Manipulating and analyzing data with dplyr

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Learning Objectives

  • Describe the purpose of the dplyr and tidyr packages.
  • Select certain columns in a data frame with the dplyr function select.
  • Select certain rows in a data frame according to filtering conditions with the dplyr function filter .
  • Link the output of one dplyr function to the input of another function with the ‘pipe’ operator %>%.
  • Add new columns to a data frame that are functions of existing columns with mutate.
  • Use the split-apply-combine concept for data analysis.
  • Use summarize, group_by, and tally to split a data frame into groups of observations, apply a summary statistics for each group, and then combine the results.
  • Describe the concept of a wide and a long table format and for which purpose those formats are useful.
  • Describe what key-value pairs are.
  • Reshape a data frame from long to wide format and back with the spread and gather commands from the tidyr package.
  • Export a data frame to a .csv file.

Data Manipulation using dplyr and tidyr

Bracket subsetting is handy, but it can be cumbersome and difficult to read, especially for complicated operations. Enter dplyr. dplyr is a package for making tabular data manipulation easier. It pairs nicely with tidyr which enables you to swiftly convert between different data formats for plotting and analysis.

Packages in R are basically sets of additional functions that let you do more stuff. The functions we’ve been using so far, like str() or data.frame(), come built into R; packages give you access to more of them. Before you use a package for the first time you need to install it on your machine, and then you should import it in every subsequent R session when you need it. You should already have installed the tidyverse package. This is an “umbrella-package” that installs several packages useful for data analysis which work together well such as tidyr, dplyr, ggplot2, tibble, etc.

The tidyverse package tries to address 3 major problems with some of base R functions: 1. The results from a base R function sometimes depend on the type of data. 2. Using R expressions in a non standard way, which can be confusing for new learners. 3. Hidden arguments, having default operations that new learners are not aware of.

We have seen in our previous lesson that when building or importing a data frame, the columns that contain characters (i.e., text) are coerced (=converted) into the factor data type. We had to set stringsAsFactors to FALSE to avoid this hidden argument to convert our data type.

This time will use the tidyverse package to read the data and avoid having to set stringsAsFactors to FALSE

To load the package type:

library("tidyverse")    ## load the tidyverse packages, incl. dplyr

What are dplyr and tidyr?

The package dplyr provides easy tools for the most common data manipulation tasks. It is built to work directly with data frames, with many common tasks optimized by being written in a compiled language (C++). An additional feature is the ability to work directly with data stored in an external database. The benefits of doing this are that the data can be managed natively in a relational database, queries can be conducted on that database, and only the results of the query are returned.

This addresses a common problem with R in that all operations are conducted in-memory and thus the amount of data you can work with is limited by available memory. The database connections essentially remove that limitation in that you can connect to a database of many hundreds of GB, conduct queries on it directly, and pull back into R only what you need for analysis.

The package tidyr addresses the common problem of wanting to reshape your data for plotting and use by different R functions. Sometimes we want data sets where we have one row per measurement. Sometimes we want a data frame where each measurement type has its own column, and rows are instead more aggregated groups - like plots or aquaria. Moving back and forth between these formats is nontrivial, and tidyr gives you tools for this and more sophisticated data manipulation.

To learn more about dplyr and tidyr after the workshop, you may want to check out this handy data transformation with dplyr cheatsheet and this one about tidyr.

We’ll read in our data using the read_csv() function, from the tidyverse package readr, instead of read.csv().

surveys <- read_csv("data/portal_data_joined.csv")
#> Parsed with column specification:
#> cols(
#>   record_id = col_integer(),
#>   month = col_integer(),
#>   day = col_integer(),
#>   year = col_integer(),
#>   plot_id = col_integer(),
#>   species_id = col_character(),
#>   sex = col_character(),
#>   hindfoot_length = col_integer(),
#>   weight = col_integer(),
#>   genus = col_character(),
#>   species = col_character(),
#>   taxa = col_character(),
#>   plot_type = col_character()
#> )
## inspect the data
str(surveys)

Notice that the class of the data is now tbl_df This is referred to as a “tibble”. Tibbles are almost identical to R’s standard data frames, but they tweak some of the old behaviors of data frames. For our purposes the only differences between data frames and tibbles are that:

  1. When you print a tibble, R displays the data type of each column under its name; it prints only the first few rows of data and only as many columns as fit on one screen.
  2. Columns of class character are never automatically converted into factors.

