Manipulating and analyzing data with dplyr

Learning Objectives

Describe the purpose of the dplyr and tidyr packages.

Select certain columns in a data frame with the dplyr function select.

Select certain rows in a data frame according to filtering conditions with the dplyr function filter .

Link the output of one dplyr function to the input of another function with the ‘pipe’ operator %>%.

Add new columns to a data frame that are functions of existing columns with mutate.

Use the split-apply-combine concept for data analysis.

Use summarize, group_by, and count to split a data frame into groups of observations, apply summary statistics for each group, and then combine the results.

Describe the concept of a wide and a long table format and for which purpose those formats are useful.

Describe what key-value pairs are.

Reshape a data frame from long to wide format and back with the pivot_wider and pivot_longer functions from the tidyr package.

Export a data frame to a .csv file.

Data Manipulation using `dplyr` and `tidyr`

Bracket subsetting is handy, but it can be cumbersome and difficult to read, especially for complicated operations. Enter dplyr. dplyr is a package for making tabular data manipulation easier. It pairs nicely with tidyr which enables you to swiftly convert between different data formats for plotting and analysis.

Packages in R are sets of additional functions that let you do more stuff. The functions we’ve been using so far, like str() or data.frame(), come built into R. Adding packages gives you access to more functions. Before you use a package for the first time you need to install it on your machine, and then you should import it in every subsequent R session when you need it. You should already have installed the tidyverse package. This is an “umbrella-package” that installs several packages useful for data analysis which work together well such as tidyr, dplyr, ggplot2, tibble, etc.

Advanced note: The tidyverse package tries to address 3 common issues that arise when doing data analysis with some of the functions that come with R: (1) The results from a base R function sometimes depend on the type of data. (2) Using R expressions in a non standard way, which can be confusing for new learners. (3) Hidden arguments, having default operations that new learners are not aware of.

We have seen in our previous lesson that when building or importing a data frame, the columns that contain characters (i.e., text) are coerced (=converted) into the factor data type. We had to set stringsAsFactors to FALSE to avoid this hidden argument to convert our data type.

This time we will use the tidyverse package to read the data and avoid having to set stringsAsFactors to FALSE

If we haven’t already done so, we can type install.packages("tidyverse") straight into the console. In fact, it’s better to write this in the console than in our script for any package, as there’s no need to re-install packages every time we run the script.

Then, to load the package type:

## load the tidyverse packages, incl. dplyr
library(tidyverse)

What are `dplyr` and `tidyr`?

The package dplyr provides easy tools for the most common data manipulation tasks. It is built to work directly with data frames, with many common tasks optimized by being written in a compiled language (C++). An additional feature is the ability to work directly with data stored in an external database. The benefits of doing this are that the data can be managed natively in a relational database, queries can be conducted on that database, and only the results of the query are returned.

This addresses a common problem with R in that all operations are conducted in-memory and thus the amount of data you can work with is limited by available memory. The database connections essentially remove that limitation in that you can connect to a database of many hundreds of GB, conduct queries on it directly, and pull back into R only what you need for analysis.

The package tidyr addresses the common problem of wanting to reshape your data for plotting and use by different R functions. Sometimes we want data sets where we have one row per measurement. Sometimes we want a data frame where each measurement type has its own column, and rows are instead more aggregated groups - like plots or aquaria. Moving back and forth between these formats is non-trivial, and tidyr gives you tools for this and more sophisticated data manipulation.

To learn more about dplyr and tidyr after the workshop, you may want to check out this handy data transformation with dplyr cheatsheet and this one about tidyr.

We’ll read in our data using the read_csv() function, from the tidyverse package readr, instead of read.csv(). (Note the underscore instead of dot.)

surveys <- read_csv("data_raw/portal_data_joined.csv")

#> Rows: 34786 Columns: 13
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (6): species_id, sex, genus, species, taxa, plot_type
#> dbl (7): record_id, month, day, year, plot_id, hindfoot_length, weight
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

You will see the message Parsed with column specification, followed by each column name and its data type. When you execute read_csv on a data file, it looks through the first 1000 rows of each column and guesses the data type for each column as it reads it into R. For example, in this dataset, read_csv reads weight as col_double (a numeric data type), and species as col_character. You have the option to specify the data type for a column manually by using the col_types argument in read_csv.

