(R-Data Analysis & Visualization In Science)

Course Description

Computer literacy is now essential in all aspects of science. Data management skills are needed for entering data without errors, storing it in a usable way, and extracting key aspects of the data for analysis. Basic programming is required for everything from accessing and managing data, data visualization, to statistical analysis, and modeling. This course will provide an introduction to data/project management, manipulation, visualization and analysis, across a broad set of ecological data (spatial, genomic, field, etc). Class will typically consist of short introductions or question & answer sessions, followed by hands on computing exercises. The course will be taught using git/Github, R/RStudio, RMarkdown, and SQLite, but the concepts learned will easily apply to all programming languages and database management systems. No background in databases or R/computational experience is required.

Prerequisite Knowledge and Skills

A willingess to practice coding and embrace the R language.

Purpose of Course

In this course you will learn all of the fundamental aspects of computer programming that are necessary for conducting ecological research. By the end of the course you will be able to use these tools to import data into R, wrangle various types of data, summarize and analyze data, create visualizations and maps, write reports/manuscripts/CV’s in RMarkdown, save and export data/figures, work with SQL databases, as well as collaborate on Github with version-controlled projects.

The focus of this course is to provide graduate students with training that develops and teaches the tools applicable to the entire process of reproducible data-driven research and encourage the use of open-source tools. By learning how to get the computer to do your work for you, you will be able to do more science faster, and your future-self will thank you.

Course Objectives

Students completing this course should be able to:

  • Read, Import/Export data
  • Tidy/summarize and analyze data
  • Write simple functions/programs in R
  • Automate data analysis
  • Scrape websites for data
  • Map/manipulate spatial (raster/vector) data
  • Learn how to apply these tools to address scientific research questions

Code of Conduct

We are dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. However, we recognise that some groups in our community are subject to historical and ongoing discrimination, and may be vulnerable or disadvantaged. Membership in such a specific group can be on the basis of characteristics such as gender, sexual orientation, disability, physical appearance, body size, race, nationality, sex, colour, ethnic or social origin, pregnancy, citizenship, familial status, veteran status, genetic information, religion or belief, political or any other opinion, membership of a national minority, property, birth, age, or choice of text editor. We do not tolerate harassment of participants on the basis of these categories, or for any other reason.

Harassment is any form of behaviour intended to exclude, intimidate, or cause discomfort. Because we are a diverse community, we may have different ways of communicating and of understanding the intent behind actions. Therefore we have chosen to prohibit certain forms of behaviour in our community, regardless of intent. Prohibited harassing behaviour includes but is not limited to:

  • written or verbal comments which have the effect of excluding people on the basis of membership of a specific group listed above
  • causing someone to fear for their safety, such as through stalking, following, or intimidation the display of sexual or violent images
  • unwelcome sexual attention
  • nonconsensual or unwelcome physical contact
  • sustained disruption of talks, events or communications
  • incitement to violence, suicide, or self-harm
  • continuing to initiate interaction (including photography or recording) with someone after being asked to stop
  • publication of private communication without consent

Behaviour not explicitly mentioned above may still constitute harassment. The list above should not be taken as exhaustive but rather as a guide to make it easier to enrich all of us and the communities in which we participate. All Carpentry interactions should be professional regardless of location: harassment is prohibited whether it occurs on- or offline, and the same standards apply to both.

Enforcement of the Code of Conduct will be respectful and not include any harassing behaviors.

Thank you for helping make this a welcoming, friendly community for all.

This code of conduct is an adaptation of the one used by the Software Carpentry Foundation and is a modified version of that used by PyCon, which in turn is forked from a template written by the Ada Initiative and hosted on the Geek Feminism Wiki. Contributors to this document: Adam Obeng, Aleksandra Pawlik, Bill Mills, Carol Willing, Erin Becker, Hilmar Lapp, Kara Woo, Karin Lagesen, Pauline Barmby, Sheila Miguez, Simon Waldman, Tracy Teal.

For more information about the Code of Conduct related to Data Carpentry, please see their website.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please see the UC Davis ombuds office.

Territory Acknowledgement

Acknowledging territory shows recognition of and respect for Native Americans. It is recognition of their presence both in the past and the present. Recognition and respect are essential elements of establishing healthy, reciprocal relations. These relationships are key to reconciliation, a process to which we are committed.

We would like to respectfully acknowledge that the land on which we gather is traditional unceded Patwin territory. We recognize and respect our role as guests here.

This territory acknowledgement is an adaptation of one written by the Canadian Association of University Teachers. For more information, please see their website.