Introduction to RStudio

Biochemistry laboratories - 201

Jean-Yves Sgro [email protected]

Find this document here (short URL) today: http://go.wisc.edu/aq1x6l


*Note*: To see as slides click on **"Gift icon"** at the top right. To revert back to page view click on **"book icon"** when on the first slide.

Set-up

  • check your name on the attendees list
  • choose an iMac
  • login with your UW NetID with @wisc.edu
  • If this is the first time this Mac "sees" you it will go through a quick set-up: simply skip using "Apple ID"

Finding RStudio on the iMac

  • Click on the "Finder" at the bottom right of the "Dock" on the bottom of the screen.
  • This will open a new window.
  • On the left click on "Applications"
  • In the alphabetical list choose "RStudio" or "RSudio.app" with a icon that looks like: RStudio icon
  • double click to open the RStudio program

RStudio Exercise Files Summary list

Hand-outs are in HTML format:

The "Freddie" reports are in HTML or "Rmd" (text) formats:

Get RStudio:

If you need to install RStudio follow this link:

Today - Part I

Using_RStudio_I.html

  • RStudio 4 quadrants interface
  • RScripts
  • Table output formats
  • Create graphics and plots

Today - Part II

Using_RStudio_II.html (UPDATED Oct18, 2018)

  • Creating a Project
  • Learn some markdown syntax
  • Add R Markdown syntax: Dynamic documents

Today - Part III

Using_RStudio_III.html

  • Dynamic reporting with simple enzymology data
  • Michaelis-Menten equation: solve Km and Vmax
  • Nonlinear least square

The Michaelis-Menten equation can be written as a function of $S$ with constant parameters to be evaluated:

$$f(S, (K, V_m)) = \frac{V_m S}{K_m+S}$$

Help Freddie!

Help Freddie create an dynamic report with the enzymology data. "Freddie" report are in HTML or "Rmd" (text) formats:

Class evaluation

After class:

  • fill-in the one page "evaluation" form for this class

The evaluation is anonymous. Evaluation link on Qualtrics or type: the short URL: http://go.wisc.edu/p1t5g3

(Note: Survey will be unlocked when workshop occurs. )