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index.Rmd
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---
output:
html_document:
theme: cosmo
pdf_document: default
---
## SISBID: Module 1 Big Data Wrangling in R
**Instructors:** [Andrew Jaffe](http://www.aejaffe.com/) and [Jeff Leek](http://www.jtleek.com/)
**Teaching assitants:**
[Jeremy Roth](http://students.washington.edu/jhroth/)
**Class Schedule:**
* [Daily schedule](https://www.biostat.washington.edu/suminst/sisbid)
* Location: FSH 102 (the big auditorium in Fisheries Sciences) [maps](https://www.biostat.washington.edu/suminst/maps)
**Ressources:**
* [R project](http://www.r-project.org/)
* [Rstudio](http://www.rstudio.com/),
* [Bioconductor](http://bioconductor.org/)
* [Rstudio's cheatsheets](http://www.rstudio.com/resources/cheatsheets/)
* [Data Wrangling cheatsheet](https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf)
* [Data.table cheatsheet](https://s3.amazonaws.com/assets.datacamp.com/img/blog/data+table+cheat+sheet.pdf)
**Getting Started:**
Please read this to setup your installation of R, git, and install required R packages
https://github.com/SISBID/Module1/blob/gh-pages/getting_started.md
**Schedule**
| Day | Date | Session | Resources | Description |
|----|------------|--------------|---------------------|--------------------------------------|
| 0 | 2016-07-11 | Background | [Try R](http://tryr.codeschool.com/) | Really simple intro to R online |
| 0 | 2016-07-11 | Background | [swirl](http://swirlstats.com/) | More tutorials on R, in R |
| 0 | 2016-07-11 | Background | [Datacamp](http://datacamp.com/) | More tutorials on R, in the browser |
| 1 | 2016-07-11 | 8:30AM - 10:00AM |[Welcome and motivation](https://docs.google.com/presentation/d/1WeOfmSZTWUm74rA-jqV-gnoQcI1oJpe6ecntWPJ-iK8/edit), [PDF](lecture_notes/SISBID_Intro.pdf)|Why you're here|
| 1 | 2016-07-11 | 8:30AM - 10:00AM | [Who assessment](https://docs.google.com/spreadsheets/d/103vUoftv2dLNZ_FcAz08b5ptIkWN4W2RaFn7VF39FJ8/edit#gid=0) | How to see who we are|
| 1 | 2016-07-11 | 8:30AM - 10:00AM | [Skills assessment](https://docs.google.com/spreadsheets/d/18KQQd4LY5k8Ucux1MvWCsQGQJlvd0ECTnn-3ixdOKFM/edit?usp=sharing) [Skills Notebook](https://raw.githubusercontent.com/SISBID/Module1/gh-pages/labs/skills_notebook.Rmd) | How to see how good we are|
| 1 | 2016-07-11 | 8:30AM - 10:00AM |[Data brainstorming](https://docs.google.com/document/d/1yxcXeKAGhu1CyPatuBmgfRp4XbVJVEhc2Zp4Yl-Q9pk/edit?usp=sharing) | How to find data |
|1 | --- | 10:00AM - 10:30AM | Break | How to rest |
|1 | 2016-07-11 | 10:30AM - 12:00PM | [Rep. Research/Version Control](https://docs.google.com/presentation/d/1F2tyP9nsHcY9DT5B6rSS95sIA9DEreDNt7s_HmbrINw/edit?usp=sharing) | How to reproduce analysis |
|1 | 2016-07-11 | 10:30AM - 12:00PM | [Try Git](https://try.github.io/levels/1/challenges/1) | How to try git|
|1 | 2016-07-11 | 10:30AM - 12:00PM | [Install Git/Github](http://stat545.com/git00_index.html) | How to install git/github|
|1 | 2016-07-11 | 10:30AM - 12:00PM | [Github lab](https://github.com/SISBID/Module1/blob/gh-pages/labs/github-lab.md) | How to practice git/github|
|1 | --- | 12:00PM - 1:30PM | Lunch| How to eat |
|1 | 2016-07-11 | 1:30PM - 3:00PM | [Data I/O and Structure](lecture_notes/Data_IO_and_structure.html)|How R sees data|
|1 | --- | 3:00PM - 3:30PM | Break | How to break |
|1 | 2016-07-11 | 3:30PM - 5:00PM |[Subsetting](lecture_notes/Subsetting_Data_in_R.html), [Lab](labs/subsetting-data-lab.Rmd), [Key](labs/subsetting-data-lab-key.Rmd)|How to select data|
|2 | 2016-07-12 | 8:30AM - 10:00AM | [Advanced data IO](https://docs.google.com/presentation/d/1KNopKzl_cR9z9HQt_22RuvIQOsZe4pxM2G7spT_AVoc/edit?usp=sharing) | Different ways of accessing big data|
|2 | --- | 10:00AM - 10:30AM | Break | --- |
|2 | 2016-07-12 | 10:30AM - 12:PMAM | [Advanced data Lab](labs/web-api-lab.Rmd) | Different ways of accessing big data|
|2 | --- | 12:00PM - 1:30PM | Lunch| --- |
|2 | 2016-07-12 | 1:30PM - 3:00PM | [Cleaning data](lecture_notes/Data_Cleaning.html)|Cleaning Data|
|2 | --- | 3:00PM - 3:30PM | Break | Break |
|2 | 2016-07-12 | 3:30PM - 5:00PM |[Data Cleaning Lab](labs/data-cleaning-lab.Rmd), [Key](labs/data-cleaning-lab-key.Rmd)|Cleaning Data|
|3 | 2016-07-13 | 8:30AM-10:00AM | [Manipulation/Summarization](https://docs.google.com/presentation/d/15meI7W3MeF0afEV5ggdqXfwOIlwy5tcFYTJM-VUGHTs/edit?usp=sharing), [Reshaping](lecture_notes/Manipulating_Data_in_R.html)| |
|3 | --- | 10:00AM - 10:30AM | Break | --- |
|3 | 2016-07-13 | 10:30AM-12:00PM | [Databases/data.tables](https://docs.google.com/presentation/d/1Er4xRtvZA6iRuuCQcVK0H-WcxMe04IEZgNlWLQCOjGM/edit?usp=sharing), [Big Data "Tricks"](lecture_notes/Big_Data_Tricks.html), [Bioconductor/Genomics](https://docs.google.com/presentation/d/1N_98xkBZmPeeYdY5jRMFHNcIKMnUK_AXyiroGH6qhhg/edit?usp=sharing) | |
**Miscellaneous**
Feel free to submit typos/errors/etc via the github repository associated with the class:
https://github.com/SISBID/Module1
This web-page is modified from Andrew Jaffe's [Summer 2016 R course](http://www.aejaffe.com/summerR_2016/), which also has great material (some overlapping with ours).
```{r, eval = FALSE, echo = FALSE}
## Render this file:
rmarkdown::render('index.Rmd')
```
This page was last updated on `r Sys.time()` Eastern Time.