Reading and Writing CSV Files
Last updated on 2024-12-07 | Edit this page
Overview
Questions
- How do I read data from a CSV file into R?
- How do I write data to a CSV file?
Objectives
- Read in a .csv, and explore the arguments of the csv reader.
- Write the altered data set to a new .csv, and explore the arguments.
The most common way that scientists store data is in Excel spreadsheets. While there are R packages designed to access data from Excel spreadsheets (e.g., gdata, RODBC, XLConnect, xlsx, RExcel), users often find it easier to save their spreadsheets in comma-separated values and then use R’s built in functionality to read and manipulate the data. In this short lesson, we’ll learn how to read data from a .csv and write to a new .csv, and explore the arguments that allow you read and write the data correctly for your needs.
Read a .csv and Explore the Arguments
Let’s start by opening a .csv file containing information on the
speeds at which cars of different colors were clocked in 45 mph zones in
the four-corners states (car-speeds.csv). We will use the
built in read.csv(...) function call, which reads the
data in as a data frame, and assign the data frame to a variable (using
<-) so that it is stored in R’s memory. Then we will
explore some of the basic arguments that can be supplied to the
function. First, open the RStudio project containing the scripts and
data you were working on in episode ‘Analyzing Patient Data’.
R
# Import the data and look at the first six rows
carSpeeds <- read.csv(file = 'data/car-speeds.csv')
head(carSpeeds)
OUTPUT
Color Speed State
1 Blue 32 NewMexico
2 Red 45 Arizona
3 Blue 35 Colorado
4 White 34 Arizona
5 Red 25 Arizona
6 Blue 41 ArizonaChanging Delimiters
The default delimiter of the read.csv() function is a
comma, but you can use other delimiters by supplying the ‘sep’ argument
to the function (e.g., typing sep = ';' allows a semi-colon
separated file to be correctly imported - see ?read.csv()
for more information on this and other options for working with
different file types).
The call above will import the data, but we have not taken advantage of several handy arguments that can be helpful in loading the data in the format we want. Let’s explore some of these arguments.
The header Argument
The default for read.csv(...) is to set the
header argument to TRUE. This means that the
first row of values in the .csv is set as header information (column
names). If your data set does not have a header, set the
header argument to FALSE:
R
# The first row of the data without setting the header argument:
carSpeeds[1, ]
OUTPUT
Color Speed State
1 Blue 32 NewMexicoR
# The first row of the data if the header argument is set to FALSE:
carSpeeds <- read.csv(file = 'data/car-speeds.csv', header = FALSE)
carSpeeds[1, ]
OUTPUT
V1 V2 V3
1 Color Speed StateClearly this is not the desired behavior for this data set, but it may be useful if you have a dataset without headers.
The stringsAsFactors Argument
In older versions of R (prior to 4.0) this was perhaps the most
important argument in read.csv(), particularly if you were
working with categorical data. This is because the default behavior of R
was to convert character strings
into factors, which may make it
difficult to do such things as replace values. It is important to be
aware of this behaviour, which we will demonstrate. For example, let’s
say we find out that the data collector was color blind, and
accidentally recorded green cars as being blue. In order to correct the
data set, let’s replace ‘Blue’ with ‘Green’ in the $Color
column:
R
# Here we will use R's `ifelse` function, in which we provide the test phrase,
# the outcome if the result of the test is 'TRUE', and the outcome if the
# result is 'FALSE'. We will also assign the results to the Color column,
# using '<-'
# First - reload the data with a header
carSpeeds <- read.csv(file = 'data/car-speeds.csv', stringsAsFactors = TRUE)
carSpeeds$Color <- ifelse(carSpeeds$Color == 'Blue', 'Green', carSpeeds$Color)
carSpeeds$Color
OUTPUT
[1] "Green" "1" "Green" "5" "4" "Green" "Green" "2" "5"
[10] "4" "4" "5" "Green" "Green" "2" "4" "Green" "Green"
[19] "5" "Green" "Green" "Green" "4" "Green" "4" "4" "4"
[28] "4" "5" "Green" "4" "5" "2" "4" "2" "2"
[37] "Green" "4" "2" "4" "2" "2" "4" "4" "5"
[46] "2" "Green" "4" "4" "2" "2" "4" "5" "4"
[55] "Green" "Green" "2" "Green" "5" "2" "4" "Green" "Green"
[64] "5" "2" "4" "4" "2" "Green" "5" "Green" "4"
[73] "5" "5" "Green" "Green" "Green" "Green" "Green" "5" "2"
[82] "Green" "5" "2" "2" "4" "4" "5" "5" "5"
[91] "5" "4" "4" "4" "5" "2" "5" "2" "2"
[100] "5" What happened?!? It looks like ‘Blue’ was replaced with ‘Green’, but every other color was turned into a number (as a character string, given the quote marks before and after). This is because the colors of the cars were loaded as factors, and the factor level was reported following replacement.
