Merge pull request #32 from StanfordHPDS/culture-policies-updates

Add documentation and onboarding content

Author: sherrirose

chapters/01-culture.qmd

@@ -25,7 +25,3 @@ We embrace time off, breaks from meetings, and vacations!
 Your physical and mental health are incredibly important. Please familiarize yourself with the [mental health](https://studentaffairs.stanford.edu/mental-health-resources-stanford) and [crisis assistance](https://glo.stanford.edu/glo-services/crisis-assistance) resources available for students at Stanford as well as mental [health resources](https://postdocbenefits.stanford.edu/my-benefits/medical-coverage/mental-health-resources) for postdoctoral scholars.
 
 Stanford is committed to providing equal educational opportunities for disabled students. Disabled students are a valued and essential part of the Stanford community. If you experience disability, please register with the [Office of Accessible Education (OAE)](https://oae.stanford.edu/). Professional staff at OAE will evaluate your needs, support appropriate and reasonable accommodations, and prepare an Academic Accommodation Letter for faculty. If you already have an Academic Accommodation Letter, Stanford invites you to share your letter with your advisor. Academic Accommodation Letters should be shared at the earliest possible opportunity so we may partner with you and OAE to identify any barriers to access and inclusion that might be encountered in your experience.
-
-## Professional Growth
-
-The Lab offer several internal opportunities for professional growth, including [trainings](https://github.com/StanfordHPDS/training), [book clubs](https://github.com/StanfordHPDS/hpds_book_club), and [journal clubs](https://github.com/StanfordHPDS/hpds_journal_club).

chapters/02-policies.qmd

@@ -4,7 +4,19 @@ It is important that each trainee and Dr. Rose have a shared understanding of ex
 
 ## Joining the Lab
 
-Dr. Rose keeps a page updated [on her website](http://drsherrirose.org/new-students-and-postdocs) regarding whether she is taking new students, hiring postdocs, or available for dissertation committees. At Stanford, we've had students from many different graduate programs join the Lab, including health policy, biomedical data science, computer science, and chemical engineering programs. 
+Dr. Rose keeps a page updated [on her website](http://drsherrirose.org/new-students-and-postdocs) regarding whether she is taking new students, hiring postdocs, or available for dissertation committees. At Stanford, we've had students from many different graduate programs join the Lab, including health policy, computer science, biomedical data science, and chemical engineering programs.
+
+## Onboarding
+
+The first step for new Lab members is to send Dr. Rose your GitHub username to be added to the Lab’s GitHub organization account. Then, review our [internal onboarding documentation](https://github.com/StanfordHPDS/onboarding) for new Lab members.
+
+*Rotation students do not need to complete these steps.*
+
+## Documentation
+
+We are a documentation-based Lab. This means that we write things down early and often. The goal is to solidify ideas as well as bring clarity and formalism (i.e., with notation) to projects. Documentation also helps team members review work asynchronously and record institutional knowledge.
+
+We document meetings with agendas (see @sec-meeting-agendas), manage projects with Git and GitHub (see @sec-git-github), and prefer reproducible documents using Quarto (see @sec-quarto).
 
 ## Recurring Meetings
 
@@ -22,13 +34,13 @@ Please also see @sec-meeting-agendas for details on recurring meeting agendas an
 
 Trainees must prepare an agenda prior to each recurring meeting with Dr. Rose. Create a google doc (invite Dr. Rose as editor) that you’ll add to in reverse chronological order for each meeting with the information below included. Update the google doc by 11AM *one business day* before our meeting. Push a commit to the project's GitHub repository at the same time, even if you plan to make further changes prior to the meeting. If additional changes are made to the repository ahead of the meeting, push a second commit. Repeatedly not creating agendas will result in cancelled meetings.
 
-**[Meeting Date]**
+**\[Meeting Date\]**
 
-- What has been completed since previous meeting:
-- Topics to discuss at the meeting:
-- What will be completed by the next meeting:
+-   What has been completed since previous meeting:
+-   Topics to discuss at the meeting:
+-   What will be completed by the next meeting:
 
-## Individual Development Plans 
+## Individual Development Plans
 
 If Dr. Rose is your primary advisor, students and postdoctoral scholars should complete the Stanford Individual Development Plan (IDP) when joining the Lab and then annually thereafter ([student forms](https://oge.stanford.edu/academics/idp/forms/), [initial form for postdocs](https://postdocs.stanford.edu/sites/default/files/opa_idp-initial_0.pdf), [annual form for postdocs](https://postdocs.stanford.edu/sites/default/files/opa_idp-annual_0.pdf)). This applies regardless of home department. Trainees should plan to check in on progress made toward IDP goals once a quarter. Dr. Rose expects that trainees will be responsible for scheduling the annual IDP meetings and adding the IDP check-ins once a quarter to the agenda for an existing recurring meeting.
 
@@ -38,29 +50,32 @@ If you are a graduate student and Dr. Rose is your primary advisor, please creat
 
 ## Registering for Units
 
-Graduate students should discuss their plans to register for research units with Dr. Rose each term (often BIOMEDIN 299 or HRP 399). Units should be taken credit/no credit and not for a letter grade. Permission codes are currently required to register for research units. 
+Graduate students should discuss their plans to register for research units with Dr. Rose each term (often BIOMEDIN 299 or HRP 399). Units should be taken credit/no credit and not for a letter grade. Permission codes are currently required to register for research units.
 
