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Data analysis using R

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Loading data into R

Overview

Teaching: 20 min
Exercises: 10 min
Questions

  • How can I read and write tabular data in R?

  • What are the basic data types in R?

Objectives

  • To be aware of the different types of data.

  • To begin exploring tibbles

  • To be able to extract parts of a tibble

One of R’s most powerful features is its ability to deal with tabular data — such as you may already have in a spreadsheet or a CSV file.

The course data contains a .csv file called feline-data.csv, which you copied to the data/ folder when we discussed managing projects in RStudio.

coat,weight,likes_string
calico,2.1,1
black,5.0,0
tabby,3.2,1

We can view the contents of the file by selecting it from the “Files” window in RStudio, and selecting “View File”. This will display the contents of the file in a new window in RStudio. We can see that the variables names are given in the first line of the file, and that the remaining lines contain the data itself. Each observation is on a separate line, and variables are separated by commas. Note that viewing the file doesn’t make its contents available to R; to do this we need to import the data.

We can import the data into R using the read_csv() function; this is part of the readr package, which is part of the tidyverse.

Let’s make a new script for this episode, by choosing the menu options File, New File, R Script.

Although we loaded the tidyverse in the previous episode, we should make our scripts self-contained, so we should include library(readr) in the new script. We could use library(tidyverse) to load all of the commonly used packages in the tidyverse. We then use the read_csv() function to import the data, which we store in the object named cats:

library(readr)
cats <- read_csv(file = "data/feline-data.csv")


── Column specification ────────────────────────────────────────────────────────
cols(
  coat = col_character(),
  weight = col_double(),
  likes_string = col_double()
)

We see that the read_csv() table reports a “column specification”. This shows the variable names that were read in, and the type of data that each column was interpreted as.

New versions of readr

Newer versions of readr don’t report the full column specification when you load a file. The spec() function will show you the full column specification:

spec(cats)

cols(
  coat = col_character(),
  weight = col_double(),
  likes_string = col_double()
)

Previewing data

cats

# A tibble: 3 × 3
  coat   weight likes_string
  <chr>   <dbl>        <dbl>
1 calico    2.1            1
2 black     5              0
3 tabby     3.2            1

When we enter cats by itself on the command line, it will print the contents of cats; we see that it consists of a 3 by 3 tibble. A tibble is a way of storing tabular data, which is part of the tidyverse. We see the variable names, and an (abbreviated) string indicating what type of data is stored in each variable.

read_csv() vs read.csv()

You may notice while typing the command that RStudio auto suggests read.csv() as a function to load a comma separated value file. This function is included as part of base R, and performs a similar job to read_csv(). We will be using read_csv() in this course; it is part of the tidyverse, so works well with other parts of the tidyverse, is faster than read.csv() and handles strings in a way that is usually more useful than read.csv().

Loading other types of data

Another type of file you might encounter are tab-separated value files (.tsv); these can be read with the read_tsv() function in the readr package. To read files with other delimiters, use the read_delim() function. If files are fixed width format (i.e. the variable is defined by its position on the line), then use the read_fwf() function.

The tidyverse comes with several packages for loading data in other formats. These include:

  • readxl for reading data from Excel spreadsheets
  • haven for reading SAS, SPSS and Stata data files
  • xml2 for reading xml data

These aren’t loaded by default (when we use library("tidyverse")), so they will need to be loaded separately, e.g. library("readxl"), etc. There are also tidyverse packages for getting data via web APIs, or by “scraping” websites.

Data types

Every piece of data in R is stored as either double, integer, complex, logical or character.

When we read the data into R using read_csv() it tries to work out what data type each variable is, which it does by looking at the data contained in the first 1000 rows of the data file. We can see from the displayed message that read_csv() has treated the coat variable as a character variable, the weight variable as a floating point number and likes_string as an double variable.

This is almost correct; likes_string is, however a logical (or boolean) value — the cat either likes string (which is represented in the data file as a 1, or doesn’t (represented by 0)). We can specify how we would like read_csv() to treat the data in each variable using the col_types option; let’s tell read_csv() to treat likes_string as a logical variable:

cats <- read_csv("data/feline-data.csv", col_types = cols(
  coat = col_character(),
  weight = col_double(),
  likes_string = col_logical()
) )

That’s a lot of typing! Fortunately, we don’t have to type everything by hand. The cols() function above may look familiar; if we load a file using read_csv() without specifying the col_types option, it will print out the cols() function it has generated during the import process. We can copy and paste this into our script, and modify it as required.

