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Introduction to the Workshop
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We follow The Carpentries Code of Conduct.
Our goal is to generate a shareable and reproducible report by the end of the workshop.
This lesson content is targeted to absolute beginners with no coding experience.
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R for Plotting
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R is a free programming language used by many for reproducible data analysis.
Use read_csv to read tabular data in R.
Geometries are the visual elements drawn on data visualizations (lines, points, etc.), and aesthetics are the visual properties of those geometries (color, position, etc.).
Use ggplot() and geoms to create data visualizations, and save them using ggsave().
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The Unix Shell
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A shell is a program whose primary purpose is to read commands and run other programs.
Tab completion can help you save a lot of time and frustration.
The shell’s main advantages are its support for automating repetitive tasks and its capacity to access network machines.
Information is stored in files, which are stored in directories (folders).
Directories nested in other directories for a directory tree.
cd [path] changes the current working directory.
ls [path] prints a listing of a specific file or directory.
ls lists the current working directory.
pwd prints the user’s current working directory.
/ is the root directory of the whole file system.
A relative path specifies a location starting from the current location.
An absolute path specifies a location from the root of the file system.
Directory names in a path are separated with / on Unix, but \ on Windows.
.. means ‘the directory above the current one’; . on its own means ‘the current directory’.
cp [old] [new] copies a file.
mkdir [path] creates a new directory.
mv [old] [new] moves (renames) a file or directory.
rm [path] removes (deletes) a file.
* matches zero or more characters in a filename.
The shell does not have a trash bin — once something is deleted, it’s really gone.
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Intro to Git & GitHub
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R for Data Analysis
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Package loading is an important first step in preparing an R environment.
Data analsyis in R facilitates reproducible research.
There are many useful functions in the tidyverse packages that can aid in data analysis.
Assessing data source and structure is an important first step in analysis.
Preparing data for analysis can take significant effort and planning.
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Writing Reports with R Markdown
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R Markdown is an easy way to create a report that integrates text, code, and figures.
Options such as include and echo determine what parts of an R code chunk are included in the R Markdown report.
R Markdown can render HTML, PDF, and Microsoft Word outputs.
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Conclusion
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When it comes to trying to figure out how to code something, and debugging, Internet searching is your best friend.
There are several resources at the University of Michigan that you can take advantage of if you need help with your code.
We didn’t have time to cover all important coding concepts in this workshop, so definitely continue trying to learn more once you get comfortable with the material we covered.
There are often packages and tools that you can leverage to perform domain-specific analyses, so search for them!
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