cct-datascience · Aariq · Jul 17, 2024 · Jul 5, 2024 · Jul 5, 2024 · Jul 5, 2024
diff --git a/.github/ISSUE_TEMPLATE/onboarding-checklist.md b/.github/ISSUE_TEMPLATE/onboarding-checklist.md
@@ -37,7 +37,7 @@ The goal in the first week is to set up your accounts and your physical and virt
 Feel free to ask anyone in the group questions about these steps, especially in the group's Slack channel (#datascience channel within CALS CCT Slack).
 
 -   [ ] Work through CCT-DS Onboarding checklist (this document). Suggest changes, comment, and ask questions as you go to make it more useful to the next person.
--   [ ] Review our group's [Code of Conduct](code-of-conduct.qmd)
+-   [ ] Review our group's [Code of Conduct](https://cct-datascience.github.io/group-procedures/code-of-conduct.html)
 
 ### HR logistics
 
@@ -92,7 +92,7 @@ Create accounts on the following collaboration tools (details provided below):
     -   [ ] You will need to create a Hackmd account, and then someone from the group will need to add you.
 -   [ ] Get added to Toggl, for time tracking
 -   [ ] Log in to get edit access to the website. Navigate to <https://datascience.cct.arizona.edu/user>. Don't log in using the obvious log in form; click on "Log in with NetAuth" (or similar) and log in using your NetID credentials.
--   [ ] Log in to [Stache](stache.arizona.edu), used for sharing passwords and other sensitive information within the university.
+-   [ ] Log in to [Stache](https://stache.arizona.edu/), used for sharing passwords and other sensitive information within the university.
 -   [ ] Get added to the group [Posit Connect](https://viz.datascience.arizona.edu/connect/)
     -   You'll have to request access and list a sponsor. This is Kristina.
 -   [ ] Log in to the group [Quarto Pub](https://quartopub.com)
@@ -116,7 +116,7 @@ Create accounts on the following collaboration tools (details provided below):
 
 -   [ ] Read about group expectations and general information [here](https://cct-datascience.github.io/group-procedures/general-info.html)
 -   [ ] Populate your calendar with the current group meeting schedule. Kristina will send you invites.
--   [ ] Participate in daily standup meetings, [biweekly sprint planning meetings](https://hackmd.io/ih-qR2B6RJ221MJEFeEqcA), [weekly outreach hour](https://hackmd.io/fxo335XYQXGUpIm6c46TkQ), and [biweekly incubator meetings](https://github.com/orgs/cct-datascience/projects/7). Review [project management page](project-management.qmd) to prepare for these.
+-   [ ] Participate in daily standup meetings, [biweekly sprint planning meetings](https://hackmd.io/ih-qR2B6RJ221MJEFeEqcA), [weekly outreach hour](https://hackmd.io/fxo335XYQXGUpIm6c46TkQ), and [biweekly incubator meetings](https://github.com/orgs/cct-datascience/projects/7). Review [project management page](https://cct-datascience.github.io/group-procedures/project-management.html) to prepare for these.
 -   [ ] Set up your standing meeting with Kristina.
 -   [ ] Begin learning about and using software and data related to projects.
     -   This can include reading about incubators (on our GitHub project board), funded projects (talk to Kristina and current team members), or trainings.

diff --git a/.github/workflows/links.yml b/.github/workflows/links.yml
@@ -28,6 +28,7 @@ jobs:
             --exclude github\.com\/orgs\/cct-datascience\/projects 
             --exclude calendar\.google\.com 
             --exclude \.php$ 
+            --exclude portal\.hpc\.arizona\.edu
             './**/*.md' './**/*.qmd'
 
       - name: Create Issue From File

diff --git a/annual-reviews.qmd b/annual-reviews.qmd
@@ -5,23 +5,27 @@ editor: visual
 
 Arizona Board of Regents requires at least one formal performance appraisal per year per employee.
 
-The University of Arizona provides a standardized process called "Career Conversations" that is described in more detail in the links below.
+The University of Arizona provides a standardized process called "[Career Conversations](https://hr.arizona.edu/career-conversations-employees)" that is described in more detail in the links below.
 We will have Annual Reviews in early January each year, prior to the first Quarterly Review.
 