## inspect the data
str(surveys)

## preview the data
View(surveys)

Notice that the class of the data is now tbl_df

This is referred to as a “tibble”. Tibbles tweak some of the behaviors of the data frame objects we introduced in the previous episode. The data structure is very similar to a data frame. For our purposes the only differences are that:

In addition to displaying the data type of each column under its name, it only prints the first few rows of data and only as many columns as fit on one screen.
Columns of class character are never converted into factors.

We’re going to learn some of the most common dplyr functions:

select(): subset columns
filter(): subset rows on conditions
mutate(): create new columns by using information from other columns
group_by() and summarize(): create summary statistics on grouped data
arrange(): sort results
count(): count discrete values

Selecting columns and filtering rows

To select columns of a data frame, use select(). The first argument to this function is the data frame (surveys), and the subsequent arguments are the columns to keep.

select(surveys, plot_id, species_id, weight)

To select all columns except certain ones, put a “-” in front of the variable to exclude it.

select(surveys, -record_id, -species_id)

This will select all the variables in surveys except record_id and species_id.

To choose rows based on a specific criterion, use filter():

filter(surveys, year == 1995)

Pipes

What if you want to select and filter at the same time? There are three ways to do this: use intermediate steps, nested functions, or pipes.

With intermediate steps, you create a temporary data frame and use that as input to the next function, like this:

surveys2 <- filter(surveys, weight < 5)
surveys_sml <- select(surveys2, species_id, sex, weight)

This is readable, but can clutter up your workspace with lots of objects that you have to name individually. With multiple steps, that can be hard to keep track of.

You can also nest functions (i.e. one function inside of another), like this:

surveys_sml <- select(filter(surveys, weight < 5), species_id, sex, weight)

This is handy, but can be difficult to read if too many functions are nested, as R evaluates the expression from the inside out (in this case, filtering, then selecting).

The last option, pipes, are a recent addition to R. Pipes let you take the output of one function and send it directly to the next, which is useful when you need to do many things to the same dataset. Pipes in R look like %>% and are made available via the magrittr package, installed automatically with dplyr. If you use RStudio, you can type the pipe with Ctrl + Shift + M if you have a PC or Cmd + Shift + M if you have a Mac.

surveys %>%
  filter(weight < 5) %>%
  select(species_id, sex, weight)

In the above code, we use the pipe to send the surveys dataset first through filter() to keep rows where weight is less than 5, then through select() to keep only the species_id, sex, and weight columns. Since %>% takes the object on its left (either an object or the result of a function call) and passes it as the first argument to the function on its right, we don’t need to explicitly include the data frame as an argument to the filter() and select() functions any more.

Some may find it helpful to read the pipe like the word “then”. For instance, in the above example, we took the data frame surveys, then we filtered for rows with weight < 5, then we selected columns species_id, sex, and weight. The dplyr functions by themselves are somewhat simple, but by combining them into linear workflows with the pipe, we can accomplish more complex manipulations of data frames.

If we want to create a new object with this smaller version of the data, we can assign as the value of a new object using the assignment operator:

surveys_sml <- surveys %>%
  filter(weight < 5) %>%
  select(species_id, sex, weight)

surveys_sml

Challenge

3.1 Using pipes, subset the surveys data to include animals collected before 1995 and retain only the columns year, sex, and weight.
Answer
surveys %>%
    filter(year < 1995) %>%
    select(year, sex, weight)

Mutate

Frequently you’ll want to create new columns based on the values in existing columns, for example to do unit conversions, or to find the ratio of values in two columns. For this we’ll use mutate().

To create a new column of weight in kg:

surveys %>%
  mutate(weight_kg = weight / 1000)

Note that we use the single = symbol here to store the value on the right in the new column named on the left.