Selecting columns and filtering rows

We’re going to learn some of the most common dplyr functions: select(), filter(), mutate(), group_by(), and summarize(). To select columns of a data frame, use select(). The first argument to this function is the data frame (surveys), and the subsequent arguments are the columns to keep.

select(surveys, plot_id, species_id, weight)

To choose rows based on a specific criteria, use filter():

filter(surveys, year == 1995)

Pipes

What if you want to select and filter at the same time? There are three ways to do this: use intermediate steps, nested functions, or pipes.

With intermediate steps, you create a temporary data frame and use that as input to the next function, like this:

surveys2 <- filter(surveys, weight < 5)
surveys_sml <- select(surveys2, species_id, sex, weight)

This is readable, but can clutter up your workspace with lots of objects that you have to name individually. With multiple steps, that can be hard to keep track of.

You can also nest functions (i.e. one function inside of another), like this:

surveys_sml <- select(filter(surveys, weight < 5), species_id, sex, weight)

This is handy, but can be difficult to read if too many functions are nested, as R evaluates the expression from the inside out (in this case, filtering, then selecting).

The last option, pipes, are a recent addition to R. Pipes let you take the output of one function and send it directly to the next, which is useful when you need to do many things to the same dataset. Pipes in R look like %>% and are made available via the magrittr package, installed automatically with dplyr. If you use RStudio, you can type the pipe with Ctrl + Shift + M if you have a PC or Cmd + Shift + M if you have a Mac.

surveys %>%
  filter(weight < 5) %>%
  select(species_id, sex, weight)

In the above code, we use the pipe to send the surveys dataset first through filter() to keep rows where weight is less than 5, then through select() to keep only the species_id, sex, and weight columns. Since %>% takes the object on its left and passes it as the first argument to the function on its right, we don’t need to explicitly include the data frame as an argument to the filter() and select() functions any more.

If we want to create a new object with this smaller version of the data, we can assign it a new name:

surveys_sml <- surveys %>%
  filter(weight < 5) %>%
  select(species_id, sex, weight)

surveys_sml

Note that the final data frame is the leftmost part of this expression.

Challenge

Using pipes, subset the surveys data to include individuals collected before 1995 and retain only the columns year, sex, and weight.

Mutate

Frequently you’ll want to create new columns based on the values in existing columns, for example to do unit conversions, or to find the ratio of values in two columns. For this we’ll use mutate().

To create a new column of weight in kg:

surveys %>%
  mutate(weight_kg = weight / 1000)

You can also create a second new column based on the first new column within the same call of mutate():

surveys %>%
  mutate(weight_kg = weight / 1000,
         weight_kg2 = weight_kg * 2)

If this runs off your screen and you just want to see the first few rows, you can use a pipe to view the head() of the data. (Pipes work with non-dplyr functions, too, as long as the dplyr or magrittr package is loaded).

surveys %>%
  mutate(weight_kg = weight / 1000) %>%
  head()

The first few rows of the output are full of NAs, so if we wanted to remove those we could insert a filter() in the chain:

surveys %>%
  filter(!is.na(weight)) %>%
  mutate(weight_kg = weight / 1000) %>%
  head()

is.na() is a function that determines whether something is an NA. The ! symbol negates the result, so we’re asking for every row where weight is not an NA.

Challenge

Create a new data frame from the surveys data that meets the following criteria: contains only the species_id column and a new column called hindfoot_half containing values that are half the hindfoot_length values. In this hindfoot_half column, there are no NAs and all values are less than 30.

Hint: think about how the commands should be ordered to produce this data frame!

Split-apply-combine data analysis and the summarize() function

Many data analysis tasks can be approached using the split-apply-combine paradigm: split the data into groups, apply some analysis to each group, and then combine the results. dplyr makes this very easy through the use of the group_by() function.

The summarize() function

group_by() is often used together with summarize(), which collapses each group into a single-row summary of that group. group_by() takes as arguments the column names that contain the categorical variables for which you want to calculate the summary statistics. So to compute the mean weight by sex:

surveys %>%
  group_by(sex) %>%
  summarize(mean_weight = mean(weight, na.rm = TRUE))

You may also have noticed that the output from these calls doesn’t run off the screen anymore. It’s one of the advantages of tbl_df over data frame.

