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index.Rmd
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---
title: "Intro R with swirl "
date: "`r format(Sys.time(), '%B %d, %Y')`"
site: bookdown::bookdown_site
documentclass: book
bibliography: book.bib
biblio-style: apalike
link-citations: yes
description: "This book provides a lab exercise that introduces students to the basics of R programming."
favicon: assets/GDSCN_style/gdscn_favicon.ico
---
# About {-}
In this exercise, students are introduced to the basics of R using the `swirl` package (https://swirlstats.com), which teaches students R from within the R console. The primary goal of this exercise is to get students comfortable interacting with the R console.
```{r, echo=FALSE, fig.alt="swirl logo"}
knitr::include_graphics("assets/swirl_logo.png")
```
## Skills Level {-}
::: {.notice}
_Genetics_
**Novice**: no genetics knowledge needed
_Programming skills_
**Novice**: no programming experience needed
:::
## Format {-}
<!--
Class Type should be one of the following (from CourseSource):
- Lecture
- Lab
- Seminar
- Discussion Section
- On-line
- Other
-->
<!--
Lesson Length should be one of the following (from CourseSource):
- Portion of one class period
- One class period
- Multiple class periods
- One term (semester or quarter)
- One year
- Other
You can then provide addtional details; e.g.
- **Lesson Length:** One class period (2-3 hr lab)
- 40 min setup and introduction (for shorter lab periods, these can be done ahead of time)
- 2 hr core lab exercises
- Optional 20 min "challenge" exercise
-->
- **Class Type:** Lab (computer based)
- **Lesson Length:** One class period (2-3 hr lab)
- 40 min setup and introduction (for shorter lab periods, these can be done ahead of time)
- 2 hr core lab exercises
- Optional 20 min "challenge" exercise
## Learning Objectives {-}
- Open RStudio and locate important panels (R console, Help)
- Run commands in the R console
- Explain what vectors and dataframes are in R
- Use common R commands to work with R objects (e.g. assign, print, subset, math operations)
- Explore a dataset using base R commands (e.g. `dim`, `summary`, `str`)
## Core Competencies {-}
This activity addresses the following core concepts and competencies:
```{r, echo=FALSE}
competencies <- tibble::tribble(
~source, ~competencies,
"**Vision and Change**", paste(
#"Concepts\n",
# "- **1**: EVOLUTION: The diversity of life evolved over time by processes of mutation, selection, and genetic change",
# "- **2**: STRUCTURE AND FUNCTION: Basic units of structure define the function of all living things",
# "- **3**: INFORMATION FLOW, EXCHANGE, AND STORAGE: The growth and behavior of organisms are activated through the expression of genetic information in context",
# "- **4**: PATHWAYS AND TRANSFORMATIONS OF ENERGY AND MATTER: Biological systems grow and change by processes based upon chemical transformation pathways and are governed by the laws of thermodynamics",
# "- **5**: SYSTEMS: Living systems are interconnected and interacting.",
"Competencies\n",
# "- **1**: Ability to apply the process of science",
"- **2**: Ability to use quantitative reasoning",
# "- **3**: Ability to use modeling and simulation",
"- **4**: Ability to tap into the interdisciplinary nature of science",
# "- **5**: Ability to communicate and collaborate with other disciplines",
# "- **6**: Ability to understand the relationship between science and society",
sep="\n"),
# "**Genetics**", paste(
# "Concepts\n",
# "- How is DNA organized?",
# "- What are the molecular components and mechanisms necessary to preserve and duplicate an organism’s genome?",
# "- What are the mechanisms by which an organism’s genome is passed on to the next generation?",
# "- How can one deduce information about genes, alleles, and gene functions from analysis of genetic crosses and patterns of inheritance?",
# "- How does the phenomenon of linkage affect the assortment of alleles during meiosis?",
# "- How is genetic information expressed so it affects an organism’s structure and function?",
# "- How can gene activity be altered in the absence of DNA changes?",
# "- How do genes and genomes control changes in an organism’s structure and function throughout its life cycle?",
# "- How do different types of mutations affect genes and the corresponding mRNAs and proteins?",
# "- What are the processes that can affect the frequency of genotypes and phenotypes in a population over time?",
# "- How do the results of molecular genetic studies in model organisms help us understand aspects of human genetics and genetic diseases?",
# "- What experimental methods are commonly used to analyze gene structure, gene expression, gene function, and genetic variants?",
# "Competencies\n",
# "- Locate, read, and comprehend primary literature research papers on genetics topics",
# "- Implement observational strategies to formulate a question",
# "- Generate testable hypotheses",
# "- Design an experiment using appropriate controls and appropriate sample sizes",
# "- Gather and evaluate experimental evidence, including qualitative and quantitative data",
# "- Apply statistical methods when analyzing their data, and use patterns to construct a model",
# "- Generate and interpret graphs displaying experimental results",
# "- Critique large data sets and use bioinformatics to assess genetics data",
# "- Communicate experimental results effectively, including writing research papers and giving presentations",
# "- Effectively explain genetics concepts to different audiences",
# "- Tap into the interdisciplinary nature of science",
# "- Identify and critique scientific issues relating to society or ethics",
# sep="\n"),
"**Bioinformatics**", paste(
# "- **C1**: Explain the role of computation and data mining in addressing hypothesis-driven and hypothesis-generating questions within the life sciences",
# "- **C2**: Summarize key computational concepts, such as algorithms and relational databases, and their applications in the life sciences",
# "- **C3**: Apply statistical concepts used in bioinformatics",
# "- **C4**: Use bioinformatics tools to examine complex biological problems in evolution, information flow, and other important areas of biology",
# "- **C5**: Find, retrieve, and organize various types of biological data",
# "- **C6**: Explore and/or model biological interactions, networks and data integration using bioinformatics",
"- **C7**: Use command-line bioinformatics tools and write simple computer scripts",
# "- **C8**: Describe and manage biological data types, structure, and reproducibility",
# "- **C9**: Interpret the ethical, legal, medical, and social implications of biological data",
sep="\n")
)
knitr::kable(competencies, col.names = NULL, format = "html")
```
Core concepts and competencies are taken from the following sources:
- [Vision and Change in Undergraduate Biology Education](https://visionandchange.org/) AAAS report
- [Genetics Core Competencies](https://genetics-gsa.org/education/genetics-learning-framework/) by [GSA](https://genetics-gsa.org/)
- [Bioinformatics core competencies for undergraduate life sciences education](https://doi.org/10.1371/journal.pone.0196878) by [NIBLSE](https://qubeshub.org/community/groups/niblse)
## GDSCN Collection {-}
This exercise is part of a collection of teaching resources developed through the *Genomic Data Science Community Network* (GDSCN). GDSCN works towards a vision where researchers, educators, and students from diverse backgrounds are able to fully participate in genomic data science research. Learn more about GDSCN by visiting https://www.gdscn.org/home or reading the [article in Genome Research](https://doi.org/10.1101/gr.276496.121).