You can also create a second new column based on the first new column within the same call of mutate():

surveys %>%
  mutate(weight_kg = weight / 1000,
         weight_lb = weight_kg * 2.2)

If this runs off your screen and you just want to see the first few rows, you can use a pipe to view the head() of the data. (Pipes work with non-dplyr functions, too, as long as the dplyr or magrittr package is loaded).

surveys %>%
  mutate(weight_kg = weight / 1000) %>%
  head()

The first few rows of the output are full of NAs, so if we wanted to remove those we could insert a filter() in the chain:

surveys %>%
  filter(!is.na(weight)) %>%
  mutate(weight_kg = weight / 1000) %>%
  head()

is.na() is a function that determines whether something is an NA. The ! symbol negates the result, so we’re asking for every row where weight is not an NA.

Challenge

3.2 Create a new data frame from the surveys data that meets the following criteria:

contains only the species_id column and a new column called hindfoot_cm, which contains the hindfoot_length values converted to centimeters.

In this hindfoot_cm column, there are no NAs and all values are less than 3.

Hint: think about how the commands should be ordered to produce this data frame
Answer
surveys_hindfoot_cm <- surveys %>%
    filter(!is.na(hindfoot_length)) %>%
    mutate(hindfoot_cm = hindfoot_length / 10) %>%
    filter(hindfoot_cm < 3) %>%
    select(species_id, hindfoot_cm)

Split-apply-combine data analysis and the `summarize()` function

Many data analysis tasks can be approached using the split-apply-combine paradigm: split the data into groups, apply some analysis to each group, and then combine the results. dplyr makes this very easy through the use of the group_by() function and the summarize() function

group_by() creates groups within your data by taking as arguments the column name(s) that contain the categorical variable(s) for which you want to make the groups (e.g. by sex and by species).

group_by() is often used together with summarize(), which collapses each group into a single-row by calculating some summary statistic(s).

So to compute the mean weight by sex, you would group by the sex column and then summarise the weight column:

surveys %>%
  group_by(sex) %>%
  summarize(mean_weight = mean(weight, na.rm = TRUE))

You may also have noticed that the output from these calls doesn’t run off the screen anymore. It’s one of the advantages of tbl_df over data frame.

The big difference between mutate() and summarize() is that mutate() adds columns while summarize() only keeps what you have grouped by and the summaries you have calculated.

You can also group by multiple columns:

surveys %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight, na.rm = TRUE)) %>% 
  tail()

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Here, we used tail() to look at the last six rows of our summary. Before, we had used head() to look at the first six rows. We can see that the sex column contains NA values because some animals had escaped before their sex and body weights could be determined. The resulting mean_weight column does not contain NA but NaN (which refers to “Not a Number”) because mean() was called on a vector of NA values while at the same time setting na.rm = TRUE. To avoid this, we can remove the missing values for weight before we attempt to calculate the summary statistics on weight. Because the missing values are removed first, we can omit na.rm = TRUE when computing the mean:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight))

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Here, again, the output from these calls doesn’t run off the screen anymore. If you want to display more data, you can use the print() function at the end of your chain with the argument n specifying the number of rows to display:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight)) %>%
  print(n = 15)

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Once the data are grouped, you can also summarize multiple variables at the same time (and not necessarily on the same variable). For instance, we could add a column indicating the minimum weight for each species for each sex:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight))

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

It is sometimes useful to rearrange the result of a query to inspect the values. For instance, we can sort on min_weight to put the lighter species first using the arrange() function:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight)) %>%
  arrange(min_weight)

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

To sort in descending order, we need to add the desc() function. If we want to sort the results by decreasing order of mean weight:

surveys %>%
  filter(!is.na(weight)) %>%
  group_by(sex, species_id) %>%
  summarize(mean_weight = mean(weight),
            min_weight = min(weight)) %>%
  arrange(desc(min_weight))

#> `summarise()` has grouped output by 'sex'. You can override using the `.groups`
#> argument.

