Data Carpentry for Biologists

Teaching the tools to get computers to do cool science

Creative Commons License

Exercises

SQL | R | Python | Access

SQL

Topic Title Output
Advanced Queries Aggregated Join [txt]
Advanced Queries Basic Join [txt]
Advanced Queries Detailed Join [txt]
Advanced Queries Filtered Join [txt]
Advanced Queries Multi-table Join [txt]
Advanced Queries Nesting Queries [txt]
Aggregation COUNT [txt]
Aggregation SUM [txt]
Basic Queries DISTINCT [txt]
Basic Queries GROUP BY [txt]
Basic Queries ORDER BY [txt]
Basic Queries SELECT [txt] [txt]
Basic Queries Simple WHERE [txt]
Basic Queries WHERE [txt] [txt] [txt]
Database Control Adding Records [txt]
Database Control Creating Tables [txt]
Database Control Importing Data [txt] [txt] [txt]
Database Control Missing Data [txt]
Database Control Updating Records [txt]
Database Structure Redundancy [txt] [txt] [txt]
Database Structure Split Cells [txt] [txt]
dplyr Databases Copy to Database [txt]
dplyr Link to Databases [txt]
QAQC Data entry validation in Excel
Tidy Data Improving Messy Data

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R

Topic Title Output
Basic Data Management Review [txt] [txt]
Basic Vector Review [txt]
Capstone Cocili Data Exploration [png] [png]
Capstone Length of Floods [txt]
Combining Basics Shrub Volume Carbon [txt]
Data Analysis Code Shuffle [jpeg]
Data Frames Database CSV [txt]
Data Frames Shrub Volume Data Frame [txt]
Debugging Debug the Code [txt]
dplyr Collect from Databases [txt]
dplyr Databases Copy to Database [txt] [txt]
dplyr Databases Link and Query
dplyr Databases Manipulate Query [txt]
dplyr Databases NEON Mammals [jpeg] [txt] [jpeg] [jpeg]
dplyr Databases Source and Query [txt]
dplyr Fix the Code [txt]
dplyr Link to Databases [txt] [txt]
dplyr Shrub Volume Aggregation [txt]
dplyr Shrub Volume Data Basics [txt]
dplyr Shrub Volume Join [txt]
Expressions & Variables Basic Expressions [txt]
Expressions & Variables Basic Variables [txt]
Expressions & Variables Modify the Code [txt]
Expressions & Variables More Variables [txt]
Expressions & Variables Variable Reassignment [txt]
Functions Built-in Functions [txt]
Functions Combining Functions [txt]
Functions Default Arguments [txt]
Functions for Loop [txt] [txt]
Functions String Data [txt]
Functions Use and Modify [txt]
Functions Writing Functions [txt]
Good Style Format the Code [jpeg]
Graphing Acacia and Ants [jpeg] [jpeg] [jpeg] [jpeg]
Graphing Acacia and Ants Data Manipulation [txt] [jpeg] [jpeg] [txt] [jpeg]
Graphing Acacia and Ants Histograms [jpeg] [jpeg] [jpeg] [jpeg]
Graphing Adult vs Newborn Size [jpeg] [jpeg] [jpeg] [jpeg] [jpeg]
Graphing Mammal Body Size Distribution [jpeg] [jpeg] [jpeg] [jpeg] [jpeg]
Graphing Mass vs Metabolism [jpeg] [jpeg] [jpeg] [jpeg]
Graphing Sexual Dimorphism Data Manipulation [jpeg] [jpeg] [jpeg] [jpeg]
Graphing Sexual Dimorphism Exploration [jpeg] [jpeg] [jpeg] [jpeg] [jpeg]
Higher Order Functions Species Area Relationship [txt]
Knitr Reproducible Breeding Bird Survey Analysis [html]
Loops Basic For Loops [txt]
Loops Basic Index [txt]
Loops Basic Vector [txt]
Loops Crown Volume Calculation [txt] [txt] [png]
Loops Improve Your Code [txt]
Loops Multi-file Analysis [png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [txt]
Loops Multiple Files [txt]
Loops Size Estimates By Name Apply [txt] [png]
Loops Size Estimates By Name Loop [txt]
Loops Size Estimates Vectorized [txt]
Loops Species Name Capitalization with Apply [txt]
