Report factor and collaboration chapters reviewed

new_pages/collaboration.qmd

@@ -71,18 +71,18 @@ However, it becomes even more powerful when used with a online repository
 such as Github to support **collaborative projects**. This facilitates:
 
 -   Collaboration: others can review, comment on, and
-    accept/decline changes
+    accept/decline changes.
 
 -   Sharing your code, data, and outputs, and invite feedback
-    from the public (or privately, with your team)
+    from the public (or privately, with your team).
 
 and avoids:
 
 -   "Oops, I forgot to send the last version and now you need to
-    redo two days worth of work on this new file"
+    redo two days worth of work on this new file".
 
 -   Mina, Henry and Oumar all worked at the same time on one script and
-    need to manually merge their changes
+    need to manually merge their changes.
 
 -   Two people try to modify the same file on Dropbox and Sharepoint 
     and this creates a synchronization error.
@@ -125,7 +125,7 @@ this chapter.
 Intermediate (more powerfull, but more complex) options include Source Tree, 
 Gitkracken, Smart Git and others.
 
-Quick explanation on [Git clients](https:/happygitwithr.com/git-client.html#git-client).
+Quick explanation on [Git clients](https://happygitwithr.com/git-client).
 
 *Note: since interfaces actually all use Git internally, you can try several of
 them, switch from one to another on a given project, use the console punctually 
@@ -139,7 +139,7 @@ Console) or the Git Bash terminal.
 
 ### Github account {.unnumbered}
 
-Sign-up for a free account at [github.com](github.com).
+Sign-up for a free account at [github.com](https://github.com/).
 
 You may be offered to set-up two-factor authentication with an app on
 your phone. Read more in the Github [help
@@ -156,7 +156,7 @@ clone a project from Github.
 As when learning R, there is a bit of vocabulary to remember to
 understand Git. Here are the [basics to get you
 going](https://www.freecodecamp.org/news/an-introduction-to-git-for-absolute-beginners-86fa1d32ff71/)
-/ [interactive tutorial](learngitbranching.js.org). In the next
+/ [interactive tutorial](https://learngitbranching.js.org/). In the next
 sections, we will show how to use interfaces, but it is good
 to have the vocabulary and concepts in mind, to build your mental model,
 and as you'll need them when using interfaces anyway.
@@ -257,8 +257,8 @@ Two general approaches to set-up are:
 
 
 -   Create a new R Project from an existing or new Github repository
-    (*preferred for beginners*), or
--   Create a Github repository for an existing R project
+    (*preferred for beginners*), or,
+-   Create a Github repository for an existing R project.
 
 
 ### Start-up files {.unnumbered}
@@ -326,13 +326,13 @@ Rstudio and Github desktop.
 #### In Rstudio {.unnumbered}
 
 In RStudio, start a new R project by clicking *File \> New Project \>
-Version Control \> Git*
+Version Control \> Git*.
 
 -   When prompted for the "Repository URL", paste the HTTPS URL from
-    Github\
--   Assign the R project a short, informative name\
--   Choose where the new R Project will be saved locally\
--   Check "Open in new session" and click "Create project"
+    Github.\
+-   Assign the R project a short, informative name.\
+-   Choose where the new R Project will be saved locally.\
+-   Check "Open in new session" and click "Create project".
 
 
 You are now in a new, local, RStudio project that is a clone of the
@@ -341,15 +341,15 @@ linked.
 
 #### In Github Desktop {.unnumbered}
 
--   Click on *File \> Clone a repository*
+-   Click on *File \> Clone a repository*.
 
--   Select the URL tab
+-   Select the URL tab.
 
--   Paste the HTTPS URL from Github in the first box
+-   Paste the HTTPS URL from Github in the first box.
 
--   Select the folder in which you want to have your local repository
+-   Select the folder in which you want to have your local repository.
 