Counting

When working with data, we often want to know the number of observations found for each factor or combination of factors. For this task, dplyr provides count(). For example, if we wanted to count the number of rows of data for each sex, we would do:

surveys %>%
    count(sex)

The count() function is shorthand for something we’ve already seen: grouping by a variable, and summarizing it by counting the number of observations in that group. In other words, surveys %>% count() is equivalent to:

surveys %>%
    group_by(sex) %>%
    summarise(count = n())

Where n() is a function that gives us the number of rows in a group.

For convenience, count() provides the sort argument:

surveys %>%
    count(sex, sort = TRUE)

If we wanted to count a combination of values, such as sex and species, we would specify the both columns as the arguments of count():

surveys %>%
  count(sex, species)

With the above code, we can proceed with arrange() to sort the table according to a number of criteria so that we have a better comparison. For instance, we might want to arrange the table above in (i) alphabetical order of the species and (ii) descending order of the count:

surveys %>%
  count(sex, species) %>%
  arrange(species, desc(n))

From the table above, we may learn that, for instance, there are 75 observations of the albigula species that have missing data for sex (i.e. NA).

Challenge

3.3 How many animals were caught in each plot_type surveyed?
Answer
surveys %>%
    count(plot_type) 
3.4 Use group_by() and summarize() to find the mean, min, and max hindfoot length for each species (using species_id). Also add the number of observations (hint: see ?n and don’t forget to handle any missing values).
Answer
surveys %>%
    filter(!is.na(hindfoot_length)) %>%
    group_by(species_id) %>%
    summarize(
        mean_hindfoot_length = mean(hindfoot_length),
        min_hindfoot_length = min(hindfoot_length),
        max_hindfoot_length = max(hindfoot_length),
        n = n()
    )
3.5 What was the heaviest animal measured in each year? Return the columns year, genus, species_id, and weight.
Answer
surveys %>%
    filter(!is.na(weight)) %>%
    group_by(year) %>%
    filter(weight == max(weight)) %>%
    select(year, genus, species, weight) %>%
    arrange(year)
3.6 Create a new data frame surveys_1977 that (i) contains only the columns year, plot_type, species, and weight and (ii) contains only the observations from the year 1977 and where weight is not NA.
Answer
surveys_1977 <- surveys %>%
    select(species, plot_type, weight, year) %>%
    filter(year == 1977 & (!is.na(weight)))
3.7 Use group_by() to group surveys_1977 by species and then arrange() by weight. What changes when you set the .by_group argument in arrange() to TRUE?
Answer
surveys_1977 %>% 
    group_by(species) %>% 
    arrange(weight)
surveys_1977 %>% 
    group_by(species) %>% 
    arrange(weight, .by_group = TRUE)

Time for a git commit

Reshaping by pivoting data wider or longer

There are many ways to store data. When working with tidyverse functions, it is helpful to follow the four rules that they define as “tidy data”:

Each variable has its own column
Each observation has its own row
Each value must have its own cell
Each type of observational unit forms a table

For more on this, after the workshop, see this Data Carpentry lesson on handling data and spreadsheets.

Here we examine the fourth rule: Each type of observational unit forms a table.

In surveys, the rows of surveys contain the values of variables associated with each record (the unit), such as the weight or sex of each animal. What if instead of comparing records, we wanted to compare the different mean weight of each genus between plots? (Ignoring plot_type for simplicity).

Note: here, “plot” means an area of land.

We’d need to create a new table where each row (the unit) is comprised of values of variables associated with each plot (so each row would be a plot). In practical terms this means the values in the genus column would become the names of columns and the values within these columns would be the mean weight observed on each plot.

Having created this new table, it would be straightforward to explore the relationship between the weight of different genera within, and between, the plots.

The key point here is that we are still following a tidy data structure, but we have reshaped the data according to the observations of interest: average genus weight per plot instead of records per date.

We can do this transformation with the tidyr function pivot_wider().

Pivoting wider

Note: in older versions of the tidyr package, this function was called spread()

pivot_wider() takes three principal arguments:

the data
the column whose values will become new column names. (The ‘key’ column.)
the column whose values will fill the new column values. (The ‘value’ column.)