Loops stringr [txt]
Loops Use and Modify with Apply [txt] [txt]
Loops Use and Modify with Loops [txt] [txt] [txt]
Loops Vectorized Genus Extraction [txt]
Making Choices Basic If Statements [txt]
Making Choices Choice Operators [txt]
Making Choices Choices with Functions [txt]
Making Choices Complete the Code [txt]
Making Choices DNA or RNA [txt]
Making Choices DNA or RNA Iteration [txt]
Making Choices Load or Download File [txt]
Making Choices Simple If Statement [txt]
Making Choices Size Estimates by Name [txt]
Making Choices Unit Conversion Challenge [txt]
Modules dplyr
NEON Canopy Height from Space [png] [png] [png] [txt]
NEON NEON Database [jpeg] [jpeg] [jpeg]
NEON NEON Raster [jpeg]
NEON Phenology from Space [png] [txt]
dplyr Portal Data Joins [txt]
dplyr Portal Data Manipulation [txt]
dplyr Portal Data Manipulation Pipes [txt]
Putting It All Together Size-biased Extinction [txt] [txt] [png]
R-SQL Automate Query [txt]
R-SQL Connect and Query [txt]
R-SQL Data Stream [txt]
R-SQL Export to Database [txt]
Regular Expressions Find the Rodents [txt]
Loops Climate Space Iteration [png] [png] [png] [png] [png] [png] [png]
Reproduction Climate Space Rewrite [png] [png] [png]
Reproduction Climate Space [png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [png] [png]
Reproduction Dinosaur Size Distribution [png]
Reproduction Megafaunal Extinction [txt] [png] [png] [png]
Scientific Mammal Body Size [txt]
Scientific Mammal Body Size by Continent [txt]
Scientific Tree Biomass Challenge [txt] [jpg]
Spatial Data Species Occurrences Elevation Histogram [png] [png] [png]
Spatial Data Species Occurrences Map [txt] [png]
SQL Practice Basic Queries Review [txt] [txt] [txt]
Statistics Adult vs Newborn Size Regression [txt] [jpeg] [jpeg]
Statistics Mammal Body Size T-test [txt]
Statistics Shrub Volume ANOVA [txt]
Strings Function with Choices [txt]
Strings Long Strings [txt]
Strings Print Strings [txt]
Strings Split Strings [txt]
Strings stringr Functions [txt]
Strings Strings and Math [txt]
Strings Strings from Data [txt]
Tests Test the Code [txt]
Tidyr Tree Biomass [txt]
Vectors Bird Banding [txt]
Vectors Shrub Volume Vectors [txt]
Version Control Add and Revert Comment
Version Control Basic Adding a Remote
Version Control Basic Commit Multiple Files
Version Control Basic Create Project Repository
Version Control Basic First Solo Commit
Version Control Basic Project Proposal
Version Control Basic Pulling and Pushing
Version Control Basic Pushing Changes
Version Control Basic Second Solo Commit
Version Control Basic Set Up Git
Version Control Fix and Commit
Version Control Git Setup
Version Control Merge Conflict
Version Control Pull and Move
Version Control Revert

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Python

Python exercises were used in previous iterations of the course at Utah State University, but are no longer under active development.

Topic Title Output
Basic Data Management Review
Basic List Review
Combining Basics Shrub Volume [txt]
Data Analysis Code Shuffle
Debugging Fix the Code 1
Dictionaries Species Composition 2
Expressions & Variables Basic Expressions [txt]
Expressions & Variables Basic Variables [txt]
Expressions & Variables Modify the Code 1 [txt]
Expressions & Variables More Variables [txt]
Expressions & Variables Variable Reassignment
For Loops Exponential Growth 1
For Loops Repeat Strings
For Loops While
Functions Built-in Functions [txt]