To see the internal structure, we can use another function,
str(). In this case, the dataframe’s internal structure
includes the format of each column, which is what we are interested in.
str() will be reviewed a little more in the lesson Data Types and Structures.
R
# Reload the data with a header (the previous ifelse call modifies attributes)
carSpeeds <- read.csv(file = 'data/car-speeds.csv', stringsAsFactors = TRUE)
str(carSpeeds)
OUTPUT
'data.frame': 100 obs. of 3 variables:
$ Color: Factor w/ 5 levels " Red","Black",..: 3 1 3 5 4 3 3 2 5 4 ...
$ Speed: int 32 45 35 34 25 41 34 29 31 26 ...
$ State: Factor w/ 4 levels "Arizona","Colorado",..: 3 1 2 1 1 1 3 2 1 2 ...We can see that the $Color and $State
columns are factors and $Speed is a numeric column.
Now, let’s load the dataset using
stringsAsFactors=FALSE, and see what happens when we try to
replace ‘Blue’ with ‘Green’ in the $Color column:
R
carSpeeds <- read.csv(file = 'data/car-speeds.csv', stringsAsFactors = FALSE)
str(carSpeeds)
OUTPUT
'data.frame': 100 obs. of 3 variables:
$ Color: chr "Blue" " Red" "Blue" "White" ...
$ Speed: int 32 45 35 34 25 41 34 29 31 26 ...
$ State: chr "NewMexico" "Arizona" "Colorado" "Arizona" ...R
carSpeeds$Color <- ifelse(carSpeeds$Color == 'Blue', 'Green', carSpeeds$Color)
carSpeeds$Color
OUTPUT
[1] "Green" " Red" "Green" "White" "Red" "Green" "Green" "Black" "White"
[10] "Red" "Red" "White" "Green" "Green" "Black" "Red" "Green" "Green"
[19] "White" "Green" "Green" "Green" "Red" "Green" "Red" "Red" "Red"
[28] "Red" "White" "Green" "Red" "White" "Black" "Red" "Black" "Black"
[37] "Green" "Red" "Black" "Red" "Black" "Black" "Red" "Red" "White"
[46] "Black" "Green" "Red" "Red" "Black" "Black" "Red" "White" "Red"
[55] "Green" "Green" "Black" "Green" "White" "Black" "Red" "Green" "Green"
[64] "White" "Black" "Red" "Red" "Black" "Green" "White" "Green" "Red"
[73] "White" "White" "Green" "Green" "Green" "Green" "Green" "White" "Black"
[82] "Green" "White" "Black" "Black" "Red" "Red" "White" "White" "White"
[91] "White" "Red" "Red" "Red" "White" "Black" "White" "Black" "Black"
[100] "White"That’s better! And we can see how the data now is read as character
instead of factor. From R version 4.0 onwards we do not have to specify
stringsAsFactors=FALSE, this is the default behavior.
The as.is Argument
This is an extension of the stringsAsFactors argument,
but gives you control over individual columns. For example, if we want
the colors of cars imported as strings, but we want the names of the
states imported as factors, we would load the data set as:
R
carSpeeds <- read.csv(file = 'data/car-speeds.csv', as.is = 1)
# Note, the 1 applies as.is to the first column only
Now we can see that if we try to replace ‘Blue’ with ‘Green’ in the
$Color column everything looks fine, while trying to
replace ‘Arizona’ with ‘Ohio’ in the $State column returns
the factor numbers for the names of states that we haven’t replaced:
R
str(carSpeeds)
OUTPUT
'data.frame': 100 obs. of 3 variables:
$ Color: chr "Blue" " Red" "Blue" "White" ...
$ Speed: int 32 45 35 34 25 41 34 29 31 26 ...