+::: callout-note
+Note that the University's career conversations cycle is on a different schedule than our groups.
+You'll fill out your career conversations form at the end of the calendar year, but be required to submit it to HR at the end of the *fiscal* year in June.
+:::
+
 Steps:
 
 1.  Define your personal goals for the year; SMART goals provide a helpful framework
 
 2.  [Review what SMART Goals are](https://www.linkedin.com/learning/setting-team-and-employee-goals-using-smart-methodology/how-to-use-smart-goals-2)
 
-3.  [SMART Goals Template](https://hr.arizona.edu/sites/default/files/SMART-Goal-Setting-Template.pdf)
+3.  [SMART Goals Template](https://hr.arizona.edu/sites/default/files/Smart-Goal-Setting-Template_rev%202021.pdf)
 
-4.  Fill out the [Career Conversations](https://hr.arizona.edu/sites/default/files/UACareerConversation%20Form.docx) form.
+4.  Fill out the [Career Conversations](https://hr.arizona.edu/career-conversations-employees) form.
 
 5.  Send this form to David the day prior to your meeting.
 
 *References:*
 
--   [Career Conversations Guide](https://hr.arizona.edu/sites/default/files/hr/forms/HR-Conversations/UACareerConversationGuide.pdf)
-    -   [Guide Supplement: "Career Conversations in a Remote Setting"](https://hr.arizona.edu/sites/default/files/Career%20Conversations%20in%20a%20Remote%20Setting.pdf)
--   [FAQs](https://hr.arizona.edu/supervisors/performance-management/performance-feedback-faqs)
+-   [Career Conversations Guide](https://hr.arizona.edu/career-conversations-employees)
+-   [FAQs](https://hr.arizona.edu/career-conversations-employees) (at bottom of page)
diff --git a/code-of-conduct.qmd b/code-of-conduct.qmd
@@ -34,12 +34,12 @@ We are committed to creating an environment that supports inclusivity and respec
 
 ### University of Arizona
 
--   **If you experience discrimination or harassment by *UA employees, visitors, vendors or contractors***, report it to the Office of Institutional Equity---<https://equity.arizona.edu/reporting>; 520‐621‐9449; [equity\@email.arizona.edu](mailto:equity@email.arizona.edu){target="_blank"}.
+-   **If you experience discrimination or harassment by *UA employees, visitors, vendors or contractors***, report it to the Office of Institutional Equity—<https://equity.arizona.edu/reporting>; 520‐621‐9449; [equity\@email.arizona.edu](mailto:equity@email.arizona.edu){target="_blank"}.
 -   **If a person complains of discrimination or harassment**, ask them to report it to OIE. Then report it immediately - <https://equity.arizona.edu/reporting>; 520‐621‐9449; [equity\@email.arizona.edu](mailto:equity@email.arizona.edu){target="_blank"}. NEVER promise to "keep it quiet." NEVER investigate the issue yourself.
-    -   ***If a student asks you for help***, refer them to OIE using this guidance---<https://equity.arizona.edu/reporting/make-referral>. NEVER promise to "keep it quiet." NEVER investigate the issue yourself.
--   **If you witness or are made aware of discrimination or harassment, you must report it immediately**---<https://equity.arizona.edu/reporting>; 520‐621‐9449; [equity\@email.arizona.edu](mailto:equity@email.arizona.edu){target="_blank"}.
-    -   **If you witness or are made aware of discrimination or harassment *by students***, submit an Incident Report Referral Form to the Dean of Students---<https://arizona-advocate.symplicity.com/public_report>
--   **All suspected or alleged criminal activity, especially sexual assault**, must be reported to UAPD immediately---<https://uapd.arizona.edu>; 911 (emergency) or 520-621-8273 (non-emergency).
+    -   ***If a student asks you for help***, refer them to OIE using this guidance—<https://equity.arizona.edu/reporting/make-referral>. NEVER promise to "keep it quiet." NEVER investigate the issue yourself.
+-   **If you witness or are made aware of discrimination or harassment, you must report it immediately**—<https://equity.arizona.edu/reporting>; 520‐621‐9449; [equity\@email.arizona.edu](mailto:equity@email.arizona.edu){target="_blank"}.
+    -   **If you witness or are made aware of discrimination or harassment *by students***, submit an Incident Report Referral Form to the Dean of Students—<https://arizona-advocate.symplicity.com/public_report/index.php>
+-   **All suspected or alleged criminal activity, especially sexual assault**, must be reported to UAPD immediately—<https://uapd.arizona.edu>; 911 (emergency) or 520-621-8273 (non-emergency).
 
