Data Cleaning and Assessment - Part I

Reviewing the dataset - for Homework 01

In today’s class we’ll get started exploring and finding the issues and problems with the dataset you’ll be working with for Homework 01. All of the files are uploaded into this Github repository https://github.com/melindahiggins2000/N736Homework01. Feel free to download the files (as a ZIP), or fork the repository to work with in your own Github repo.

Exploring this test dataset

During class we identified a number of issues and put them up on the whiteboard. Here is a screenshot of the issues we found:

https://raw.githubusercontent.com/melindahiggins2000/N736Homework01/master/screenshot_20170830_150136.jpg

Class discussion and video

The discussion and video of my lecture on 08/30/2017 is now posted on Echo360 available through canvas and at this link: https://echo360.org/lesson/2ca62f2a-5cad-41b9-b111-596d4e5e55b4/classroom#sortDirection=desc You will need to login “via institution” - choose Emory and use your Emory login credentials to see the video.

Weblinks discussed in the video and during class:

• Journal of Biostatistics - author guidelines for “Reproducible Research” https://academic.oup.com/biostatistics/pages/General_Instructions.

• Gitbook https://www.gitbook.com/.

• Bookdown https://bookdown.org.

• Yihui Xie’s book on the bookdown package https://bookdown.org/yihui/bookdown/.

• Github repo for Yihui Xie’s “Dynamic Documents with R and knitr” - 1st 3 chapters available online https://github.com/yihui/knitr-book.

• Garrett Grolemund and Hadley Wickham’s book “R for Data Science” - also online at http://r4ds.had.co.nz/ & if you’re interested, here is the Github repo for their book https://github.com/hadley/r4ds.

• Tidyverse https://www.tidyverse.org/.

• Washington Post Article on “An Alarming Number of Scientific Papers Contain Excel Errors” https://www.washingtonpost.com/news/wonk/wp/2016/08/26/an-alarming-number-of-scientific-papers-contain-excel-errors/?utm_term=.8ec47ce8bc16.

• Genome Biology 2016 Paper on “Gene name error are widespread in the scientific literature” https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7.

• “The Excel Error heard Around the World” https://newrepublic.com/article/112951/rogoff-reinhart-and-world-excel-error-research & more at http://nymag.com/daily/intelligencer/2013/04/grad-student-who-shook-global-austerity-movement.html.

• “How Bright Promise in Cancer Testing Fell Apart” - Duke cancer trials controversy http://www.nytimes.com/2011/07/08/health/research/08genes.html?mcubz=1 & “An array of errors” http://www.economist.com/node/21528593.

• “A Manifesto for Reproducible Science” https://www.nature.com/articles/s41562-016-0021.

• Center for Open Science https://cos.io/ & COS History https://cos.io/about/brief-history-cos-2013-2017/.

• Science “One in Five Genetics Papers Contains Errors Thanks to Microsoft Excel” http://www.sciencemag.org/news/sifter/one-five-genetics-papers-contains-errors-thanks-microsoft-excel.