dplyr Aggregation

Setup

install.packages(c('dplyr', 'readr', 'tidyr'))
download.file("https://ndownloader.figshare.com/files/2292172", "surveys.csv")
download.file("https://ndownloader.figshare.com/files/3299474", "plots.csv")
download.file("https://ndownloader.figshare.com/files/3299483", "species.csv")
download.file("https://www.datacarpentry.org/semester-biology/data/shrub-volume-data.csv", "shrub-volume-data.csv")

Basic aggregation

surveys <- read_csv("surveys.csv")

Aggregation combines rows into groups based on one of more columns.
Calculates combined values for each group.
First step, group the data frame.
Let’s group it by year
group_by
Arguments: 1) table to work on; 2) columns to group by

group_by(surveys, year)

The tibble produced by this function has grouping information
Store the data frame in a variable to use in the next step

surveys_by_year <- group_by(surveys, year)

After grouping a data frame use summarize() to calculate values for each group.
Count the number of rows for each group (individuals in each species).
First argument is the table to work on
Needs to be a grouped table
One additional argument for each calculation we want to do for each group
Column name to store calculated value, =, calculation to perform for each group
We’ll use the function n which is a special function that counts the rows in the table

counts_by_year <- summarize(surveys_by_year, abundance = n())

Can group by multiple columns
Count the number of individuals in each plot in each year

surveys_by_plot_year <- group_by(surveys, plot_id, year)
counts_by_plot_year <- summarize(surveys_by_plot_year, abundance = n())

Just like with other dplyr functions we could write this using pipes instead

plot_year_counts <- surveys |>
  group_by(plot_id, year) |>
  summarize(abundance = n())

Do Portal Data Aggregation 1-2.

We can also do multiple calculations using summarize
Use any function that returns a single value from one or more vectors
E.g., mean, max, min
We’ll calculate the number of individuals in each plot year combination and their average weight

size_abundance_data <- surveys |>
  group_by(plot_id, year) |>
  summarize(abundance = n(), avg_weight = mean(weight))

Open table
Why did we get NA?
mean(weight) returns NA when weight has missing values (NA)
Can fix using drop_na(weight)

size_abundance_data <- surveys |>
  drop_na(weight) |>
  group_by(plot_id, year) |>
  summarize(abundance = n(), avg_weight = mean(weight))

Also note the message about “grouped output”
It says that the resulting data frame is grouped by year
When we group by more than one column the resulting data frame is grouped by all but the last group
Can be useful in some more complicated circumstances
Can also make things not work if functions don’t support grouped data frames
To remove these groups add .groups = "drop" as an optional arugment

size_abundance_data <- surveys |>
  drop_na(weight) |>
  group_by(plot_id, year) |>
  summarize(abundance = n(), avg_weight = mean(weight), .groups = "drop")

Or you can add ungroup() to the end of the pipeline
But then the message still prints because it happens as part of the summarize step
Looking at the resulting data frame

size_abundance_data

Shows us that the final data frame is ungrouped

Do Portal Data Aggregation 3.

Notes

Setup

Basic aggregation