If we look at the imported data, we will now see that the likes_string variable is recorded as a logical. The strict approach to specifying data types has another benefit, as we’ll see…

A user has added details of another cat. This information is in the file data/feline-data_v2.csv, included in the course data download.

file.show("data/feline-data_v2.csv")

coat,weight,likes_string
calico,2.1,1
black,5.0,0
tabby,3.2,1
tabby,2.3 or 2.4,1

Let’s load this in, using the read_csv() command we have just written:

cats2 <- read_csv("data/feline-data_v2.csv", col_types = cols(
  coat = col_character(),
  weight = col_double(),
  likes_string = col_logical()
) )

Warning: 1 parsing failure.
row    col               expected     actual                      file
  4 weight no trailing characters 2.3 or 2.4 'data/feline-data_v2.csv'

We see that a parsing failure message has been printed when we load the data. If we look at the cats2 data, we will see that the invalid weight 2.3 or 2.4 has been replaced with an NA. This illustrates one of the benefits of specifying the column types when we load the data; it alerts us when something has gone wrong with the data-import. If we hadn’t specified the type of data that we expect to be stored in each column, read_csv() will read the weight variable as a character variable.

We don’t have to specify a column type for each variable; the cols() function will guess the data types for the columns we don’t specify. It is, however, a good idea to be explicit about the type of data we expect to be in each column.

Importing data using RStudio

You may have noticed when we viewed the feline-data.csv file in RStudio, before importing it, that another option appeared, labelled “Import Dataset”. This lets us import the data interactively. It can be more convenient to use this approach, rather than manually writing the required code. If you do this, you will find that the code RStudio has written is put into the console and run (and will appear in the history tab in RStudio). It’s fine to do this initially, but you should copy the generated code to your script, so that you can reproduce your analysis.

Exploring tibbles

We can “unpick” the contents of a tibble in several ways. We can return a vector containing the values of a variable using the dollar symbol, $:

cats$weight

[1] 2.1 5.0 3.2

We can also use the subsetting operator [] directly on tibbles. In contrast to a vector, a tibble is two dimensional. We pass two arguments to the [] operator; the first indicates the row(s) we require and the second indicates the columns. So to return rows 1 and 2, and columns 2 and 3 we can use:

cats[1:2,2:3]

# A tibble: 2 × 2
  weight likes_string
   <dbl> <lgl>       
1    2.1 TRUE        
2    5   FALSE

If we leave an index blank, this acts as a wildcard and matches all of the rows or columns:

cats[1,]

# A tibble: 1 × 3
  coat   weight likes_string
  <chr>   <dbl> <lgl>       
1 calico    2.1 TRUE        

cats[,1]

# A tibble: 3 × 1
  coat  
  <chr> 
1 calico
2 black 
3 tabby

Subsetting a tibble returns another tibble; using $ to extract a variable returns a vector:

cats$coat

[1] "calico" "black"  "tabby" 

cats[,1]

# A tibble: 3 × 1
  coat  
  <chr> 
1 calico
2 black 
3 tabby

Tibbles vs data frames

Tibbles are used to represent tabular data in the tidyverse. In contrast, base R uses data frames to represent tabular data. One of the differences between these two types of object is what is returned when you extract a subset of rows/columns. In contrast to a tibble, taking a subset of a data frame doesn’t always return another data frame. For more details see the callout at the end of this episode.

Writing data in R

We can save a tibble (or data frame) to a csv file, using readr’s write_csv() function. For example, to save the cat data to mycats.csv:

write_csv(cats, "data/mycats.csv")

Categorical data (self study)

Another data structure is called a factor. Factors usually look like character data, but are used to represent categorical information. We don’t handle much categorical data in this course, so this session is left for self study.

Let’s work with the coat colours of the cats in our dataset:

catCoats <- cats$coat
catCoats

[1] "calico" "black"  "tabby"

Let’s assume that only specific values of coat colour are allowed:

validCoatColours <- c("white", "black", "calico", "tabby")

We can convert our character vector of coat colours into a factor using the parse_factor() function:

coatFactor <- parse_factor(catCoats, levels = validCoatColours)
coatFactor 

[1] calico black  tabby 
Levels: white black calico tabby

You might be wondering what the point of defining a factor is. If we’re fitting, e.g. a linear regression with a categorical variable we would need to generate indicator variables for it. By defining our data as categorical, R will take care of this for us. The factor levels will be defined in the order we specify in the vector we pass as the levels argument to parse_factor; so the baseline treatment would usually be specified as the first level.

