Remember to

  • Load surveys.csv data into surveys

Basic aggregation

  • 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 species_id
  • group_by
  • Arguments: 1) table to work on; 2) columns to group by
group_by(surveys, species_id)
  • Different looking kind of data.frame
    • Source, grouping, and data type information
  • Store the data frame in a variable to use in the next step
surveys_by_species <- group_by(surveys, species_id)
  • 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).
  • summarize
  • Arguments
    • Table to work on, which needs to be a grouped table
    • One additional argument for each calculation we want to do for each group
      • New column name to store calculated value
      • =
      • Calculation that we want to perform for each group
      • We’ll use the function n which is a special function that counts the rows in the table
summarize(surveys_by_species, abundance = n())
  • Can group by multiple columns
  • Count the number of individuals in each species and plot
surveys_by_species_plot <- group_by(surveys, species_id, plot_id)
species_plot_counts <- summarize(surveys_by_species_plot, abundance = n())
  • Use any function that returns a single value from a vector.
  • E.g., mean, max, min
  • We’ll calculate the average weight of each species on each plot
species_weight <- summarize(surveys_by_species_plot, avg_weight = mean(weight))
  • Open table
  • Why did we get NA?
    • mean(weight) returns NA when weight has missing values (NA)
  • Can fix using mean(weight, na.rm = TRUE)
species_weight <- summarize(surveys_by_species,
                            avg_weight = mean(weight, na.rm = TRUE))
  • Still has NaN for species that have never been weighed
  • Can filter using !is.na
filter(species_weight, !is.na(avg_weight))

Do Shrub Volume Aggregation.