add more editing suggestions

README.md

@@ -26,6 +26,9 @@ I'll turn this into instructions later, but here's a running list of things you'
 
 -   `repo_url` in `_quarto.yml`
 
+-   Red callout boxes titled "Group Edit" hold suggestions for what content to include on that page/section.
+    These should be deleted or commented out once the edits happen.
+
 ## To publish
 
 You only have to do this once.

authorship.qmd

@@ -14,4 +14,6 @@ Some ideas of things to discuss:
     (e.g. requirements of publishers vs. collaborator expectations)
 
 -   Under what circumstances, if any, should authors be removed?
+
+-   Are there any circumstances where {{< var pi_name >}} wouldn't be an author on a student/mentee paper?
 :::

code-of-conduct.qmd

@@ -53,7 +53,8 @@ Members of the community who violate these rules—no matter how much they have
 If inappropriate behavior persists after a discussion with {{< var pi_name >}}, the issue will be escalated according to procedures laid out by the relevant entities in University of Arizona's [Office of Institutional Equity](https://equity.arizona.edu/)
 
 **To report an issue** please contact [{{< var pi_name >}}](mailto:{{< var pi_contact >}}).
-All communication will be treated as confidential. If you feel you cannot contact {{< var pi_name >}}, contact the [Office of Institutional Equity](https://equity.arizona.edu/reporting)
+All communication will be treated as confidential.
+If you feel you cannot contact {{< var pi_name >}}, contact the [Office of Institutional Equity](https://equity.arizona.edu/reporting)
 
 ## University of Arizona Policies
 

contributing.qmd

@@ -2,42 +2,51 @@
 number-sections: false
 editor:
   markdown:
-    canonical: false #visual editor mangles shortcodes in links, but fixed in upcoming version https://github.com/quarto-dev/quarto/issues/337#issuecomment-1873437524
+    canonical: true #FYI visual editor mangles shortcodes in links in older versions of RStudio https://github.com/quarto-dev/quarto/issues/337#issuecomment-1873437524
 ---
 
 # Editing This Book {.unnumbered}
 
-Prerequisites: 
+Prerequisites:
 
-- Create an account on GitHub if you don't already have one.
-- Basic understanding of [markdown](https://quarto.org/docs/authoring/markdown-basics.html).
-- Optionally, knowledge of [Quarto](https://quarto.org/).
+-   Create an account on GitHub if you don't already have one.
+-   Basic understanding of [markdown](https://quarto.org/docs/authoring/markdown-basics.html).
+-   Optionally, knowledge of [Quarto](https://quarto.org/).
 
 ### Suggesting a change
 
 To suggest a change, click the "Report an issue" link on any page or go to the [GitHub repository]({{< meta book.repo-url >}}) and open an issue.
 
 ### Small edits
 
-To make an edit directly on GitHub, click the "{{< fa brands github >}} Edit this page" link on any page. This will open a page where you can make edits. When you are done, click the green "Commit changes..." button.  If you do not have the ability to push directly to the repo it may prompt you to create a fork and submit changes as a pull request. Your edits won't be "live" until someone (such as {{< var pi_name >}}) merges these changes. Don't worry if you don't know what "fork" and "pull request" mean yet—you should still be able to make edits this way!
+To make an edit directly on GitHub, click the "{{< fa brands github >}} Edit this page" link on any page.
+This will open a page where you can make edits.
+When you are done, click the green "Commit changes..." button.
+If you do not have the ability to push directly to the repo it may prompt you to create a fork and submit changes as a pull request.
+Your edits won't be "live" until someone (such as {{< var pi_name >}}) merges these changes.
+Don't worry if you don't know what "fork" and "pull request" mean yet—you should still be able to make edits this way!
 
 ### More substantial edits or new sections
 
 To make more extensive edits or to add new sections, it's probably best if you fork and clone the GitHub repository for this book and work on it on your computer using either RStudio or VSCode where you can take advantage of the [visual markdown editor](https://quarto.org/docs/visual-editor/) for Quarto.
 
 If you are an R user, there are some helpful functions in the [`usethis` package](https://usethis.r-lib.org/index.html) that can help with this workflow.
 
-1. Use `usethis::create_from_github("{{< meta book.repo-url >}}")` to fork and clone the repository.[^1]
-2. Use `usethis::pr_init("name-of-my-branch")` to create a new branch for your changes.
-3. Edit existing .qmd, .md, or .Rmd files or create new ones.
-4. If you've created a new file, be sure to add the path to it as a chapter in `_quarto.yml`.
-5. Preview your changes by running `quarto preview` in the terminal.
-6. Commit your changes with git.
-7. Run `usethis::pr_push()` to push your changes and open a pull request on GitHub.
-8. Once the pull request is merged on GitHub, run `usethis::pr_finish()` to clean things up.
+1.  Use `usethis::create_from_github("{{< meta book.repo-url >}}")` to fork and clone the repository.[^contributing-1]
+2.  Use `usethis::pr_init("name-of-my-branch")` to create a new branch for your changes.
+3.  Edit existing .qmd, .md, or .Rmd files or create new ones.
+4.  If you've created a new file, be sure to add the path to it as a chapter in `_quarto.yml`.
+5.  Preview your changes by running `quarto preview` in the terminal.
+6.  Commit your changes with git.
+7.  Run `usethis::pr_push()` to push your changes and open a pull request on GitHub.
+8.  Once the pull request is merged on GitHub, run `usethis::pr_finish()` to clean things up.
 