$ State: Factor w/ 4 levels "Arizona","Colorado",..: 3 1 2 1 1 1 3 2 1 2 ...R
carSpeeds$Color <- ifelse(carSpeeds$Color == 'Blue', 'Green', carSpeeds$Color)
carSpeeds$Color
OUTPUT
[1] "Green" " Red" "Green" "White" "Red" "Green" "Green" "Black" "White"
[10] "Red" "Red" "White" "Green" "Green" "Black" "Red" "Green" "Green"
[19] "White" "Green" "Green" "Green" "Red" "Green" "Red" "Red" "Red"
[28] "Red" "White" "Green" "Red" "White" "Black" "Red" "Black" "Black"
[37] "Green" "Red" "Black" "Red" "Black" "Black" "Red" "Red" "White"
[46] "Black" "Green" "Red" "Red" "Black" "Black" "Red" "White" "Red"
[55] "Green" "Green" "Black" "Green" "White" "Black" "Red" "Green" "Green"
[64] "White" "Black" "Red" "Red" "Black" "Green" "White" "Green" "Red"
[73] "White" "White" "Green" "Green" "Green" "Green" "Green" "White" "Black"
[82] "Green" "White" "Black" "Black" "Red" "Red" "White" "White" "White"
[91] "White" "Red" "Red" "Red" "White" "Black" "White" "Black" "Black"
[100] "White"R
carSpeeds$State <- ifelse(carSpeeds$State == 'Arizona', 'Ohio', carSpeeds$State)
carSpeeds$State
OUTPUT
[1] "3" "Ohio" "2" "Ohio" "Ohio" "Ohio" "3" "2" "Ohio" "2"
[11] "4" "4" "4" "4" "4" "3" "Ohio" "3" "Ohio" "4"
[21] "4" "4" "3" "2" "2" "3" "2" "4" "2" "4"
[31] "3" "2" "2" "4" "2" "2" "3" "Ohio" "4" "2"
[41] "2" "3" "Ohio" "4" "Ohio" "2" "3" "3" "3" "2"
[51] "Ohio" "4" "4" "Ohio" "3" "2" "4" "2" "4" "4"
[61] "4" "2" "3" "2" "3" "2" "3" "Ohio" "3" "4"
[71] "4" "2" "Ohio" "4" "2" "2" "2" "Ohio" "3" "Ohio"
[81] "4" "2" "2" "Ohio" "Ohio" "Ohio" "4" "Ohio" "4" "4"
[91] "4" "Ohio" "Ohio" "3" "2" "2" "4" "3" "Ohio" "4" We can see that $Color column is a character while
$State is a factor.
Updating Values in a Factor
Suppose we want to keep the colors of cars as factors for some other
operations we want to perform. Write code for replacing ‘Blue’ with
‘Green’ in the $Color column of the cars dataset without
importing the data with stringsAsFactors=FALSE.
R
carSpeeds <- read.csv(file = 'data/car-speeds.csv')
# Replace 'Blue' with 'Green' in cars$Color without using the stringsAsFactors
# or as.is arguments
carSpeeds$Color <- ifelse(as.character(carSpeeds$Color) == 'Blue',
'Green',
as.character(carSpeeds$Color))
# Convert colors back to factors
carSpeeds$Color <- as.factor(carSpeeds$Color)
The strip.white Argument
It is not uncommon for mistakes to have been made when the data were
recorded, for example a space (whitespace) may have been inserted before
a data value. By default this whitespace will be kept in the R
environment, such that ‘\ Red’ will be recognized as a different value
than ‘Red’. In order to avoid this type of error, use the
strip.white argument. Let’s see how this works by checking
for the unique values in the $Color column of our
dataset:
Here, the data recorder added a space before the color of the car in one of the cells:
R
# We use the built-in unique() function to extract the unique colors in our dataset
unique(carSpeeds$Color)
OUTPUT
[1] Green Red White Red Black
Levels: Red Black Green Red WhiteOops, we see two values for red cars.
Let’s try again, this time importing the data using the
strip.white argument. NOTE - this argument must be
accompanied by the sep argument, by which we indicate the
type of delimiter in the file (the comma for most .csv files)
R
carSpeeds <- read.csv(
file = 'data/car-speeds.csv',
stringsAsFactors = FALSE,
strip.white = TRUE,
sep = ','
)
unique(carSpeeds$Color)
OUTPUT
[1] "Blue" "Red" "White" "Black"That’s better!