 ## Deadlines
 
 We aim to set ambitious yet feasible target deadlines for work product in a collaborative process. It is often the case that research takes longer than we expect, and an internal agreed-upon deadline is no longer possible. If you anticipate missing a deadline, contact Dr. Rose. It is an expectation in the Lab that all members are proactive about discussing revised deadlines rather than waiting until after the deadline has passed. If a trainee is repeatedly missing deadlines, we should discuss the underlying reasons.
 
-## Lab Meetings & Events
+## Lab Meetings
+
+We hold Lab Meetings approximately weekly to increase visibility across Lab projects, brainstorm ideas, and discuss research-related topics.
 
-The Lab holds Lab Meetings and various types of events throughout the year, including lunches, data jamborees, coffee chats, and journal clubs. If you have ideas for events, suggestions are always welcome.
+## Professional Development & Events
+
+The Lab offers several internal opportunities for professional growth, including [trainings](https://github.com/StanfordHPDS/training), [book clubs](https://github.com/StanfordHPDS/hpds_book_club), and [journal clubs](https://github.com/StanfordHPDS/hpds_journal_club). We also host informal lunches and coffee chats. If you have ideas for events, suggestions are always welcome.
 
 Food at Lab events is funded by the Lab and free to Lab attendees. We expect that trainees who RSVP and submit food orders will show up to the event, barring illness or personal situation. If you need to change your RSVP, please contact Dr. Rose to help us avoid food waste.
 
 ## Recommendation Letters
 
 Dr. Rose receives a variety of requests for letters from current and former trainees, including for graduate school, job applications, fellowships, and awards. Please know she treats your letter requests with the seriousness they deserve and recognizes their importance. Dr. Rose asks that you respect the time it takes her to write, revise, and send letters by giving plenty of notice and being organized with your requests.
 
-It essential that you ask Dr. Rose if she can write you a recommendation letter before submitting her name as a recommender. It may be the case that a letter from someone else will be more beneficial for you or that the deadline is too soon for her to accommodate your request. 
+It essential that you ask Dr. Rose if she can write you a recommendation letter before submitting her name as a recommender. It may be the case that a letter from someone else will be more beneficial for you or that the deadline is too soon for her to accommodate your request.
 
-In general, please give Dr. Rose at least 4 weeks notice when requesting a letter, and more time than that when possible. If the deadline is sooner than 4 weeks, she may not be able to write the letter, particularly during times of the year when she receives a high volume of letter requests. 
+In general, please give Dr. Rose at least 4 weeks notice when requesting a letter, and more time than that when possible. If the deadline is sooner than 4 weeks, she may not be able to write the letter, particularly during times of the year when she receives a high volume of letter requests.
 
 ## Communication
 
 We have a Lab **slack**. Lab members can search for "HPDS Lab" in the [Workspaces at Stanford](https://stanford.enterprise.slack.com/) and request to join.
 
 Please keep in mind our Lab philosophy on working hours in @sec-working-hours. Do not assume that because you have sent a slack message or email that you should get an instant reply.
-

chapters/07-publications.qmd

@@ -8,7 +8,7 @@ We aim to discuss authorship early in the research process and have continuing c
 
 The Lab follows the [ICMJE recommendations](http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html) regarding who is included as an author.
 
-What does first authorship mean in our Lab? Being the first author typically means that you are: (1) an intellectual lead on the project, (2) making major contributions conducting the scientific work (e.g., developing methodology, analyzing data), and (3) a main writer on the manuscript, typically crafting the first draft. For some projects, a first authorship role may also involve project management with collaborators and partners. All of these activities are done under the mentorship of Dr. Rose as the PI with substantial feedback in an apprenticeship model.
+What does first authorship mean in our Lab? Being the first author typically means that you are: (1) an intellectual lead on the project, (2) making major contributions conducting the scientific work (e.g., developing methodology, analyzing data), and (3) a main writer on the manuscript, usually crafting the first draft. For some projects, a first authorship role may also involve project management with collaborators and partners. All of these activities are done under the mentorship of Dr. Rose as the PI with substantial feedback in an apprenticeship model.
 
 ## Acknowledgments
 

chapters/09-code-workflow-agreements.qmd

@@ -253,7 +253,7 @@ Prefer Quarto `.qmd` files over Jupyter files; Quarto can run interactively like
 The best way to use Quarto for Python projects is [VS Code](https://quarto.org/docs/tools/vscode.html) using the Quarto extension. This extension allows you to render files easily while also running code interactively. RStudio also supports Python projects, so it's another good option if you also use R.
 :::
 
-## Use Git and GitHub
+## Use Git and GitHub {#sec-git-github}
 
 You should manage your project with version control and hosted for collaborators to access. We use [Git](https://www.atlassian.com/git) and [GitHub](https://docs.github.com/en/get-started/start-your-journey/hello-world) for managing and hosting version-controlled repositories, respectfully. We also have a [GitHub organization](https://github.com/StanfordHPDS) where we keep team projects.