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More on data frames
Data Carpentry contributors
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Learning Objectives

  • understand the concept of a data.frame
  • using sequences to index data
  • know how to access any element of a data.frame

What are data frames?

data.frame is the de facto data structure for most tabular data and what we use for statistics and plotting.

A data.frame is a collection of vectors of identical lengths. Each vector represents a column, and each vector can be of a different data type (e.g., characters, integers, factors). The str() function is useful to inspect the data types of the columns.

Creating data.frames by importing data

A data.frame can be created by the functions read.csv() or read.table(), in other words, when importing spreadsheets from your hard drive (or the web).

By default, data.frame converts (= coerces) columns that contain characters (i.e., text) into the factor data type. Depending on what you want to do with the data, you may want to keep these columns as character. To do so, read.csv() and read.table() have an argument called stringsAsFactors which can be set to FALSE:

>some_data <- read.csv("data/some_file.csv", stringsAsFactors=FALSE)

Creating data.frames manually

You can also create data.frame manually with the function data.frame(). This function can also take the argument stringsAsFactors. Compare the output of these examples, and compare the difference between when the data are being read as character and when they are being as factor.

>example_data <- data.frame(
                            animal=c("dog", "cat", "sea cucumber", "sea urchin"),
                            feel=c("furry", "furry", "squishy", "spiny"),
                            weight=c(45, 8, 1.1, 0.8)
                            )
>str(example_data)
>

#> 'data.frame':    4 obs. of  3 variables:
#>  $ animal: Factor w/ 4 levels "cat","dog","sea cucumber",..: 2 1 3 4
#>  $ feel  : Factor w/ 3 levels "furry","spiny",..: 1 1 3 2
#>  $ weight: num  45 8 1.1 0.8

>example_data <- data.frame(
                            animal=c("dog", "cat", "sea cucumber", "sea urchin"),
                            feel=c("furry", "furry", "squishy", "spiny"),
                            weight=c(45, 8, 1.1, 0.8),
                            stringsAsFactors=FALSE)
                            )
>
>str(example_data)

#> 'data.frame':    4 obs. of  3 variables:
#>  $ animal: chr  "dog" "cat" "sea cucumber" "sea urchin"
#>  $ feel  : chr  "furry" "furry" "squishy" "spiny"
#>  $ weight: num  45 8 1.1 0.8

Challenge

  1. There are a few mistakes in this hand crafted data.frame, can you spot and fix them? Don't hesitate to experiment!

    author_book <- data.frame(author_first=c("Charles", "Ernst", "Theodosius"),
                          author_last=c(Darwin, Mayr, Dobzhansky),
                          year=c(1942, 1970))

  2. Can you predict the class for each of the columns in the following example?

    country_climate <- data.frame(country=c("Canada", "Panama", "South Africa", "Australia"),
                               climate=c("cold", "hot", "temperate", "hot/temperate"),
                               temperature=c(10, 30, 18, "15"),
                               northern_hemisphere=c(TRUE, TRUE, FALSE, "FALSE"),
                               has_kangaroo=c(FALSE, FALSE, FALSE, 1))

Check your guesses using str(country_climate). Are they what you expected? Why? Why not?

R coerces (when possible) to the data type that is the least common denominator and the easiest to coerce to.

Inspecting data.frame objects

We already saw how the functions head() and str() can be useful to check the content and the structure of a data.frame. Here is a non-exhaustive list of functions to get a sense of the content/structure of the data.

  • Size:
    • dim() - returns a vector with the number of rows in the first element, and the number of columns as the second element (the dimensions of the object)
    • nrow() - returns the number of rows
    • ncol() - returns the number of columns
  • Content:
    • head() - shows the first 6 rows
    • tail() - shows the last 6 rows
  • Names:
    • names() - returns the column names (synonym of colnames() for data.frame objects)
    • rownames() - returns the row names
  • Summary:
    • str() - structure of the object and information about the class, length and content of each column
    • summary() - summary statistics for each column

Note: most of these functions are "generic", they can be used on other types of objects besides data.frame.

Indexing and sequences

If we want to extract one or several values from a vector, we must provide one or several indices in square brackets, just as we do in math. For instance try the following:

>animals <- c("mouse", "rat", "dog", "cat")
>animals[2]
>
>animals[c(3, 2)]
>animals[2:4]
>
>more_animals <- animals[c(1:3, 2:4)]
>more_animals

R indexes start at 1. Programming languages like Fortran, MATLAB, and R start counting at 1, because that's what human beings typically do. Languages in the C family (including C++, Java, Perl, and Python) count from 0 because that's simpler for computers to do.

: is a special function that creates numeric vectors of integers in increasing or decreasing order, test 1:10 and 10:1 for instance. The function seq() (for sequence) can be used to create more complex patterns:

>seq(1, 10, by=2)
>seq(5, 10, length.out=3)
>seq(50, by=5, length.out=10)
>seq(1, 8, by=3) # sequence stops to stay below upper limit

Our survey data frame has rows and columns (it has 2 dimensions), if we want to extract some specific data from it, we need to specify the "coordinates" we want from it. Row numbers come first, followed by column numbers.

>surveys[1, 1]   # first element in the first column of the data frame
>surveys[1, 6]   # first element in the 6th column
>surveys[1:3, 7] # first three elements in the 7th column
>surveys[3, ]    # the 3rd element for all columns
>surveys[, 8]    # the entire 8th column
>head_surveys <- surveys[1:6, ] # surveys[1:6, ] is equivalent to head(surveys)

Challenge

  1. The function nrow() on a data.frame returns the number of rows. Use it, in conjuction with seq() to create a new data.frame called surveys_by_10 that includes every 10th row of the survey data frame starting at row 10 (10, 20, 30, ...)