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Author: actions-user

docs/03-project-organization.md

@@ -89,7 +89,8 @@ project-name/
 But you don't have to take my organizational strategy, there are lots of ideas out there.
 You can read through some of these articles to think about what kind of organizational strategy might work for you and your team:   
 
-- [Jenny Bryan's organizational strategy](https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html) [@Bryan2021].
+- [Jenny Bryan's organizational strategies](https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html) [@Bryan2021].
+- [Danielle Navarro's organizational strategies](https://www.youtube.com/playlist?list=PLRPB0ZzEYegPiBteC2dRn95TX9YefYFyy) @Navarro
 - [Jenny Bryan on Project-oriented workflows](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/)[@Bryan2017].
 - [Data Carpentry mini-course about organizing projects](https://datacarpentry.org/organization-genomics/) [@DataCarpentry2021].
 - [Andrew Severin's strategy for organization](https://bioinformaticsworkbook.org/projectManagement/Intro_projectManagement.html#gsc.tab=0) [@Severin2021].

docs/04-open-source-with-github.md

@@ -76,14 +76,14 @@ Now that we understand how useful GitHub is for creating reproducible analyses,
 
 Git and GitHub have a whole rich world of tools and terms that can get complex quickly, but for this exercise, we will not worry about those terms and functionalities just yet, but focus on getting code up on GitHub so we are ready to collaborate and conduct open analyses!
 
-- Go to [Github's main page](https://github.com/) and click Sign Up if you don't have an account.
-- Follow [these instructions to create a repository](https://docs.github.com/en/get-started/quickstart/create-a-repo). As a general, but not absolute rule, you will want to keep one GitHub repository for one analysis project.
+- Go to <a href="https://github.com/" target="_blank">Github's main page</a> and click Sign Up if you don't have an account.
+- Follow <a href="https://docs.github.com/en/get-started/quickstart/create-a-repo" target="_blank">these instructions to create a repository</a>. As a general, but not absolute rule, you will want to keep one GitHub repository for one analysis project.
   - Name the repository something that reminds you what its related to.
   - Choose `Public`.
   - Check the box that says `Add a README`.
-- Follow [these instructions](https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github) to add the example files you downloaded to your new repository.
+- Follow <a href="https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github" target="_blank">these instructions</a> to add the example files you downloaded to your new repository.
 
 Congrats! You've started your very own project on GitHub!
 We encourage you to do the same with your own code and other projects!
-  
+
 **Any feedback you have regarding this exercise is greatly appreciated; you can fill out [this form](https://forms.gle/ygSSwoGaEATA2S65A)!**

docs/07-durable-code.md

@@ -130,7 +130,7 @@ You should see you no longer have `some_obj` listed as being defined in your env
 some_obj <- c()
 ls()
 ```
-Now refresh your ession and re-run `ls()`
+Now refresh your session and re-run `ls()`
 ```
 ls()
 ```

docs/Introduction-to-Reproducibility.docx

@@ -89,7 +89,8 @@ project-name/
 But you don't have to take my organizational strategy, there are lots of ideas out there.
 You can read through some of these articles to think about what kind of organizational strategy might work for you and your team:   
 
-- [Jenny Bryan's organizational strategy](https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html) [@Bryan2021].
+- [Jenny Bryan's organizational strategies](https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html) [@Bryan2021].
+- [Danielle Navarro's organizational strategies](https://www.youtube.com/playlist?list=PLRPB0ZzEYegPiBteC2dRn95TX9YefYFyy) @Navarro
 - [Jenny Bryan on Project-oriented workflows](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/)[@Bryan2017].
 - [Data Carpentry mini-course about organizing projects](https://datacarpentry.org/organization-genomics/) [@DataCarpentry2021].
 - [Andrew Severin's strategy for organization](https://bioinformaticsworkbook.org/projectManagement/Intro_projectManagement.html#gsc.tab=0) [@Severin2021].

docs/coursera/03-project-organization.md

@@ -76,14 +76,14 @@ Now that we understand how useful GitHub is for creating reproducible analyses,
 
 Git and GitHub have a whole rich world of tools and terms that can get complex quickly, but for this exercise, we will not worry about those terms and functionalities just yet, but focus on getting code up on GitHub so we are ready to collaborate and conduct open analyses!
 
-- Go to [Github's main page](https://github.com/) and click Sign Up if you don't have an account.
-- Follow [these instructions to create a repository](https://docs.github.com/en/get-started/quickstart/create-a-repo). As a general, but not absolute rule, you will want to keep one GitHub repository for one analysis project.
+- Go to <a href="https://github.com/" target="_blank">Github's main page</a> and click Sign Up if you don't have an account.
+- Follow <a href="https://docs.github.com/en/get-started/quickstart/create-a-repo" target="_blank">these instructions to create a repository</a>. As a general, but not absolute rule, you will want to keep one GitHub repository for one analysis project.
   - Name the repository something that reminds you what its related to.
   - Choose `Public`.
   - Check the box that says `Add a README`.
-- Follow [these instructions](https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github) to add the example files you downloaded to your new repository.
+- Follow <a href="https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github" target="_blank">these instructions</a> to add the example files you downloaded to your new repository.
 
 Congrats! You've started your very own project on GitHub!
 We encourage you to do the same with your own code and other projects!
-  
+
 **Any feedback you have regarding this exercise is greatly appreciated; you can fill out [this form](https://forms.gle/ygSSwoGaEATA2S65A)!**

docs/coursera/04-open-source-with-github.md

@@ -130,7 +130,7 @@ You should see you no longer have `some_obj` listed as being defined in your env
 some_obj <- c()
 ls()
 ```
-Now refresh your ession and re-run `ls()`
+Now refresh your session and re-run `ls()`
 ```
 ls()
 ```