Let’s use pivot_wider() to transform surveys to find the mean weight of each genus in each plot over the entire survey period. We use filter(), group_by() and summarise() to filter our observations and variables of interest, and create a new variable for the mean_weight.

surveys_gw <- surveys %>%
  filter(!is.na(weight)) %>%
  group_by(plot_id, genus) %>%
  summarize(mean_weight = mean(weight))

#> `summarise()` has grouped output by 'plot_id'. You can override using the
#> `.groups` argument.

str(surveys_gw)

This yields surveys_gw where the observations for each plot are spread across multiple rows (196 observations of 3 variables).

Using pivot_wider() we can make a new column for each value in the genus column with values for those new columns coming from the mean_weight column.

surveys_wide <- surveys_gw %>%
  pivot_wider(names_from = genus, 
              values_from = mean_weight)

head(surveys_wide)

Here we now have 24 observations of 11 variables, one row for each plot.

After the workshop, see the tidyr documentation for more details. This documentation format is called a ‘vignette’ and is popular in the R community. You may want to use this term when googling.

Pivoting longer

Note: in older versions of the tidyr package, this function was called gather()

The opposing situation could occur if we had been provided with data in the form of surveys_wide, where the genus names are column names, but we wish to treat them as values of a genus variable instead.

In this situation we are gathering the column names and turning them into a pair of new variables. One variable represents the column names as values, and the other variable contains the values previously associated with the column names.

pivot_longer() takes four principal arguments:

the data
which columns we want to gather (pivot on)
the name of the column we wish to create from the column names we will gather. (key)
the name of the column we wish to create that will contain the values that used to be in the gathered colums (values)

To recreate surveys_gw from surveys_wide we would create a key called genus and value called mean_weight and use all columns except plot_id for the key variable. Here we exclude plot_id from being used in the pivot.

surveys_longer <- surveys_wide %>%
  pivot_longer( cols = -plot_id, 
          # columns to pivot into longer format, here we want
          # everything *except* the plot_id (note the minus sign)
          
          names_to = "genus", 
          # name of the new column that will store the old column names
          
          values_to = "mean_weight" 
          # name of the new column that will store the old column values)
  )
head(surveys_longer)
str(surveys_longer)

Why are some words quoted here (“genus” and “mean_weight”) and others are not (plot_id)? It’s because plot_id refers to an existing column in the data frame. The quoted words “genus” and “mean_weight” are the names of new columns. Since the columns don’t exist yet, these words need quotation marks because they don’t refer to variables that exist in R yet. If you don’t include the quotation marks then R will look for a column called genus and will throw an error because it doesn’t exist.

Note that now the NA genera are included in the re-gathered format. Spreading and then gathering can be a useful way to balance out a dataset so every replicate has the same composition.

Alternatively, we could have specified which columns to include in the cols argument (instead of what not to include). This can be useful if you have a large number of identifying columns that you don’t want to pivot longer, because then it’s easier to specify what to pivot (gather) than what to leave alone.

surveys_wide %>%
  pivot_longer( cols = c(Baiomys, Chaetodipus, Dipodomys, Neotoma, 
                         Onychomys, Perognathus, Peromyscus, Reithrodontomys, 
                         Sigmodon, Spermophilus), 
          # columns to pivot into longer format, here we specify
          # all the genera with a vector of names
          names_to = "genus", 
          values_to = "mean_weight" ) %>% 
  head()

There are many shortcuts for selecting columns. For more on that after the workshop, see the tidyr package documentation on pivoting.

