class: center, middle, inverse, title-slide # Practical R: About the class ### Abhijit Dasgupta ### BIOF 339 --- layout: true <div class="my-header"> <span>BIOF339</span></div> </div> --- class: middle, center, inverse name: about # About this class --- ## Learning Objectives - Run R and RStudio, making use of inherent R features - Find and make use of the extensive packages (R add-ons) available for analyzing biological and other forms of data - Load, manipulate, and combine data to make it amenable to further analyses - Visualize data with extensive graphics capabilities of R (including ggplot) - Use R to run statistical models and hypothesis tests and report results conforming to standards expected in scientific journals - Write reports using the powerful `rmarkdown` package and its derivatives --- # Plan <table> <thead> <tr> <th style="text-align:left;"> Week </th> <th style="text-align:left;"> Topic </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> Week 1 </td> <td style="text-align:left;"> Introduction to R: Working environmnent and data structures </td> </tr> <tr> <td style="text-align:left;"> Week 2 </td> <td style="text-align:left;"> Using packages to enhance data ingestion, munging, and reporting </td> </tr> <tr> <td style="text-align:left;"> Week 3 </td> <td style="text-align:left;"> Data visualization for exploration and reporting </td> </tr> <tr> <td style="text-align:left;"> Week 4 </td> <td style="text-align:left;"> Statistical analyses using R </td> </tr> <tr> <td style="text-align:left;"> Week 5 </td> <td style="text-align:left;"> Statistical learning using R </td> </tr> <tr> <td style="text-align:left;"> Week 6 </td> <td style="text-align:left;"> Designing and analyzing experiments, with a sprinkling of bioinformatics </td> </tr> <tr> <td style="text-align:left;"> Week 7 </td> <td style="text-align:left;"> Reproducible documents for analytic reporting </td> </tr> </tbody> </table> --- ## Teaching materials 1. The main ideas for the week will be developed through videos, screencasts and slides 1. I will assign tutorials where you can interactively work with R to improve your understanding + [RStudio Primers](https://rstudio.cloud/learn/primers) + I will create and periodically update a R package of R tutorials, that will be called `BIOF339Tutorials`. Instructions are forthcoming --- # Grading rubric 1. Homeworks for each week are due Sunday at 11:59pm (50%) - No late homeworks - We'll have 6 homeworks, I'll score the top 4 for grade 1. Final project: A RMarkdown report/presentation demonstrating an end-to-end data analysis in R using your own data, from data ingestion to munging to analyses and graphics, with a brief introduction and conclusion (30%) 1. Class participation (20%): Discussion topics each week --- # Submitting assignments ## Homework + All homework will be submitted via Canvas + You must submit your homework using R Markdown - The submission will consist of 2 files: A Rmd file and the corresponding HTML file. Both are required for full credit. + I will initially provide templates for the homework, but you will be expected to create your own R Markdown documents by week 4. --- # Communication - Primarily via <svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M94.12 315.1c0 25.9-21.16 47.06-47.06 47.06S0 341 0 315.1c0-25.9 21.16-47.06 47.06-47.06h47.06v47.06zm23.72 0c0-25.9 21.16-47.06 47.06-47.06s47.06 21.16 47.06 47.06v117.84c0 25.9-21.16 47.06-47.06 47.06s-47.06-21.16-47.06-47.06V315.1zm47.06-188.98c-25.9 0-47.06-21.16-47.06-47.06S139 32 164.9 32s47.06 21.16 47.06 47.06v47.06H164.9zm0 23.72c25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06H47.06C21.16 243.96 0 222.8 0 196.9s21.16-47.06 47.06-47.06H164.9zm188.98 47.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06h-47.06V196.9zm-23.72 0c0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06V79.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06V196.9zM283.1 385.88c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06v-47.06h47.06zm0-23.72c-25.9 0-47.06-21.16-47.06-47.06 0-25.9 21.16-47.06 47.06-47.06h117.84c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06H283.1z"></path></svg> [Slack](http://www.slack.com). - Please join the BIOF339 Slack channel using [this link](https://join.slack.com/t/biof339/shared_invite/zt-hczp2mg1-Yh0yqms52wAA8H445jkBUg). - You will see a channel `#fall2020-a`. Please join this channel - Slack for broadcasting messages, answering questions and the like. - If you have a question, you can directly message me on Slack. Expect an answer within 24 hours. - Office hours by appointment --- # Class project - Create a R Markdown document or presentation - Use your own data, or data available on the web (legally) - Show me that you can - import data into R - manipulate (munge) the data - perform some analysis on the data - create a visualization - create a report in R Markdown - 5 minute _lightning talks_ that can be recorded using Quicktime or [Screencastify](https://www.screencastify.com/)