Data Science Research in Biology -
Fall 2022

A course for UC Merced undergraduates in data science applications for research in ecology and evolution

Creative Commons License

Intro to version control

Activities

Day1

Individual activity: Tropical plan traits data

The goals of this activity are:

  • To practice usage of main R functions to process data tables (read, summarize and write as CSV files) using RStudio.
  • To apply a good workflow of version control with git on a local repository using RStudio.
  1. For this assignment, we are going to use the plant trait data from:
    • Razafindratsima OH, Brown KA, Carvalho F, Johnson SE, Wright PC, Dunham AE (2017) Data from: Edge effects on components of diversity and above-ground biomass in a tropical rainforest. Dryad Digital Repository. https://doi.org/10.5061/dryad.jn743
  2. Follow the link to the dataset and download the .xlsx file.
  3. Open the file in a spreadsheet program (like excel) and save the trait tab as a CSV (comma delimited) file. Make sure you saved the CSV file in the data-raw folder of your project.
  4. Create a new file called “tropical-plant-trait.R” file.
  5. In this file, write the necessary R code to perform the following challenges. After each challenge, add and commit the R script file, using an informative commit message for each commit:
    • Read the CSV file using the function read.csv and assign it to an object called data_table.
    • Use the functions unique and length to show the number of unique families found in the data frame. First, you will need to subset accordingly your data_table object using square brackets [ ].
    • Do the same to find the number of unique “dispersal modes” and “fruit colors”.
    • Use the mean function to calculate the average fruit width in cm.
    • Use the function summary on your data_table object. Can you find the average fruit width in the output of the function? Is it the same as the one you obtained using the function mean?
    • Look at the output of the function summary. What is the average fruit length in cm?
    • Create the following subset tables from your original data_table object. Use square brackets to create:
      • A subset of data_table that contains the first 10 rows.
      • A subset of data_table that contains the last 20 rows.
      • A subset of data_table that contains rows 12, 17, 23 and 145.
      • A subset of data_table that contains the first 10 rows and rows 12, 17, 23 and 145.
      • A subset of data_table that contains the first 5 columns and all rows.
      • A subset of data_table that contains the last 2 columns and all rows.
      • A subset of data_table that contains columns with “family”, “fruit_color” and “growth_rate”, and all rows.
      • A subset of data_table that contains the first 5 columns and rows 12, 17, 23 and 145.
    • Remember to comment your code.
    • Use the function write.csv to write CSV files for each subset into the data folder. Note: you have to use the argument file to provide the path and name for the subset CSV files, otherwise they will not be written to the correct folder or at all. If you do not know how to use the file argument, run help(write,csv) or ?write.csv.
  6. Add and commit all CSV files that you generated. Use an informative commit message.
  7. Display your git history and take a snapshot. Send the snapshot to your instructor.

Day2

Group activity: absolute and relative paths

The goals of this activity are:

  • To practice usage of absolute and relative paths.
  1. For this activity we will use a section of the code from the previous activity.
  2. Go into groups and compare the file paths you used to save the CSV files in the data folder, and answer:
    • Did you use relative or absolute paths?
    • If you all used the absolute path to save any CSV file, what does the path look like? Do you all have the same path? What are the differences?
    • If you all used relative paths to save any of your CSV files, what does the path look like? Do you all have the same path? What are the differences?
  3. Create a script called paths.R, save it to your scripts folder, and write the code to:
    • Write the data_table object as a CSV file in your computer’s home directory using an absolute path and a relative path.
    • Write the data_table object as a CSV file in your project’s home directory using an absolute path and a relative path.
  4. Add and commit all the files that you generated. Use an informative commit message.
  5. Display your git history and take a snapshot. Send the snapshot to your instructor.

Individual activity: logical comparisons

  1. For this assignment, we are going to keep on working with the plant trait data from:
    • Razafindratsima OH, Brown KA, Carvalho F, Johnson SE, Wright PC, Dunham AE (2017) Data from: Edge effects on components of diversity and above-ground biomass in a tropical rainforest. Dryad Digital Repository. https://doi.org/10.5061/dryad.jn743
  2. Create a new file called logical-comparisons.R and save it in your scripts folder.
  3. Write the necessary code to:
    1. Read the CSV file with trait plant data using the function read.csv and assign it to an object called data_table.
    2. Subset your data table and create an object called all_dispersal_modes that contains all rows from column “dispersal mode”.
    3. Run the following code all_dispersal_modes == "lemur". What is the class of this output? What is it telling you about dispersal mode?
    4. Besides the indices of rows and columns, we can use logical operators to subset a data frame. Use the code from the previous line to subset your data_table object to keep only those rows that have a dispersal_mode equal to “lemur”. Create an object called data_table_lemur.
    5. Apply the function nrow to your newly created object. How many plant species are dispersed by lemurs?
    6. Use the same logic and procedure to find out the follwing:
      1. how many plant species in data_table are dispersed by birds?
      2. how many plant species have an average height above 10?
      3. how many plant species have an average height exactly equal to 10?
      4. how many plant species have an average height below 10?
      5. how many plant species belong to the family Lauraceae?
  4. Add and commit all the files that you generated. Use an informative commit message.
  5. Display your git history and take a snapshot. Send the snapshot to your instructor.