You can also group by multiple columns:

surveys %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight, na.rm = TRUE))

When grouping both by sex and species_id, the first rows are for individuals that escaped before their sex could be determined and weighted. You may notice that the last column does not contain NA but NaN (which refers to “Not a Number”). To avoid this, we can remove the missing values for weight before we attempt to calculate the summary statistics on weight. Because the missing values are removed first, we can omit na.rm = TRUE when computing the mean:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight))

Here, again, the output from these calls doesn’t run off the screen anymore. If you want to display more data, you can use the print() function at the end of your chain with the argument n specifying the number of rows to display:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight)) %>%
  print(n = 15)

Once the data are grouped, you can also summarize multiple variables at the same time (and not necessarily on the same variable). For instance, we could add a column indicating the minimum weight for each species for each sex:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight))

Tallying

When working with data, we often want to know the number of observations found for each factor or combination of factors. For this task, dplyr provides tally(). For example, if we wanted to group by sex and find the number of rows of data for each sex, we would do:

surveys %>%
  group_by(sex) %>%
  tally()

Here, tally() is the action applied to the groups created by group_by() and counts the total number of records for each category.

Challenge

  1. How many individuals were caught in each plot_type surveyed?

  2. Use group_by() and summarize() to find the mean, min, and max hindfoot length for each species (using species_id).

  3. What was the heaviest animal measured in each year? Return the columns year, genus, species_id, and weight.

  4. You saw above how to count the number of individuals of each sex using a combination of group_by() and tally(). How could you get the same result using group_by() and summarize()? Hint: see ?n.

Reshaping with gather and spread

In the spreadsheet lesson we discussed how to structure our data:

  1. Each variable has its own column
  2. Each observation has its own row
  3. Each value must have its own cell

However, these rules a little trickier than they seem: what counts as an “observation”? Is it an individual, or the individual measurements taken on an individual (weight, hindfoot length, etc.), or all the individuals caught in a given plot on a given day? Consider two tables:

  • all of the individuals caught in a given plot one one day count as a single observation (many columns, few rows)
  • every single individual has its own observation (many rows and few columns)

Many researchers store data in the former (wider) format by default, because it’s often easier for data entry and for human readability. However, most statistical tools (including R, and especially tidyverse) work better with the latter (longer) format.

Suppose we are given a data table with species counts per plot and date for observations taken in 1977, like this:

month day year plot_id DM OT DS DO …
7 16 1977 1 2 0 0 0 …
7 16 1977 2 1 0 0 0 …
7 16 1977 3 2 0 1 0 …
7 16 1977 4 1 0 0 0 …
7 16 1977 5 0 0 1 0 …
7 16 1977 6 1 0 0 0 …

where each of the column names after plot_id represents a species abbreviation.

You can get this file by retrieving it from the course web page:

download.file("tinyurl.com/dcmac2017dec/data/surveys_wide.csv",dest="surveys_wide.csv")

Save it in your working directory and read it in with

surveys_wide <- read.csv("surveys_wide.csv")

In order to work with this data set effectively in R, we need to convert it to long format. We want to convert all of the columns corresponding to species abbreviations into a single pair of columns, one (the key) containing the species abbreviation and the other (the value) containing the number of that species counted on a given date in a given location. The key point here is that the data structure is tidy, but but we are reshaping the data according to the observations of interest: numbers of a particular species observed in a plot rather than the numbers of all species observed in that plot.

Here’s an illustration of how gather() works to convert a (relatively) wide data set to a longer format:

The opposite transformation would transform a single pair of columns (species_id and count) with many rows into many columns (one for each species) with fewer rows (only one per plot/date). We can do both these of transformations with two tidyr functions, spread() and gather().

Gathering

In this situation we are gathering the column names and turning them into a pair of new variables. One variable represents the column names as values, and the other variable contains the values previously associated with the column names.

gather() takes four principal arguments:

  1. the data
  2. the key column variable we wish to create from column names.
  3. the values column variable we wish to create and fill with values associated with the key.
  4. the names of the columns we use to fill the key variable (or the ones we want to ignore).

To make a longer data set with one species count per row, we would create a key called species_abbrev and value called count from all of the columns except the date columns ( month, day, year) and plot_id: we use c() preceded by a minus sign to exclude these columns.

surveys_gather <- surveys_wide %>%
  gather(key = species_abbrev, value = count, -c(month, day, year, plot_id))

str(surveys_gather)

There are other ways to specify columns to exclude or include: if you have a small number of columns to gather, then specifying which ones to include is easier. And if the columns are in a row, you don’t even need to list them all - just use the : operator!

surveys_long <- surveys_wide %>%
  gather(key = species_abbrev, value = count, -(month:plot_id))

## equivalently:
## specify columns to include (here columns are specified by number:
##  a dot (.) is a shortcut for the original data set that you can use
##  inside tidyverse functions)
surveys_wide %>%
  gather(key = species_abbrev, value = count, 5:ncol(.))