 ### CCT-Data Science
 

diff --git a/general-info.qmd b/general-info.qmd
@@ -7,9 +7,9 @@ title: Campus Logistics
 We work in the Bioscience Research Laboratory (BSRL)
 
 -   General issues in the building
-    -   Submit a ticket for either IT support or miscellaneous building-related issues: <https://keating.bio5.org/ticket_support/tickets.php>
+    -   Submit a ticket for either IT support or miscellaneous building-related issues: <https://keating.bio5.org/ticket_support/>
 -   Copy machine and fax use
-    -   Lomax can connect you to the color copier downstairs; create a ticket to request his help: <https://keating.bio5.org/ticket_support/tickets.php>
+    -   Create a ticket if you need help connecting to the color copier downstairs: <https://keating.bio5.org/ticket_support/>
 -   Mail: there is a group mailbox in the mailroom on the N(orth) side of the building.
 -   Packages: if you receive a package you will be notified by email.
 

diff --git a/group-expectations.qmd b/group-expectations.qmd
@@ -21,13 +21,13 @@ See the rest of this page for when to use the group's calendar.
 -   Everyone is expected to be in during normal working hours. Since we are distributed across time zones, work with Kristina to establish your working hours.
 -   Please let Kristina know at least 2 weeks in advance of any vacation time.
 -   You can ask HR (or look in UAccess) to track your available sick and vacation time. This is an important and valuable part of your compensation!
--   Please be sure to update the CCT Group Calendar with your time off. The calendar entry only needs to include your name and when you will be out; details about the what or why are not necessary. 
+-   Please be sure to update the CCT Group Calendar with your time off. The calendar entry only needs to include your name and when you will be out; details about the what or why are not necessary.
 
 # Communication
 
 -   We use multiple methods of communication: In Person, Email, Slack, GitHub, Zoom, Google Drive, Google Calendars; see [Group Communication](group-communication.qmd) for details.
 -   We should all aim to reply to inquiries within a day. If someone doesn't reply in a timely fashion, please remind them **early**, **often**, and through **multiple channels**.
-- Everyone should do their best to keep their calendars up to date, to make scheduling meetings with collaborators, etc. easier. 
+-   Everyone should do their best to keep their calendars up to date, to make scheduling meetings with collaborators, etc. easier.
 
 # Feedback and Iteration
 
@@ -39,7 +39,7 @@ Please let me know if you have any questions.
 
 -   Inform Kristina by email of upcoming vacation or leave as soon as is practical; *at least two weeks in advance*.
 -   Employees must report their time by 10:00 a.m. on the Friday of a non-pay week. Supervisors (time approvers) must approve time by 5:00 p.m. on that day. See <https://hr.arizona.edu/supervisors/compensation>
--   For Appointed personnel, you only need to report leave time (sick, vacation, jury duty, etc). Holidays and campus closures are automatically added to your time sheet. For more information on winter holiday closure: <https://hr.arizona.edu/employees-affiliates/leaves/university-winter-closure>
+-   For Appointed personnel, you only need to report leave time (sick, vacation, jury duty, etc). Holidays and campus closures are automatically added to your time sheet. For more information on winter holiday closure: <https://hr.arizona.edu/events/winter-closure>
 
 # Computer backups
 

diff --git a/hiring.qmd b/hiring.qmd
@@ -33,7 +33,6 @@ All members of the hiring committee should be involved in all steps of the hirin
 -   ES Jobs `Es_jobs_net@ucar.edu`
 -   Academic Data Science Jobs Board <https://academicdatascience.org/jobs>
 -   US-RSE Job Board <https://us-rse.org/jobs/policy/>
--   Rstudio Community <https://community.rstudio.com/t/post-jobs-gigs-here/9254>
 -   NAU ecoinformatics: email katharyn.duffy\@nau.edu
 -   [Other resources (places to advertise) from UA HR](https://hr.arizona.edu/supervisors/recruitment-hiring/guide-successful-searches/advertising-position)
 -   Mastodon
@@ -153,13 +152,13 @@ The University has a structured system called UCAP, defined below, for standardi
 