--   Click "CLONE"
+-   Click "CLONE".
 
 ```{r echo=F, out.width = '100%', out.height='100%', fig.align = "center"}
 knitr::include_graphics(here::here("images", "github_clone_desktop.png"))
@@ -361,8 +361,8 @@ An alternative setup scenario is that you have an existing R project
 with content, and you want to create a Github repository for it.
 
 1)  Create a new, empty Github repository for the project (see
-    instructions above)\
-2)  Clone this repository locally (see HTTPS instructions above)\
+    instructions above).\
+2)  Clone this repository locally (see HTTPS instructions above).\
 3)  Copy all the content from your pre-existing R
     project (codes, data, etc.) into this new empty, local, repository (e.g. use copy and paste).\
 4)  Open your new project in RStudio, and go to the Git pane. The new files should
@@ -388,17 +388,17 @@ Please note the buttons circled in the image above, as they will be
 referenced later (from left to right):
 
 -   Button to *commit* the saved file changes to the local
-    branch (this will open a new window)
+    branch (this will open a new window).
 -   Blue arrow to *pull* (update your local version of the branch with
-    any changes made on the remote/Github version of that branch)
+    any changes made on the remote/Github version of that branch).
 -   Green arrow to *push* (send any commits/changes for your local
     version of the branch to the remote/Github version of that branch)
--   The Git tab in RStudio
+-   The Git tab in RStudio.
 -   Button to create a NEW branch using whichever local branch is shown
     to the right as the base. *You almost always want to branch off from
-    the main branch (after you first pull to update the main branch)*
--   The branch you are currently working in
--   Changes you made to code or other files will appear below
+    the main branch (after you first pull to update the main branch)*.
+-   The branch you are currently working in.
+-   Changes you made to code or other files will appear below.
 
 #### In Github Desktop {-}
 
@@ -428,20 +428,20 @@ easy and fast.
 A typical workflow is as follow:
 
 1.  Make sure that your local repository is up-to-date, update it if
-    not
+    not.
 
 2.  Go to the branch you were working on previously, or create a new
-    branch to try out some things
+    branch to try out some things.
 
 
 3.  Work on the files locally on your computer, make one or several
-    commits to this branch
+    commits to this branch.
 
-4.  Update the remote version of the branch with your changes (push)
+4.  Update the remote version of the branch with your changes (push).
 
 5.  When you are satisfied with your branch, you can merge the online
     version of the working branch into the online "main" branch to
-    transfer the changes
+    transfer the changes.
 
 Other team members may be doing the same thing with their own branches,
 or perhaps contributing commits into your working branch as well. 
@@ -464,7 +464,7 @@ knitr::include_graphics(here::here("images", "GitHub-Flow.png"))
 ```
 
 Image
-[source](https://build5nines.com/introduction-to-git-version-control-workflow/)
+[source](https://build5nines.com/introduction-to-git-version-control-workflow/).
 
 ## Create a new branch
 
@@ -549,7 +549,7 @@ knitr::include_graphics(here::here("images", "github_tracking2.png"))
 
 You might be wondering what the yellow, blue, green, and red squares next to
 the file names represent. Here is a snapshot from the [RStudio
-cheatsheet](https://www.rstudio.com/wp-content/uploads/2016/01/rstudio-IDE-cheatsheet.pdf)
+cheatsheet](https://raw.githubusercontent.com/rstudio/cheatsheets/refs/heads/main/pngs/rstudio-ide.png)
 that explains their meaning. Note that changes with yellow "?" can still
 be staged, committed, and pushed.
 
@@ -558,18 +558,18 @@ knitr::include_graphics(here::here("images", "github_tracking.png"))
 ```
 
 -   Press the "Commit" button in the Git tab, which will open a new
-    window (shown below)
+    window (shown below).
 
--   Click on a file name in the upper-left box
+-   Click on a file name in the upper-left box.
 
 -   Review the changes you made to that file (highlighted below in green
-    or red)
+    or red).
 
 -   "Stage" the file, which will include those changes in the commit. Do
     this by checking the box next to the file name. Alternatively, you
-    can highlight multiple file names and then click "Stage"
+    can highlight multiple file names and then click "Stage".
 
--   Write a commit message that is short but descriptive (required)
+-   Write a commit message that is short but descriptive (required).
 
 -   Press the "Commit" button. A pop-up box will appear showing success
     or an error message.
@@ -685,9 +685,9 @@ on Git commands.
 
 ***TIP:*** Asked to provide your password too often? See these chapters
 10 & 11 of this
-[tutorial](https://happygitwithr.com/credential-caching.html#credential-caching)
+[tutorial](https://happygitwithr.com/ssh-keys)
 to connect to a repository using a SSH key (more
-complicated)  
+complicated) .
 
 
 #### In Github Desktop {.unnumbered}
@@ -817,9 +817,9 @@ github](https://github.com/tidyverse/dplyr/pulls).
 You can submit a pull request (PR) directly form the website (as
 illustrated bellow) or from Github Desktop.
 
--   Go to Github repository (online)
--   View the tab "Pull Requests" and click the "New pull request" button
--   Select from the drop-down menu to merge your branch into main
+-   Go to Github repository (online).
+-   View the tab "Pull Requests" and click the "New pull request" button.
+-   Select from the drop-down menu to merge your branch into main.
 -   Write a detailed Pull Request comment and click "Create Pull
     Request".
 
@@ -906,12 +906,12 @@ a branch
 Be sure to also delete the branch locally on your computer. This will
 not happen automatically.
 
--   From RStudio, make sure you are in the Main branch
+-   From RStudio, make sure you are in the Main branch.
 -   Switch to typing Git commands in the RStudio "Terminal" (the tab
     adjacent to the R console), and type: **git branch -d
     branch_name**, where "branch_name" is the name of your branch to be
-    deleted
--   Refresh your Git tab and the branch should be gone
+    deleted.
+-   Refresh your Git tab and the branch should be gone.
 
 
 #### In Github Desktop
@@ -1059,7 +1059,7 @@ website](https://learngitbranching.js.org/).
 
 You enter commands in a Git shell.
 
-*Option 1* You can open a new Terminal in RStudio. This tab is next to
+*Option 1*: You can open a new Terminal in RStudio. This tab is next to
 the R Console. If you cannot type any text in it, click on the
 drop-down menu below "Terminal" and select "New terminal". Type the
 commands at the blinking space in front of the dollar sign "\$".
@@ -1068,12 +1068,12 @@ commands at the blinking space in front of the dollar sign "\$".
 knitr::include_graphics(here::here("images", "github_terminal.png"))
 ```
 
