--- title: "Welcome & Syllabus" subtitle: "Lecture 01" author: "Dr. Colin Rundel" footer: "Sta 323 - Spring 2024" format: revealjs: theme: slides.scss transition: fade slide-number: true self-contained: true --- ```{r setup} #| message: False #| warning: False #| include: False options( width=80 ) ``` # Course Details ## Course Team ### Instrutor * Dr. Colin Rundel - [colin.rundel@duke.edu](mailto:colin.rundel@duke.edu) / [cr173@duke.edu](mailto:cr173@duke.edu) / [rundel@gmail.com ](mailto:rundel@gmail.com) - Office hours: Wednesdays 2-3 pm, 204 Old Chem (or Zoom)
### TAs * Alonso Guerrero Castañeda * Olivier Binette ## Course website(s) * GitHub pages - - HTML, PDF, and qmds of Slides - Readings and other notes * Canvas - - Announcements - Gradebook ## Course Timetable * Lectures (weekly) - Old Chemistry 116 - Wednesdays, 11:45 - 1:00 pm - Fridays, 11:45 - 1:00 pm * Labs (weekly) - Reuben-Cooke Building 129 - Tuesdays, 11:45 - 1:00 pm ## Labs - Attendance is expected - Opportunity to work on course assignments with TA support - Labs will begin in Week 2 (January 23rd) ## Announcements Will be posted on Canvas (Announcements tool) * email notification * also check Canvas regularly ## Grading This course is assessed 100% on your coursework (there is no exam). We will be assessing you based on the following assignments,
::: {.medium} |Assignment|Type |Value | n |Assigned | |:---------|:---------|:------|:--:|:--------------------| |Homeworks |Team |50% | ~6 | ~ Every other week | |Midterms |Individual|40% | 2 | ~ Week 6 and 14 | |Project |Team |10% | 1 | ~ Week 10 | ::: ## Teams * Team assignments + Roughly biweekly assignments + Open ended, ~5 - 15 hours of work + Peer evaluation after completion * Expectations and roles: + Everyone is expected to contribute equal *effort* + Everyone is expected to understand *all* code turned in + Individual contribution evaluated by peer evaluation, commits, etc. ## Collaboration policy - Only work that is clearly assigned as team work should be completed collaboratively (Homeworks + Project). - Individual assignments (Midterms) must be completed individually, you may not directly share or discuss answers / code with anyone other than the myself and the TAs. - On Homeworks you should not directly share answers / code with other teams, however you are welcome to discuss the problems in general and ask for advice. ## Sharing / reusing code policy - We are aware that a huge volume of code is available on the web, and many tasks may have solutions posted. - Unless explicitly stated otherwise, this course's policy is that you may make use of any online resources (e.g. Google, StackOverflow, etc.) but you must explicitly cite where you obtained any code you directly use or use as inspiration in your solution(s). - Any recycled code that is discovered and is not explicitly cited will be treated as plagiarism, regardless of source. - The same applies to the use of LLM like ChatGPT or GitHub Copilot - you are welcome to make use of these tools as the basis for your solutions but you must cite the tool when using it. ## Academic integrity
::: {.medium} > To uphold the Duke Community Standard: > > - I will not lie, cheat, or steal in my academic endeavors; > - I will conduct myself honorably in all my endeavors; and > - I will act if the Standard is compromised. ::: # Course Tools ## Accessing RStudio Workbench To reduce friction, the preferred method is to use the department's RStudio server(s). To access RStudio/Posit Workbench: 1. Navigate to 2. Log-in with your Duke NetID and password. ::: aside If off campus, use the VPN to create a secure connection from your computer to Duke. If you are on campus, be sure you are connected to the DukeBlue network. ::: ## DSS RStudio alternatives If you cannot access RStudio via the DSS servers: - Make sure you are on authenticated Duke network (e.g. DukeBlue or VPN if off campus) - Make sure you are not using a custom DNS server - e.g. `1.1.1.1` or `8.8.8.8` - Use a Docker container from Duke OIT 1. Go to and login 2. Select `Reserve a Container` and find `RStudio (statistics application with Rmarkdown and knitr support)` 3. Click the link under my reservations to create your environment ## Local R + RStudio If working locally you should make sure that your environment meets the following requirements: * latest R (4.3.2) * latest RStudio (2023.12) * working git installation * ability to create ssh keys (for GitHub authentication) * *All* R packages updated to their latest version from CRAN . . . Support policy for local installs - we will try to help you troubleshoot if we can but reserve the right to say go use the server. ## GitHub - We will be using an organization specifically to this course [github.com/sta323-sp24](https://github.com/sta323-sp24) - All assignments will be distributed and collected via GitHub - All of your work and your membership (enrollment) in the organization is private - We will be distributing a survey this weekend to collection your GitHub account names - Before lab you will be invited to the course organization. - All course related repositories will be created for you ## Before next week * Create a GitHub account if you don't have one * Complete the course survey * Make sure you can login in to the Department's RStudio server * Setup ssh key authentication with GitHub, see ## Account names A few suggestions on picking a GitHub username: - Incorporate your actual name! People like to know who they're dealing with. It makes your username easier for people to guess or remember. - Pick a username you will be comfortable revealing to your future boss. - Shorter is better than longer. - Be as unique as possible in as few characters as possible. In some settings GitHub auto-completes or suggests usernames. - Make it timeless. Don't highlight your current university, employer, or place of residence. - Avoid words laden with special meaning in programming. # git and GitHub setup demo ## Configure git The following will tell git who you are, and other common configuration tasks. ``` r usethis::use_git_config( user.name = "Colin Rundel", user.email = "rundel@gmail.com", push.default = "simple" ) ``` You will need to do this configuration once on each machine in which you use git (e.g. the server and your laptop). This can also be done via the terminal with, ```{bash eval=FALSE} #| echo: true git config --global user.name "Colin Rundel" git config --global user.email "rundel@gmail.com" git config --global push.default simple ``` ::: aside All of these values will be saved in the `.gitconfig` file in your home directory ::: ## Configure git verification To verify you configured git correctly, run ```{r} #| echo: true #| eval: false #| code-line-numbers: "|3,4" usethis::git_sitrep() ## Git config (global) ## ● Name: 'Colin Rundel' ## ● Email: 'rundel@gmail.com' ## ● Vaccinated: FALSE ## ℹ See `?git_vaccinate` to learn more ## ● Default Git protocol: 'https' ## GitHub ## ● Default GitHub host: 'https://github.com' ## ● Personal access token for 'https://github.com': ## x Call `gh_token_help()` for help configuring a token ## Git repo for current project ## ℹ No active usethis project ``` You should see output similar to above with your details. ## Configure SSH and GitHub (authentication) We will be authenticating with GitHub using SSH via public / private keys. We can create a new key pair (if necessary) by running the following in RStudio's *console*: ```{r eval=FALSE} credentials::ssh_setup_github() ``` . . . ```{r} #| echo: true #| code-line-numbers: "|1-4|6|7-16|10|18" ## No SSH key found. Generate one now? ## ## 1: Yes ## 2: No ## ## Selection: 1 ## Generating new RSA keyspair at: /home/guest/.ssh/id_rsa ## Your public key: ## ## ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC/wH7pT3UXdOMJSX2wMaPVTyGnYkS8OPmcfjct6h8Q+44/9UG3sOibjjUCxIxVeCWAoYFB0rDI3/Ljf2EWozLlpeGzAe7xsg6A+MHtUObZnfzXSB/NnOhZymD2u8Nh+py07aojVdKAPBkRH3nHA+rljidc3gXZkqseetYEI1N79OQUshp2P+Qm6Vab4I5OCnfAwLFkR7Sw7J9hvZN1qUmM0DB0WTWSlNmPSMsASMe/6Nz30IRoBh35Z7tgF79rlIW385giCkEeD20Le9EOueGoTWarJWylE1RWnUyig2mZ9JK/rYTw4KBXacPhBwn+MgGC+r8xY5IEX78xkeXW9q2z #<< ## ## Please copy the line above to GitHub: https://github.com/settings/ssh/new ## Would you like to open a browser now? ## ## 1: Yes ## 2: No ## ## Selection: 1 ``` ## Testing things out If you were successful with all of the above then you should be able to do the following, * Create a new *private* repository on GitHub (e.g. `test_repo`) * Add a `README` or similar file * Clone the repository into RStudio * Using `File` > `New Project` > `Version Control` > `Git` * Modify the `README` or other file * Stage, commit, and push