Data Science in Omics Introduction

An OMICS Course Part 1: Shell, Organizing and Genomics

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Integrating R and SQL

Assignment

Learning Objectives

Following this assignment students should be able to:

  • connect to a remote database and execute simple queries
  • integrate database and R workflow
  • export output data from R to database
  • tidy data table with redundant fields or overfilled cells

Reading

Lecture Notes

Exercises

  1. Connect and Query

    This is a follow up to the Basic Queries filtering problem.

    It is clear Dr. Undómiel appreciates your skill working with large databases and she seems to expect you will maintain your benevolence. (Such is a fair expectation of a true wizard). This time though, she’s looking for some extra detail in her queries. She’s curious if desert rodents are dimorphic in size.

    1. Download a new copy of the Portal database.
    2. Connect to portal_mammals.sqlite using the RSQLite package.
    3. Start by reminding yourself about which tables are in the database using dbListTables()
    4. Then remind yourself of the fields in the surveys and plots tables using dbListFields().
    5. Select and print out the average hind foot length and average weight of:
      • all Dipodomys spectabilis individuals on the control plots
      • male D. spectabilis on the control plots
      • female D. spectabilis on the control plots
    [click here for output]

  2. Automate Query

    This is a follow-up to Connect and Query.

    Dr. Undómiel agrees with you that the difference in male and female D. spectabilis hind foot length and weight seems pretty small, but wants to have a reference point for comparison. She wants you to find the male and female hind foot length and weight for all species of rodent on all of the plots (not just the controls).

    Produce a data frame with species_id, sex, avg_hindfoot_length, and avg_weight for each species. Your data frame should have two rows for each species, one row for each sex.

    You can solve this problem in a variety of ways including using dplyr, a GROUP BY in your SQL query, a for loop, or using apply statements. Take whichever approach you like best.

    [click here for output]

  3. Export to Database

    Dr. Undómiel has decided to focus on the change in size of a few target rodent species over the course of the experiment(1977-2002). She has chosen , Dipodymys spectabilis, Onychomys torridus, Perymiscus erimicus, Chaetodipus penicillatus.

    Write a script that uses R and SQL to:

    1. Connect to the portal_mammals.sqlite.
    2. Generate a data frame with year, species_id, and the average weight per year (avg_weight) for each target species.
    3. Use dbWriteTable() to include your new data frame in the portal_mammals.sqlite. Call it something informative so that Dr. Undómiel can find it easily.
    [click here for output]

  4. NEON Database

    The National Ecological Observatory Network has entered into the construction phase of development and they are already making their data available! NEON collects ecological and environmental data for representative regions of the United States at local to continental scales, including, of course!, small mammal box trapping. We’ve retrieved NEON’s existing small mammal data from Ordway-Swisher Biological Station [NEON Data Use Policy].

    1. Create a SQLite database called ordway_mammals.sqlite.
    2. Download the three data tables (capture, plots, traps) and import them into the SQLite database.
    3. Connect to the database and familiarize yourself with its tables and structure.
    4. Write a query to determine the total number of traps that have been disturbed at each plot. Plot a histogram of the results.
    5. Determine the average hind foot length and weight of each species collected for each National Landcover Database (nlcd) class. Plot the average weight of all species with weight measurements from the woody wetlands.
    6. Write a set of nested queries to determine the total number of disturbed traps and average weight of Podimus floridanus for each sampling event (eventID).
    [click here for output] [click here for output] [click here for output]

  5. Tree Biomass

    Estimating the total amount of biomass (the total mass of all individuals) in forests is important for understanding the global carbon budget and how the earth will respond to increases in carbon dioxide emissions. Measuring the mass of whole trees is a major effort and requires destructive harvest of the tree. Fortunately, we can estimate the mass of a tree based on its diameter.

    There are lots of equations for estimating the mass of a tree from its diameter, but one good option is the equation:

    Mass = 0.124 * Diameter2.53

    where Mass is measured in kg of dry above-ground biomass and Diameter is in cm DBH (Brown 1997).

    We’re going to estimate the total tree biomass for trees in a 96 hectare area of the Western Ghats in India. The raw data is available on Ecological Archives. Unfortunately, the data is stored in a poor database structure and using all of the tree stems would be difficult without first tidying up the data. You can have a look at the metadata to get familiar with the data structure.

    1. Use tidyr to gather() the raw data into rows for each measured stem.
    2. Write a function that takes a vector of tree diameters as an argument and
      returns a vector of tree masses.
    3. Stems are measured in girth (or circumference) rather than diameter. Write a function that takes a vector of circumferences as an argument and returns a vector of diameters (circumference = pi * diameter).
    4. Use the two functions you’ve written to estimate the total biomass (i.e., the sum of the masses) of trees in this dataset and print the result to the screen.
    5. separate() the SpCode into GenusCode and SpEpCode and estimate the total biomass per genus in a table. Technically the four letter code doesn’t uniquely identify all of the genera in the dataset, but we’ll assume it does for the purpose of this exercise.
    [click here for output]