-*Option 2* You can also open a *shell* (a terminal to enter commands) by
+*Option 2*: You can also open a *shell* (a terminal to enter commands) by
 clicking the blue "gears" icon in the Git tab (near the RStudio
 Environment). Select "Shell" from the drop-down menu. A new window will
 open where you can type the commands after the dollar sign "\$".
 
-*Option 3* Right click to open "Git Bash here" which will open the same
+*Option 3*: Right click to open "Git Bash here" which will open the same
 sort of terminal, or open *Git Bash* form your application list.
 [More beginner-friendly informations on Git Bash](https://happygitwithr.com/shell.html), 
 how to find it and some bash commands you will need.
@@ -1118,32 +1118,33 @@ The [Github.com documentation and start
 guide](https://docs.github.com/en/github).
 
 The RStudio ["IDE"
-cheatsheet](https://www.rstudio.com/wp-content/uploads/2016/01/rstudio-IDE-cheatsheet.pdf)
+cheatsheet](https://rstudio.github.io/cheatsheets/html/rstudio-ide.html)
 which includes tips on Git with RStudio.
 
-<https://ohi-science.org/news/github-going-back-in-time>
+[GitHub: A beginner's guide to going back in time (aka fixing mistakes)](https://ohi-science.org/news/github-going-back-in-time)
 
 **Git commands for beginners**
 
 An [interactive
-tutorial](learngitbranching.js.org) to learn
+tutorial](https://learngitbranching.js.org/) to learn
 Git commands.
 
-<https://www.freecodecamp.org/news/an-introduction-to-git-for-absolute-beginners-86fa1d32ff71/>:
+[Git for Absolute Beginners](https://www.freecodecamp.org/news/an-introduction-to-git-for-absolute-beginners-86fa1d32ff71)
 good for learning the absolute basics to track changes in one folder on
 you own computer.
 
-Nice schematics to understand branches:
-<https://speakerdeck.com/alicebartlett/git-for-humans>
+Nice schematics to [understand branches](https://speakerdeck.com/alicebartlett/git-for-humans)
 
 
 **Tutorials covering both basic and more advanced subjects**
 
-<https://tutorialzine.com/2016/06/learn-git-in-30-minutes>
+[Learn Git in 30 Minutes](https://tutorialzine.com/2016/06/learn-git-in-30-minutes)
 
-<https://dzone.com/articles/git-tutorial-commands-and-operations-in-git>
-<https://swcarpentry.github.io/git-novice/> (short course)
-<https://rsjakob.gitbooks.io/git/content/chapter1.html>
+[Commands and Operations in Git](https://dzone.com/articles/git-tutorial-commands-and-operations-in-git)
+
+[Version Control with Git (short course)](https://swcarpentry.github.io/git-novice/)
+
+[Introduction to Git (book)](https://rsjakob.gitbooks.io/git/content/chapter1.html)
 
 The [Pro Git book](https://git-scm.com/book/en/v2) is considered an official reference. 
 While some chapters are ok, it is usually a bit _technical_. It is probably a good resource