Specify Missing Data When Loading
It is common for data sets to have missing values, or mistakes. The
convention for recording missing values often depends on the individual
who collected the data and can be recorded as n.a.,
--, or empty cells ” “. R recognises the reserved character
string NA as a missing value, but not some of the examples
above. Let’s say the inflammation scale in the data set we used earlier
inflammation-01.csv actually starts at 1 for
no inflammation and the zero values (0) were a missed
observation. Looking at the ?read.csv help page is there an
argument we could use to ensure all zeros (0) are read in
as NA? Perhaps, in the car-speeds.csv data
contains mistakes and the person measuring the car speeds could not
accurately distinguish between”Black or “Blue” cars. Is there a way to
specify more than one ‘string’, such as “Black” and “Blue”, to be
replaced by NA
R
read.csv(file = "data/inflammation-01.csv", na.strings = "0")
or , in car-speeds.csv use a character vector for
multiple values.
R
read.csv(
file = 'data/car-speeds.csv',
na.strings = c("Black", "Blue")
)
Write a New .csv and Explore the Arguments
After altering our cars dataset by replacing ‘Blue’ with ‘Green’ in
the $Color column, we now want to save the output. There
are several arguments for the write.csv(...) function call, a few of which
are particularly important for how the data are exported. Let’s explore
these now.
R
# Export the first rows of data. The write.csv() function requires a minimum of
# two arguments, the data to be saved and the name of the output file.
write.csv(head(carSpeeds), file = 'data/car-speeds-cleaned.csv')
If you open the file, you’ll see that it has header names, because the data had headers within R, but that there are numbers in the first column.
"","Color","Speed","State"
"1","Blue",32,"NewMexico"
"2","Red",45,"Arizona"
"3","Blue",35,"Colorado"
"4","White",34,"Arizona"
"5","Red",25,"Arizona"
"6","Blue",41,"Arizona"The row.names Argument
This argument allows us to set the names of the rows in the output
data file. R’s default for this argument is TRUE, and since
it does not know what else to name the rows for the cars data set, it
resorts to using row numbers. To correct this, we can set
row.names to FALSE:
R
write.csv(head(carSpeeds), file = 'data/car-speeds-cleaned.csv', row.names = FALSE)
Now we see:
"Color","Speed","State"
"Blue",32,"NewMexico"
"Red",45,"Arizona"
"Blue",35,"Colorado"
"White",34,"Arizona"
"Red",25,"Arizona"
"Blue",41,"Arizona"Setting Column Names
There is also a col.names argument, which can be used to
set the column names for a data set without headers. If the data set
already has headers (e.g., we used the headers = TRUE
argument when importing the data) then a col.names argument
will be ignored.
The na Argument
There are times when we want to specify certain values for
NAs in the data set (e.g., we are going to pass the data to
a program that only accepts -9999 as a nodata value). In this case, we
want to set the NA value of our output file to the desired
value, using the na argument. Let’s see how this works:
R
# First, replace the speed in the 3rd row with NA, by using an index (square
# brackets to indicate the position of the value we want to replace)
carSpeeds$Speed[3] <- NA
head(carSpeeds)
OUTPUT
Color Speed State
1 Blue 32 NewMexico
2 Red 45 Arizona
3 Blue NA Colorado
4 White 34 Arizona
5 Red 25 Arizona
6 Blue 41 ArizonaR
write.csv(carSpeeds, file = 'data/car-speeds-cleaned.csv', row.names = FALSE)
Now we’ll set NA to -9999 when we write the new .csv
file:
R
# Note - the na argument requires a string input
write.csv(head(carSpeeds),
file = 'data/car-speeds-cleaned.csv',
row.names = FALSE,
na = '-9999')
And we see:
"Color","Speed","State"
"Blue",32,"NewMexico"
"Red",45,"Arizona"
"Blue",-9999,"Colorado"
"White",34,"Arizona"
"Red",25,"Arizona"
"Blue",41,"Arizona"Key Points
- Import data from a .csv file using the
read.csv(...)function. - Understand some of the key arguments available for importing the
data properly, including
header,stringsAsFactors,as.is, andstrip.white. - Write data to a new .csv file using the
write.csv(...)function - Understand some of the key arguments available for exporting the
data properly, such as
row.names,col.names, andna.