George G. Vega Yon
University of Southern California
Department of Preventive Medicine
USC Integrative Methods of Analysis for Genomic Epidemiology (IMAGE)
Department of Preventive Medicine
July 7th, 2018
Part 1: Talk about the basics: What is R? How to get help!?
Part 2: R language fundamentals.
Part 3: An extended example using HPCC
We will be using:
R (of course), and you can get it from https://cloud.r-project.org/
RStudio (highly recommended), an IDE for R, and you can get if from https://www.rstudio.com/products/rstudio/
Materials for this presentation (including the presentation itself) can be downloaded from https://github.com/USCbiostats/intro2r-hcp-edition
Free software oriented for statistical computing and graphics (although people use for everything now a days)
Is maintain mostly by the R Core Team (about 20 members worldwide), with the support of The R Foundation
Has a thriving community of users and developers worldwide:
Institutional support from: rOpenSci, R Consortium, etc.
About 13,000 packages(libraries) on CRAN (The Comprehensive R Archive Network)
More than 1,000 attendees in useR!2017 conference
R (R Core Team 2018) is an implementation of the S (Statistics) programming language, which was created in 1976 by John Chambers while at Bell Labs.
R itself was created by Ross Ihaka and Robert Gentleman at the University of Auckland, New Zealand. First release in 1995.
Currently developed by the R Development Core Team, of which Chambers is a member.
(Source wiki)
In R, if you want to:
Know about the sqrt
function? ?sqrt
, or help("sqrt")
Know about the makeCluster
function in the R package parallel
? ?parallel::makeCluster
, or help("makeCluster", package="parallel")
Know about the Regular Expressions? ??"Regular Expressions"
, or help.search("Regular Expressions")
See a full list of the functions and help files available in the package boot
: help(package="boot")
.
Look at more in deph information about the Matrix package? vignette(package="Matrix")
Checkout the CRAN Task Views
Take a look at the rstats tag on StackOverflow.com
Visit the r-bloggers.com website
Read one of the dozens of online free books about R created with the R package bookdown at bookdown.org
Ask a question on twitter using the #rstats hashtag.
The art of R programming https://nostarch.com/artofr.htm (Matloff 2011)
Advanced R http://adv-r.had.co.nz/ (Wickham 2015)
R Programming for Data Science https://bookdown.org/rdpeng/rprogdatascience/ (Peng 2012)
R for Data Science http://r4ds.had.co.nz/ (Wickham and Grolemund 2016)
Scientific Programming and Simulation using R (Jones, Maillardet, and Robinson 2009)
Using the stats
package, How can you estimate a generalized linear model in R?
What is the command to transpose a matrix in R? What about the command for inverting a matrix?
Looking at CRAN task Views, what R packages are available for convex optimization? What about stochastic optimization?
Create a list of R packages that provide wrappers for working with Slurm.
What does return the function for fitting nonlinear least squares in the stats
package?