 ::: callout-warning
-The GitHub action to deploy this book as a website does not have the ability to run any code! If you include any code chunks in your edits, you will need to render them locally before making your pull request by running `quarto render` in the terminal and commiting any changes to the `_freeze/` directory.
+The GitHub action to deploy this book as a website does not have the ability to run any code!
+If you include any code chunks in your edits, you will need to render them locally before making your pull request by running `quarto render` in the terminal and commiting any changes to the `_freeze/` directory.
 :::
 
-[^1]: If you haven't set up git and GitHub on your computer, you'll get an (hopefully informative) error.  `usethis::git_sitrep()` can help you troubleshoot and we also recommend reading/searching [happygitwithr.com](https://happygitwithr.com/). You only need to run this the first time you contribute to the book.  For subsequent contributions, just open the RStudio project and start with step 2.
+[^contributing-1]: If you haven't set up git and GitHub on your computer, you'll get an (hopefully informative) error.
+    `usethis::git_sitrep()` can help you troubleshoot and we also recommend reading/searching [happygitwithr.com](https://happygitwithr.com/).
+    You only need to run this the first time you contribute to the book.
+    For subsequent contributions, just open the RStudio project and start with step 2.

group-expectations.qmd

@@ -1,3 +1,57 @@
 # Group Expectations
 
-group expectations go here
+Beyond abiding by the [code of conduct](code-of-conduct.qmd), we expect all group members to ...
+
+::: callout-important
+## Group Edit
+
+Some discussion topics to get you started:
+
+-   Expected work hours
+
+    -   Should group members be expected to be available evenings and weekends?
+
+    -   Should group members be expected to be in the lab/office certain hours or days of the week?
+
+-   Communication expectations
+
+    -   How quickly should group members be expected to respond to emails/slack messages?
+
+    -   Is there a preferred method of communication for the group (e.g. email, Slack, carrier pigeon)?
+
+-   Attendance at meetings
+
+    -   Are there certain meetings or seminars everyone is expected to attend?
+:::
+
+## Mentee expectations
+
+::: callout-important
+## Group Edit
+
+Some discussion topics to get you started:
+
+-   When should mentees ask questions?
+    Who should they ask first?
+
+-   Is it the mentee's responsibility to schedule regular meetings with mentors?
+    If so, how often should these be?
+
+-   
+:::
+
+## Mentor/PI expectations
+
+::: callout-important
+## Group Edit
+
+Some discussion topics to get you started:
+
+-   How often and in what way are mentors expected to check in with mentees?
+
+-   Is it the mentor's responsibility to schedule regular meetings with mentees?
+
+-   How available are mentors expected to be and in what format (email, face-to-face, zoom, slack, etc.)?
+
+-   
+:::

offboarding.qmd

@@ -1,5 +1,28 @@
 # Offboarding
 
+::: callout-important
+## Group Edit
+
+This may be difficult to finalize until someone goes through the offboarding process and takes thorough notes (ideally by [editing](contributing.qmd) this page).
+Here are some discussion topics to get you started though:
+
+-   What are the group expectations for what to do with unpublished data collected during your time in the lab when you leave?
+
+-   What about code used to analyze data?
+    Where should it be stored and what are the expectations around reproducibility/usability of such code?
+
+-   What kinds of keys (physical or otherwise) or passwords might someone need to pass on?
+
+-   What kinds of shared drives does the lab group use?
+    Do you need to explicitly transfer ownership of documents on any of them?
+
+-   Are there official university or department offboarding steps to take?
+    E.g. something mandated by HR or the graduate school like an exit interview?
+
+-   What is the timeline for all of this?
+    Don't wait until the last week of work to complete all these tasks!
+:::
+
 Offboarding is important to our group because we want to get feedback and also not lose your data and stuff
 
 Steps to take:

onboarding.qmd

@@ -1,5 +1,28 @@
 # Onboarding
 
+::: callout-important
+## Group Edit
+
+This is most easily edited by someone actively going through the onboarding process (or someone who recently joined the lab group).
+That being said, here are some discussion questions to get you started:
+
+-   How long is "onboarding"?
+    When can you say it is over and someone has completed it?
+
+-   What do you feel was most difficult when you first joined the lab?
+    What tips would you want to pass along to someone on their first day, first week, etc.
+
+-   Who are the people to talk to in your department/college who hold the knowledge a newcomer might need to get settled in?
+    E.g. who does payroll, who can get you a spare monitor and keyboard, who can get you key card access, etc.
+
+-   What are good ways to get to know people (personally and professionally) in your lab group/department/school/college?
+:::
+
+::: callout-note
+We expect this checklist to be constantly evolving and encourage you to edit it as *part of onboarding*.
+See [Editing This Book](contributing.qmd).
+:::
+
 ## First day
 
 1.  Find your desk