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index.Rmd
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---
title: "SISBID Module 1"
output:
html_document:
theme: cosmo
pdf_document: default
---
## Data Wrangling with R
**Instructors:** `r config::get("instructors")`
**Class Schedule:**
* M/T: 8am-2:30pm PST, W: 8am-11am PST
* Location: Zoom (see class email or Slack for link)
**Software:**
Please install the latest versions of R and RStudio:
https://sisbid.github.io/Data-Wrangling/lecture_notes/Setup.html
Make sure you have git installed: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
Make sure you have a GitHub profile: https://github.com/
<!--
**Resources:**
* [Rstudio Cloud Class Project Homepage](https://rstudio.cloud/spaces/21228/projects)
* [Rstudio's cheatsheets](http://www.rstudio.com/resources/cheatsheets/)
* [R for Data Science](http://r4ds.had.co.nz/)
* [JHU Cloud-Based Data Science](https://leanpub.com/universities/set/jhu/cloud-based-data-science)
* [Git for Humans](https://speakerdeck.com/alicebartlett/git-for-humans)
* [GitHub Labs](https://lab.github.com/)
* [swirl](http://swirlstats.com/)
* [Datacamp](http://datacamp.com/)
-->
**Schedule**
| | **Lecture** | **Lab** | **Lab Key** |
|-------------|----------------------------------------------|-----------------------|--------------------------------------|
| **Day 0** | | | |
| | [Setup][x1] ([PDF][x2]) | | |
| **Day 1** | | | |
| 8:00-8:50 | [Introduction][01] ([PDF][02]) | | |
| 8:50-9:05 | Break | | |
| 9:05-9:55 | [Data Input/Output Part 1][03] ([PDF][04]) | [lab][05] | [lab key][06] / [lab key output][07] |
| 9:55-10:10 | Break | | |
| 10:10-11:00 | [Data Input/Output Part 2][08] ([PDF][09]) | [lab][10] | [lab key][11] / [lab key output][12] |
| 11:00-11:30 | Break | | |
| 11:30-12:20 | [Reproducible Research][13] ([PDF][14]) | [lab][15] | [lab key][16] / [lab key output][17] |
| 12:20-12:35 | Break | | |
| 12:35-1:25 | [Data Subsetting Part 1][22] ([PDF][23]) | [lab][24] | [lab key][25] / [lab key output][26] |
| 1:25-1:40 | Break | | |
| 1:40-2:30 | [Missing Data][x5] ([PDF][x6]) | [lab][x7] | [lab key][x8]/[lab key output][x9] |
| **Day 2** | | | |
| 8:00-8:50 | [Data Subsetting Part 2][27] ([PDF][28]) | [lab][29] | [lab key][30] / [lab key output][31] |
| 8:50-9:05 | Break | | |
| 9:05-9:55 | [Data Summarization][32] ([PDF][33]) | [lab][34] | [lab key][35] / [lab key output][36] |
| 9:55-10:10 | Break | | |
| 10:10-11:00 | [Data Cleaning Part 1][37] ([PDF][38]) | [lab][39] | [lab key][40] / [lab key output][41]|
| 11:00-11:30 | Break | | |
| 11:30-12:20 | [Data Cleaning Part 2][x10] ([PDF][x11]) | [lab][x12] | [lab key][x13] / [lab key output][x14] |
| 12:20-12:35 | Break | | |
| 12:35-1:25 | [Data Reshaping][42] ([PDF][43]) | [lab][44] | [lab key][45] / [lab key output][46] |
| 1:25-1:40 | Break | | |
| 1:40-2:30 | [Data Merging and Joining][47] ([PDF][48]) | [lab][49] | [lab key][50] / [lab key output][51] |
| **Day 3** | | | |
| 8:00-8:50 | [Functionally Programming][57] ([PDF][58]) | [lab][59] | [lab key][60] / [lab key output][61] |
| 8:50-9:05 | Break | | |
| 9:05-9:55 | [Advanced Data Input/Output][52] ([PDF][53]) | [lab][54] | [lab key][55] / [lab key output][56] |
| 9:55-10:10 | Break | | |
| 10:10-11:00 | [GitHub Concepts][18] ([PDF][19]) | [lab][21] | |
| | [Wrap Up][64] ([PDF][65]) | | |
[x1]: lecture_notes/Setup.html
[x2]: lecture_notes/Setup.pdf
[01]: https://docs.google.com/presentation/d/1gy9KJt2FZv8p85rhFKFOlFXRr9v7rz0nMnrws8g5mdc/edit?usp=sharing