 #### The University Career Architecture Project (UCAP)
 
-Salaries, raises, and promotion are governed by the [University Career Architecture Project](https://ucap.arizona.edu/).
-As an overview, most full time developers in our group will fall in the PC1-PC3 category as defined by the [UA Work Dimensions spreadsheet](https://ucap.arizona.edu/career-architecture/work-dimensions-staff-pay-structure).
+Salaries, raises, and promotion are governed by the [University Career Architecture Project](https://hr.arizona.edu/compensation/staff-compensation-program).
+As an overview, most full time developers in our group will fall in the PC1-PC4 category as defined by the [UA Work Dimensions spreadsheet](https://hr.arizona.edu/compensation/staff-compensation-program/career-levels-streams).
 They will be in either the Research and Data Analysis or Research Engineering Job functions within the [Research Job families](arizona.edu/job-functions-families).
 
 We strive to have transparency and equity within the group as well as among our peers.
 Like most public institutions, salaries at the University of Arizona are public ([the library lists salary databases by year](https://new.library.arizona.edu/find/ua-info)).
-Salaries follow the [University of Arizona Pay Structure](https://ucap.arizona.edu/content/university-staff-pay-structure).
+Salaries follow the [University of Arizona Pay Structure](https://hr.arizona.edu/compensation/staff-compensation-program/university-staff-pay-structure).
 
 Salaries in DIAG range from \$30k for a recent graduate to \$85k for developers with 10-15 years of experience in relevant technologies and the ability to take on substantial leadership and mentoring roles.
 

diff --git a/incubator.qmd b/incubator.qmd
@@ -129,7 +129,7 @@ Take notes on the answers and share them with the team at the next incubator mee
 Members of the CCT-Data Science team who make substantial and substantive contributions to incubator projects should be acknowledged or included as co-authors as appropriate.
 This should be discussed early in the project.
 
-The [CRedIT Taxonomy](https://casrai.org/credit/) provides a list of contribution types that may warrant co-authorship.
+The [CRedIT Taxonomy](https://credit.niso.org/) provides a list of contribution types that may warrant co-authorship.
 All DIAG contributors should be involved in review and revision---as co-authors, we should feel comfortable with the content.
 
 More details in the [Authorship and Licensing Guidelines](getting-credit.qmd) page.
diff --git a/offboarding.qmd b/offboarding.qmd
@@ -26,7 +26,7 @@ Websites and passwords (Kristina)
 
 -   change permissions as appropriate in group organizations (optional, depending on planned future work)
 
-    -   github organizations
+    -   github organizations <!--# probably needs updating -->
 
         -   az-digitalag
         -   agpipeline
@@ -37,19 +37,19 @@ Websites and passwords (Kristina)
 
     -   Google Drive "Group" and other project-specific folders
 
-    -   Openstack CALS group
+    -   Openstack CALS group <!--# probably not relevant anymore -->
 
 -   Make sure any accounts and websites are transitioned
 
     -   E.g. dockerhub, google drive
 
--   Remove user accounts and home directories from machines
+-   Remove user accounts and home directories from machines <!--# probably not relevant anymore -->
 
-    -    `sudo userdel $name && sudo rm -r /home/$name`
+    -   `sudo userdel $name && sudo rm -r /home/$name`
 
 -   Remove from UA HPC group
 
-    -   go to <https://portal.hpc.arizona.edu/portal/> \> Manage Groups \> kristinariemer
+    -   go to <https://portal.hpc.arizona.edu> \> Manage Groups \> kristinariemer
 
