Data Carpentry for Biologists

Combining Data Manipulations in dplyr

Notes

Setup

install.packages('dplyr')
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")

Introduction

  • Combine a series of data manipulation actions
  • Do each action in sequential order

Intermediate variables

  • Run a command
  • Store the output in a variable
  • Use that variable later in the code

  • Repeat

  • Obtain the data for only DS, sorted by year, with only the year and and weight columns
ds_data <- filter(surveys, species_id == "DS", !is.na(weight))
ds_data_by_year <- arrange(ds_data, year)
ds_weight_by_year <- select(ds_data_by_year, year, weight)

Do Portal Data Manipulation Exercise 1-2

Pipes

  • Intermediate variables can get cumbersome if their are lots of steps.
  • |> (“pipe”) takes the output of one command and passes it as input to the next command
  • Want to take the mean of a vector
  • Normally we would run the mean function with the vector as the input:
x = c(1, 2, 3)
mean(x)
  • Instead we could pipe the vector into the function
x |> mean()
  • So x becomes the first argument in mean
  • If we want to add other arguments they get added to the function call
x = c(1, 2, 3, NA)
mean(x, na.rm = TRUE)
x |> mean(na.rm = TRUE)
  • Questions?
surveys |>
  filter(species_id == "DS", !is.na(weight))

ds_weight_by_year <- surveys |>
  filter(species_id == "DS", !is.na(weight)) |>
  arrange(year) |>
  select(year, weight)

Do Portal Data Manipulation Pipes 1.

The magrittr pipe

  • You will also see another type of pipe character %>%
  • This is the original pipe in R and you had to load the magrittr package to use it (this gets loaded automatically by dplyr)
  • Either pipe is fine for this class
    • |> will work everywhere as long as you have a new enough version of R
    • magrittr has some fancier functionality that may be useful in some cases

Keyboard Shortcut

  • Shortcut: Ctrl-Shift-m
  • You can change this to give the base R pipe
    • Tools -> Global Options -> Code -> Use native pipe operator

Pipe to other arguments

  • To pipe the result of a line to something other than the first argument use the placehold _
  • This only works for named arguments
  • Let’s fit a linear model at the end of our dplyr pipeline
  • lm takes a formula as the first argument tells it what columns to use for the response and driver variables
  • The second argument tells it where the data is
  • It needs to be named for the place holder to work
surveys |>
  filter(species_id == "DS", !is.na(weight)) |>
  arrange(year) |>
  select(year, weight) |>
  lm(weight ~ year, data = _)