docs/coursera/07-durable-code.md

@@ -363,14 +363,14 @@ <h2><span class="header-section-number">4.3</span> Exercise: Set up a project on
 <p>Now that we understand how useful GitHub is for creating reproducible analyses, it’s time to set ourselves up on GitHub.</p>
 <p>Git and GitHub have a whole rich world of tools and terms that can get complex quickly, but for this exercise, we will not worry about those terms and functionalities just yet, but focus on getting code up on GitHub so we are ready to collaborate and conduct open analyses!</p>
 <ul>
-<li>Go to <a href="https://github.com/">Github’s main page</a> and click Sign Up if you don’t have an account.</li>
-<li>Follow <a href="https://docs.github.com/en/get-started/quickstart/create-a-repo">these instructions to create a repository</a>. As a general, but not absolute rule, you will want to keep one GitHub repository for one analysis project.
+<li>Go to <a href="https://github.com/" target="_blank">Github’s main page</a> and click Sign Up if you don’t have an account.</li>
+<li>Follow <a href="https://docs.github.com/en/get-started/quickstart/create-a-repo" target="_blank">these instructions to create a repository</a>. As a general, but not absolute rule, you will want to keep one GitHub repository for one analysis project.
 <ul>
 <li>Name the repository something that reminds you what its related to.</li>
 <li>Choose <code>Public</code>.</li>
 <li>Check the box that says <code>Add a README</code>.</li>
 </ul></li>
-<li>Follow <a href="https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github">these instructions</a> to add the example files you downloaded to your new repository.</li>
+<li>Follow <a href="https://docs.github.com/en/repositories/working-with-files/managing-files/adding-a-file-to-a-repository#adding-a-file-to-a-repository-on-github" target="_blank">these instructions</a> to add the example files you downloaded to your new repository.</li>
 </ul>
 <p>Congrats! You’ve started your very own project on GitHub!
 We encourage you to do the same with your own code and other projects!</p>

docs/coursera/making-your-project-open-source-with-github.html

@@ -390,7 +390,8 @@ <h2><span class="header-section-number">3.3</span> Readings about organizational
 <p>But you don’t have to take my organizational strategy, there are lots of ideas out there.
 You can read through some of these articles to think about what kind of organizational strategy might work for you and your team:</p>
 <ul>
-<li><a href="https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html">Jenny Bryan’s organizational strategy</a> <span class="citation">(<a href="#ref-Bryan2021" role="doc-biblioref">Bryan and Hester 2021</a>)</span>.</li>
+<li><a href="https://www.stat.ubc.ca/~jenny/STAT545A/block19_codeFormattingOrganization.html">Jenny Bryan’s organizational strategies</a> <span class="citation">(<a href="#ref-Bryan2021" role="doc-biblioref">Bryan and Hester 2021</a>)</span>.</li>
+<li><a href="https://www.youtube.com/playlist?list=PLRPB0ZzEYegPiBteC2dRn95TX9YefYFyy">Danielle Navarro’s organizational strategies</a> <span class="citation">(<a href="#ref-Navarro" role="doc-biblioref"><strong>Navarro?</strong></a>)</span></li>
 <li><a href="https://www.tidyverse.org/blog/2017/12/workflow-vs-script/">Jenny Bryan on Project-oriented workflows</a><span class="citation">(<a href="#ref-Bryan2017" role="doc-biblioref">Bryan 2017</a>)</span>.</li>
 <li><a href="https://datacarpentry.org/organization-genomics/">Data Carpentry mini-course about organizing projects</a> <span class="citation">(<a href="#ref-DataCarpentry2021" role="doc-biblioref"><span>“Project <span>Organization</span> and <span>Management</span> for <span>Genomics</span>”</span> 2021</a>)</span>.</li>
 <li><a href="https://bioinformaticsworkbook.org/projectManagement/Intro_projectManagement.html#gsc.tab=0">Andrew Severin’s strategy for organization</a> <span class="citation">(<a href="#ref-Severin2021" role="doc-biblioref">Severin 2021</a>)</span>.</li>