2fea8805c08_0_1337") +``` + ## Handy R Tools ### here package + + +https://here.r-lib.org/ + +https://www.tidyverse.org/blog/2017/12/workflow-vs-script/ + ### RProj files +https://bookdown.org/ndphillips/YaRrr/projects-in-rstudio.html + ### ProjectTemplate +http://projecttemplate.net/ + ### R Markdown files +https://rmarkdown.rstudio.com/articles_intro.html + ### Quarto files + +https://quarto.org/docs/get-started/hello/rstudio.html From d45de4f9ce5540b12036b42fecd36ff7d525601e Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Wed, 13 Nov 2024 12:03:46 -0500 Subject: [PATCH 5/6] Rearrange chapters --- 06-setting-up.Rmd => 05-setting-up.Rmd | 0 05-rmarkdown.Rmd => 06-rmarkdown.Rmd | 0 _bookdown.yml | 4 ++-- 3 files changed, 2 insertions(+), 2 deletions(-) rename 06-setting-up.Rmd => 05-setting-up.Rmd (100%) rename 05-rmarkdown.Rmd => 06-rmarkdown.Rmd (100%) diff --git a/06-setting-up.Rmd b/05-setting-up.Rmd similarity index 100% rename from 06-setting-up.Rmd rename to 05-setting-up.Rmd diff --git a/05-rmarkdown.Rmd b/06-rmarkdown.Rmd similarity index 100% rename from 05-rmarkdown.Rmd rename to 06-rmarkdown.Rmd diff --git a/_bookdown.yml b/_bookdown.yml index ab4a42c5..f3f90e3b 100644 --- a/_bookdown.yml +++ b/_bookdown.yml @@ -7,8 +7,8 @@ rmd_files: ["index.Rmd", "02-why-R.Rmd", "03-components.Rmd", "04-rstudio-tour.Rmd", - "05-rmarkdown.Rmd", - "06-setting-up.Rmd", + "05-setting-up.Rmd", + "06-rmarkdown.Rmd", "07-code.Rmd", "08-github-workflow.Rmd", "09-software-versions.Rmd", From c4419eb78ea35b27bfd930decfdffe7673b7163f Mon Sep 17 00:00:00 2001 From: carriewright11 Date: Wed, 13 Nov 2024 11:07:09 -0700 Subject: [PATCH 6/6] fix spelling --- quizzes/quiz_ch3.md | 4 ++-- resources/dictionary.txt | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/quizzes/quiz_ch3.md b/quizzes/quiz_ch3.md index 3a158e66..7a7ce20c 100644 --- a/quizzes/quiz_ch3.md +++ b/quizzes/quiz_ch3.md @@ -44,14 +44,14 @@ m) It helps others to be able to publish conclusions about our data m) It exposes personal identifiable information to the public {choose-answers: 4} -? Which of the following is correct about this statement - if your data has PHI or PII you cannot make your analysis open source or reproducible. +? Which of the following is correct about this statement - if your data has protected data that you cannot make your analysis open source or reproducible. C) These are not mutually exclusive goals! Some thoughtful planning and use of controlled access methods can ensure that all individuals' data are well protected! C) You can protect data and not share it, but share the code in a careful manner that does not expose details about the data. o) You can make your analysis reproducible but not open source o) You can make your analysis open source but not reproducible m) There are no methods that will allow you to share your methods and data in a safe way. -m) Sharing your code is always unsafe when it comes to PHI or PII +m) Sharing your code is always unsafe when it comes to protected data {/quiz} diff --git a/resources/dictionary.txt b/resources/dictionary.txt index 5b482a35..c4d99af5 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -74,9 +74,14 @@ NIGMS ottrpal Pandoc PBC +PII +ProjectTemplate reproducibility RStudio +rstudio +rmarkdown Rmarkdown +RProj Sys UE UE5