As desired, the result now has a single row for each combination of month/day/year/plot_id/species_abbrev.

Spreading

spread() takes three principal arguments:

  1. the data
  2. the key column variable whose values will become new column names.
  3. the value column variable whose values will fill the new column variables.

Further arguments include fill which, if set, fills in missing values with the value provided.

For our first use of spread(), we’ll show how to reverse the gather() operation we just did:

spread(surveys_long,key=species_abbrev,value=count)

This takes us back to our previous arrangement.

The second most common use of tidyr is to reshape data after summarizing it, so that the results are more human-readable (by you, your supervisor/boss, or readers of your scientific reports).

As an example, we’re going to go back to the original surveys data set, find the mean weight of each species in each plot over the entire survey period, and use spread() to reshape the results. We use filter(), group_by() and summarise() to filter our observations and variables of interest, and create a new variable for the mean_weight. We use pipes as before too:

surveys_gw <- surveys %>%
  filter(!is.na(weight)) %>%
  group_by(genus, plot_id) %>%
  summarize(mean_weight = mean(weight))

str(surveys_gw)

This yields surveys_gw where the observations for each plot are spread across multiple rows, 196 observations of 13 variables. Using spread() to key on genus with values from mean_weight this becomes 24 observations of 11 variables, one row for each plot. We again use pipes:

surveys_spread <- surveys_gw %>%
  spread(key = genus, value = mean_weight)

str(surveys_spread)

We could now plot comparisons between the weight of species in different plots, although we may wish to fill in the missing values first.

surveys_gw %>%
  spread(genus, mean_weight, fill = 0) %>%
  head()

Challenge

  1. Spread the surveys data frame with year as columns, plot_id as rows, and the number of genera per plot as the values. You will need to summarize before reshaping, and use the function n_distinct() to get the number of unique types of a genera. It’s a powerful function! See ?n_distinct for more.

  2. Now take that data frame and gather() it again, so each row is a unique plot_id by year combination.

  3. The surveys data set has two measurement columns: hindfoot_length and weight. This makes it difficult to do things like look at the relationship between mean values of each measurement per year in different plot types. Let’s walk through a common solution for this type of problem. First, use gather() to create a dataset where we have a key column called measurement and a value column that takes on the value of either hindfoot_length or weight. Hint: You’ll need to specify which columns are being gathered.

  4. With this new data set, calculate the average of each measurement in each year for each different plot_type. Then spread() them into a data set with a column for hindfoot_length and weight. Hint: You only need to specify the key and value columns for spread().

Exporting data

Now that you have learned how to use dplyr to extract information from or summarize your raw data, you may want to export these new data sets to share them with your collaborators or for archival.

Similar to the read_csv() function used for reading CSV files into R, the tidyverse includes a write_csv() function that generates CSV files from data frames.

Before using write_csv(), we are going to create a new folder, data_output, in our working directory that will store this generated data set. We don’t want to write generated data sets in the same directory as our raw data. It’s good practice to keep them separate. The data folder should only contain the raw, unaltered data, and should be left alone to make sure we don’t delete or modify it. In contrast, our script will generate the contents of the data_output directory, so even if the files it contains are deleted, we can always re-generate them.

In preparation for our next lesson on plotting, we are going to prepare a cleaned up version of the data set that doesn’t include any missing data.

Let’s start by removing observations for which the species_id is missing. In this data set, the missing species are represented by an empty string and not an NA. Let’s also remove observations for which weight and the hindfoot_length are missing. This data set should also only contain observations of animals for which the sex has been determined:

surveys_complete <- surveys %>%
  filter(species_id != "",         # remove missing species_id
         !is.na(weight),           # remove missing weight
         !is.na(hindfoot_length),  # remove missing hindfoot_length
         sex != "")                # remove missing sex

Because we are interested in plotting how species abundances have changed through time, we are also going to remove observations for rare species (i.e., that have been observed less than 50 times). We will do this in two steps: first we are going to create a data set that counts how often each species has been observed, and filter out the rare species; then, we will extract only the observations for these more common species:

## Extract the most common species_id
species_counts <- surveys_complete %>%
  group_by(species_id) %>%
  tally() %>%
  filter(n >= 50)

## Only keep the most common species
surveys_complete <- surveys_complete %>%
  filter(species_id %in% species_counts$species_id)

To make sure that everyone has the same data set, check that surveys_complete has 30463 rows and 13 columns by typing dim(surveys_complete).

Now that our data set is ready, we can save it as a CSV file in our data_output folder.

write_csv(surveys_complete, path = "data_output/surveys_complete.csv")

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