[02]: lecture_notes/sisbid_intro_2024.pdf
[03]: lecture_notes/Data_IO_Part1.html
[04]: lecture_notes/Data_IO_Part1.pdf
[05]: labs/data-io-lab-part1.Rmd
[06]: labs/data-io-lab-part1-key.Rmd
[07]: labs/data-io-lab-part1-key.html
[08]: lecture_notes/Data_IO_Part2.html
[09]: lecture_notes/Data_IO_Part2.pdf
[10]: labs/data-io-lab-part2.Rmd
[11]: labs/data-io-lab-part2-key.Rmd
[12]: labs/data-io-lab-part2-key.html
[13]: https://docs.google.com/presentation/d/19HPlH3jLCzdjZYWS1jpYB7IIlj-YCSGCq1E-FpGJzAw/edit?usp=sharing
[14]: lecture_notes/sisbid_rep_research_2024.pdf
[15]: labs/rmarkdown-lab.Rmd
[16]: labs/rmarkdown-lab-key.Rmd
[17]: labs/rmarkdown-lab-key.html
[18]: https://docs.google.com/presentation/d/1-mSv1WMFmlu_93-cMKKHqD1zi8Q6meLVUV7S_G0ZBTo/edit?usp=sharing
[19]: lecture_notes/sisbid_github_2024.pdf
[20]: https://lab.github.com/githubtraining/introduction-to-github
[21]: labs/github-lab.md
[x5]: lecture_notes/Data_Missing.html
[x6]: lecture_notes/Data_Missing.pdf
[x7]: labs/missing-data-lab.Rmd
[x8]: labs/missing-data-lab-key.Rmd
[x9]: labs/missing-data-lab-key.html
[x3]: lecture_notes/Updating_files_with_github.html
[x4]: lecture_notes/Updating_files_with_github.pdf
[22]: lecture_notes/Data_Subsetting_Part1.html
[23]: lecture_notes/Data_Subsetting_Part1.pdf
[24]: labs/data-subsetting-lab-part1.Rmd
[25]: labs/data-subsetting-lab-part1-key.Rmd
[26]: labs/data-subsetting-lab-part1-key.html
[27]: lecture_notes/Data_Subsetting_Part2.html
[28]: lecture_notes/Data_Subsetting_Part2.pdf
[29]: labs/data-subsetting-lab-part2.Rmd
[30]: labs/data-subsetting-lab-part2-key.Rmd
[31]: labs/data-subsetting-lab-part2-key.html
[32]: lecture_notes/Data_Summarization.html
[33]: lecture_notes/Data_Summarization.pdf
[34]: labs/data-summarization-lab.Rmd
[35]: labs/data-summarization-lab-key.Rmd
[36]: labs/data-summarization-lab-key.html
[37]: lecture_notes/Data_Cleaning.html
[38]: lecture_notes/Data_Cleaning.pdf
[39]: labs/data-cleaning-lab.Rmd
[40]: labs/data-cleaning-lab-key.Rmd
[41]: labs/data-cleaning-lab-key.html
[x10]:lecture_notes/Data_Cleaning_Part2.html
[x11]:lecture_notes/Data_Cleaning_Part2.pdf
[x12]:labs/data-cleaning-lab-part2.Rmd
[x13]:labs/data-cleaning-lab-part2-key.Rmd
[x14]:labs/data-cleaning-lab-part2-key.html
[42]: lecture_notes/Data_Reshaping.html
[43]: lecture_notes/Data_Reshaping.pdf
[44]: labs/data-reshaping-lab.Rmd
[45]: labs/data-reshaping-lab-key.Rmd
[46]: labs/data-reshaping-lab-key.html
[47]: lecture_notes/Merging_Join.html
[48]: lecture_notes/Merging_Join.pdf
[49]: labs/merging-lab.Rmd
[50]: labs/merging-lab-key.Rmd
[51]: labs/merging-lab-key.html
[52]: lecture_notes/Advanced_Data_IO.html
[53]: lecture_notes/Advanced_Data_IO.pdf
[54]: labs/advanced-io-lab.Rmd
[55]: labs/advanced-io-lab-key.Rmd
[56]: labs/advanced-io-lab-key.html
[57]: lecture_notes/Functional_Programming.html
[58]: lecture_notes/Functional_Programming.pdf
[59]: labs/functional-program-lab.Rmd
[60]: labs/functional-program-lab-key.Rmd
[61]: labs/functional-program-lab-key.html
[62]: lecture_notes/Bioconductor_intro.html
[63]: lecture_notes/Bioconductor_intro.pdf
[64]: https://docs.google.com/presentation/d/1Q8CnyHd3YJMUxoRNk5611GmPN-cBks5TfWoDMWZT6Eg/edit?usp=sharing
[65]: lecture_notes/sisbid_wrap_up_2024.pdf
**Miscellaneous**
Feel free to submit typos/errors/etc via the github repository associated with the class:
https://github.com/SISBID/Data-Wrangling
```{r, eval = FALSE, echo = FALSE}
## Render this file:
rmarkdown::render('index.Rmd')
```
This page was last updated on `r Sys.time()` Eastern Time.