Defining variables as factors also helps us to ensure data integrity. Consider the vector below:

catCoats2 <- c("calic0", "black", "tabby")

If we try to convert this to a factor it won’t work:

parse_factor(catCoats2, levels = validCoatColours)

Warning: 1 parsing failure.
row col           expected actual
  1  -- value in level set calic0

[1] <NA>  black tabby
attr(,"problems")
# A tibble: 1 × 4
    row   col expected           actual
  <int> <int> <chr>              <chr> 
1     1    NA value in level set calic0
Levels: white black calico tabby

Remember that we specified the column types when we loaded the data using read_csv(); we can take this idea a step further, and define coat as a factor when we load the data.

Challenge 1

Assume that the valid values for the coats variable are black, white, calico and tabby. Read in the cats data, treating the coat variable as a factor with these levels.

Hint: col_factor() and its help page may be useful.

Solution to challenge 1

cats <- read_csv("data/feline-data.csv", col_types = cols(
 coat = col_factor(levels = c("black", "white", "calico",  "tabby")),
 weight = col_double(),
 likes_string = col_logical()
) )
cats

# A tibble: 3 × 3
  coat   weight likes_string
  <fct>   <dbl> <lgl>       
1 calico    2.1 TRUE        
2 black     5   FALSE       
3 tabby     3.2 TRUE

You may have noticed while reading the help file for col_factor() and parse_factor() that we can pass the option levels = NULL. This will cause R to generate the factor levels automatically. This can be a bad idea, since invalid data (such as “calic0” in the example above) will get their own factor level. If, on the other hand you’ve got hundreds of possible values, that’s a lot of typing.

A compromise between these two approaches is to look at the levels your factor has having loaded the data, using the levels() function: e.g. levels(cats$coat). By testing the length of this vector you can check that you have as many factor levels as you expect.

Doing more with factors

If you wish to perform more complex operations on factors, such as recoding level names, changing level order, and collapsing multiple levels into one, the forcats package, which is part of the tidyverse makes this easy. Note that forcats isn’t loaded by default, so you will need to use library("forcats") before using it.

Matrices

We can also define matrices in R. We don’t cover this in this course, since we are focussing on data-analysis, rather than maths and algorithms. For details of the matrix class, you can refer to the original Software Carpentry version of these notes.

Differences with base R

In this lesson we’ve taught you how to read files and make factors using the functionality in the readr package, which is part of the tidyverse.
This section highlights some of the differences between the tidyverse and its equivalent functionality in base R.

R’s standard data structure for tabular data is the data.frame. In contrast, read_csv() creates a tibble (also referred to, for historic reasons, as a tbl_df). This extends the functionality of a data.frame, and can, for the most part, be treated like a data.frame.

You may find that some older functions don’t work on tibbles. A tibble can be converted to a dataframe using as.data.frame(mytibble). To convert a data frame to a tibble, use as.tibble(mydataframe).

Tibbles behave more consistently than data frames when subsetting with []; this will always return another tibble. This isn’t the case when working with data.frames. You can find out more about the differences between data.frames and tibbles by typing vignette("tibble").

read_csv() will always read variables containing text as character variables. In contrast, the base R function read.csv() will, by default, convert any character variable to a factor. This is often not what you want, and can be overridden by passing the option stringsAsFactors = FALSE to read.csv().

We used parse_factor() to define factors. The base R equivalent is the factor() function. The main differences between the two approaches are:

  • factor() will assign factor levels automatically; it does not require us to pass levels = NULL.
  • The automatic levels generated by factor() will be alphabetical (rather than according to the order that each level is encountered in parse_factor())
  • factor() does not warn us if we have data that doesn’t match any of the levels we have specified.

It is chiefly for the final reason that we recommend using parse_factor() instead of factor(). You should be aware that the default ordering of factor levels differs between factor() and parse_factor().

Key Points

  • Tibbles let us store tabular data in R. Tibbles are an extension of the base R data frame.

  • Use read_csv to read tabular data into a tibble R.

  • User write_csv to write tabular data to a comma separated value file.

  • Use factors to represent categorical data in R. You should specify the levels of your factors.

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