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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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Python for Plotting
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Python is a free general purpose programming language used by many for reproducible data analysis.
Use Python library pandas’ read_csv() function to read tabular data.
Use Python library seaborn to create and save data visualizations.
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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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Python for Data Analysis
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Library importing is an important first step in preparing a Python environment.
Data analysis in Python facilitates reproducible research.
There are many useful methods in the pandas library 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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Jupyter Notebook and Markdown
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Jupyter Notebook is an easy way to create a report that integrates text, code, and figures.
A Jupyter Notebook can be exported to HTML, PDF, and other formats.
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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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