Introduction

This page contains information and slides for many of the Happy Scientist seminar conducted in the department.

2020

Git & Github - What is it and why should I use it?

Abstract: The vast majority of this talk is based on the paper Excuse me, do you have a moment to talk about version control? and accompanied resources are HappyGitWithR.com and gitexplorer.com.

Date: January 23rd 2020

Speaker: Emil Hvitfeldt

Slides can be found here

2019

Research Pipelines

Abstract On this edition of the “Happy Scientist”, we will discuss about practices and tools that you may, and probably should, include in your research pipeline. The presentation will be mostly focused on summarizing and showing resources for the modern researcher, most of which have been developed in-house by our division.

Date: October 24th, 2019

Speaker: George G. Vega Yon

The slides can be view directly here

How R Markdown helped me thrive in scientific research 📚 and advance my career development 👔

Abstract Description: R has made it easy for us to wrangle data and build models. With the power of the R Markdown family packages, your analysis can be easily turned into high-quality reproducible documents including reports, presentations, posters, webpages, dashboards, scientific articles, websites and more. We will look at a couple of real-life case studies in which R Markdown helps a graduate student navigate scientific research and career development.

Date: October 17th, 2019

Speaker: Zhi Yang Twitter: zhiiiyang

The slides can be view directly here

The demos can be accessed here

HPC with Slurm, R and the slurmR package Contents

Abstract The Slurm job-scheduler (currently used by USC) provides a flexible infrastructure for all your computing needs. From submitting a single-core-long-running-job to complex multi-node-tasks, Slurm covers all scientists’ needs in terms of computational resources management. The R programming language, although not HPC-ready, has multiple community-based solutions to integrate your computational pipeline with HPC settings, including Slurm. In this workshop, we will illustrate how to use R with USC’s HPC cluster, covering from the very basics, like submitting a simple R script, to the more complex-powerful settings, like using multinode socket clusters using dozens or hundreds of cores in the same R session. The workshop will be led by USC’s Division of Biostatistics at the Keck School of Medicine.

Speaker George G. Vega Yon

Slides can be viewed here

Building an R package

Abstract: Building a R package can seem daunting with its many files and structure. This seminar will go through the different use cases for a R package, dos and don’ts and best practices. Finally a live demonstration starting with the creation of a R package ending with release on CRAN.

Date: March 28th 2019

Speaker: Emil Hvitfeldt

Slides can be found here

Additional resources

Usethis package
https://github.com/r-lib/usethis

Writing a R package slides
https://github.com/jalapic/RPackage/blob/master/Writing%20an%20R%20Package.pdf

Cran documentation
https://cran.r-project.org/doc/manuals/R-exts.html

Pick a license
https://blog.codinghorror.com/pick-a-license-any-license/
https://choosealicense.com/licenses/
https://tldrlegal.com/
https://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file

Build a Basic Package
http://rpubs.com/jennybc/build-a-basic-package

Deployment options
https://twitter.com/WeAreRLadies/status/1110694338068140032

R Packages
https://r-pkgs.org/

https://www.hvitfeldt.me/blog/usethis-workflow-for-package-development/

https://usethis.r-lib.org/

You can make a package in 20 minutes - Rstudio Conf Talk by Jim Hester
https://www.rstudio.com/resources/videos/you-can-make-a-package-in-20-minutes/

https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

https://cran.r-project.org/doc/manuals/r-release/R-exts.html

https://ropensci.github.io/dev_guide/

Debugging and Profiling in R

Abstract: Hitting an error or a speed-bump while working in R can be a frustration. This seminar will cover strategies and techniques for performing debugging and code profiling in R. We will look at some different ways to identify bugs, how to fix them and how to prevent them from coming back again. We will also look at a couple of typical patterns seen in slow code and at what can be done to fix it.

Date: February 19th 2019

Speaker: Emil Hvitfeldt

Slides can be found here

Additional resources

https://adv-r.hadley.nz/debugging.html

https://support.rstudio.com/hc/en-us/articles/205612627-Debugging-with-RStudio

https://CRAN.R-project.org/package=tictoc

https://CRAN.R-project.org/package=bench

Rstudio and R Resources

Abstract: Getting started working with R can be an overwhelming task with the vast amount of information available. This presentation will cover a wide array of things you can do in R and RStudio as well as where to find complementary information. We will go over how RStudio can enhance your workflow experience, using R Markdown to generate documents, shiny for interactive web applications and how we can extend to work with other programs/facilities for even greater applications.

Date: January 22th 2019

Speaker: Emil Hvitfeldt

Slides can be found here

Additional resources

Rstudio

RStudio IDE
https://www.rstudio.com/products/RStudio/

RStudio features
https://www.rstudio.com/products/rstudio/features/

Packages

CRAN homepage
https://cran.r-project.org/

Available CRAN Packages By Name
https://cran.r-project.org/web/packages/available_packages_by_name.html

CRAN Task Views
https://cran.r-project.org/web/views/

Bioconducter homepage
https://www.bioconductor.org/