 ### Exit Interview
 

diff --git a/outreach-communication.qmd b/outreach-communication.qmd
@@ -29,7 +29,7 @@ editor:
     -   [prupert\@arizona.edu](mailto:prupert@arizona.edu) Peggy Rupert for Nutritional Sciences and Wellness
     -   [pnielsen322\@arizona.edu](mailto:pnielsen322@arizona.edu) Paula Nielsen for Entomology
     -   [thodges\@arizona.edu](mailto:thodges@arizona.edu) Tanya Hodges for AETI (Yuma)
--   Data Science Institute ["Data Drip"](https://bcf.arl.arizona.edu/news) at [Rii-datascienceinstitute\@arizona.edu](mailto:Rii-datascienceinstitute@arizona.edu)
+-   Data Science Institute ["The Data Drip"](https://datascience.arizona.edu/news/data-drip-enews) at [Rii-datascienceinstitute\@arizona.edu](mailto:Rii-datascienceinstitute@arizona.edu)
 -   R-Users AZ listserv, send announcement to Jeff Oliver [jcoliver\@email.arizona.edu](mailto:jcoliver@email.arizona.edu)
 -   CALES [Data Science Ambassadors](https://datascience.arizona.edu/dsa)
 -   EEB grad student coordinator: send announcement to Pennie Rabago-Liebig [pliebig\@arizona.edu](mailto:pliebig@arizona.edu)
@@ -130,7 +130,7 @@ To log in, you'll find the password on [stache](https://stache.arizona.edu/) (yo
 -   Short summary & link to a recent publication from the group or collaborators
 -   Notification of recent release of group's software or documentation
 -   Relevant upcoming events, e.g., conferences or hackathons that group members are attending
--   Link to recently posted news article on [group website](https://datascience.cct.arizona.edu/all-news) (new and improved website coming soon!)
+-   Link to recently posted news article on [group website](https://datascience.cct.arizona.edu/news) (new and improved website coming soon!)
 -   Link to good resources for the type of work we do, e.g., blog post for how to use an R package
 -   Live coverage of an event like a conference talk—this can be a difficult thing to do
 
@@ -156,7 +156,7 @@ To log in, you'll find the password on [stache](https://stache.arizona.edu/) (yo
 
 ### Resources
 
--   [Benefits and how to for scientists using Twitter](https://www.labsexplorer.com/c/twitter-and-scientists-a-love-story_185)
+-   [Benefits and how to for scientists using Twitter](https://app.scientist.com/blog/2019/01/31/twitter-and-scientists-a-love-story)
 -   [UA Brand Resources](https://brand.arizona.edu/)
 -   [Requesting an official UA Tweet](https://uarizona.co1.qualtrics.com/jfe/form/SV_1Nh6GSKXPDQlsKF)
 

diff --git a/publishing-to-web.qmd b/publishing-to-web.qmd
@@ -5,7 +5,7 @@ editor: visual
 
 We have many options for publishing html documents, html-based slides, websites, shiny apps, APIs, etc. to the web.
 
--   **Posit Connect (previously 'RStudio Connect')**: UA has access to a Posit Connect server at viz.datascience.arizona.edu. This is an appropriate venue for publishing Shiny apps, Quarto or RMarkdown documents, datasets using the `pins` package, and `plumber` APIs [**for research purposes**](https://datascience.arizona.edu/analytics-powerhouse/rstudio-connect). Shiny for Python or Flask APIs can also be published to Posit Connect.
+-   **Posit Connect (previously 'RStudio Connect')**: UA has access to a Posit Connect server at viz.datascience.arizona.edu. This is an appropriate venue for publishing Shiny apps, Quarto or RMarkdown documents, datasets using the `pins` package, and `plumber` APIs [**for research purposes**](https://datascience.arizona.edu/analytics-powerhouse/posit-connect). Shiny for Python or Flask APIs can also be published to Posit Connect.
 -   **Quarto Pub**: Our group has a Quarto Pub account that allows publishing of Quarto documents to [cct-datascience.quarto.pub](https://cct-datascience.quarto.pub/). This is appropriate for slides and notes used for teaching workshops. Course websites can be published here also, but because of size and traffic limitations, GitHub pages might be a better choice.
 -   **GitHub pages**: We also have the ability to use GitHub pages for publishing content to the web. This is an appropriate venue for package documentation (e.g. `pkgdown` sites), project websites, and websites for short courses. This venue is also not limited to websites created via Quarto, RMarkdown, etc. so it is possibly an appropriate venue if there is a need for more flexible deployment.