As an example, if the columns are directly adjacent, we don’t even need to list them all out - just use the : operator!

surveys_wide %>%
  pivot_longer( cols = Baiomys:Spermophilus, 
          # columns to pivot into longer format, here we specify
          # all the genera between the first and last
          names_to = "genus", 
          values_to = "mean_weight" ) %>% 
  head()

Challenge

3.8 Widen the surveys data frame with years as columns, plot_ids as rows, and the number of genera per plot as the values. You will need to summarize before reshaping. You can use the function n_distinct() to get the number of unique genera within a particular group of data. It’s a powerful function! See ?n_distinct for more.
Answer
surveys_wide_genera <- surveys %>%
  group_by(plot_id, year) %>%
  summarize(n_genera = n_distinct(genus)) %>%
  pivot_wider(names_from = year,
              values_from = n_genera)
#> `summarise()` has grouped output by 'plot_id'. You can override using the
#> `.groups` argument.
head(surveys_wide_genera)
3.9 Now take that data frame and pivot_longer() it again, so each row is a unique plot_id by year combination.
Answer
surveys_wide_genera %>%
  pivot_longer(cols = -plot_id,
               names_to = "year",
               values_to = "n_genera")
3.10 The surveys data set has two measurement columns: hindfoot_length and weight. This makes it difficult to do things like look at the relationship between mean values of each measurement per year in different plot types. Let’s walk through a common solution for this type of problem. First, use pivot_longer() to create a dataset where we have a key column called measurement and a value column that takes on the value of either hindfoot_length or weight. Hint: You’ll need to specify which columns are being pivoted on (gathered). Which columns have the values that we want to put into one column?
Answer
surveys_long <- surveys %>% 
    pivot_longer(cols=c(hindfoot_length,weight),
                 names_to = "measurement",
                 values_to = "value")
3.11 With this new data set (surveys_long): (a) calculate the mean of each measurement in each year for each different plot_type (Hint: How do you need to group your data to answer this question? What column values do you need to summarise?) (b) Then separate out the mean values into separate columns for hindfoot_length and weight using pivot_wider()
Answer
surveys_long %>%
  group_by(year, measurement, plot_type) %>%
  summarize(mean_value = mean(value, na.rm=TRUE)) %>%
  pivot_wider(names_from = measurement, values_from = mean_value)
#> `summarise()` has grouped output by 'year', 'measurement'. You can override
#> using the `.groups` argument.

Exporting data

Now that you have learned how to use dplyr to extract information from or summarize your raw data, you may want to export these new data sets to share them with your collaborators or for archival.

Similar to the read_csv() function used for reading CSV files into R, there is a write_csv() function that generates CSV files from data frames.

Before using write_csv(), we are going to create a new folder, data, in our working directory that will store this generated dataset. We don’t want to write generated datasets in the same directory as our raw data. It’s good practice to keep them separate. The data_raw folder should only contain the raw, unaltered data, and should be left alone to make sure we don’t delete or modify it. In contrast, our script will generate the contents of the data directory, so even if the files it contains are deleted, we can always re-generate them.

In preparation for our next lesson on plotting, we are going to prepare a cleaned up version of the data set that doesn’t include any missing data.

Let’s start by removing observations of animals for which weight and hindfoot_length are missing, or the sex has not been determined:

surveys_complete <- surveys %>%
  filter(!is.na(weight),           # remove missing weight
         !is.na(hindfoot_length),  # remove missing hindfoot_length
         !is.na(sex))                # remove missing sex

Because we are interested in plotting how species abundances have changed through time, we are also going to remove observations for rare species (i.e., that have been observed less than 50 times). We will do this in two steps: first we are going to create a data set that counts how often each species has been observed, and filter out the rare species; then, we will extract only the observations for these more common species:

## Extract the most common species_id 
species_counts_min50 <- surveys_complete %>%
    count(species_id) %>% 
  # count() gets the number of times each species_id occurs in the data
    filter(n >= 50) 
# count() created a column called "n" for its results. Here we keep
# only those rows where the number of times a species_id was observed is > 50

## Only keep the most common species
surveys_complete <- surveys_complete %>%
  filter(species_id %in% species_counts_min50$species_id) 
# remember %in% from the previous lesson?

To make sure that everyone has the same data set, check that surveys_complete has 30463 rows and 13 columns by typing dim(surveys_complete).

If dim(surveys_complete) returns different numbers (e.g. 30521 instead of 30463), make sure the original data was loaded with read_csv and not read.csv. Some NAs are handled differently by the two functions. See for instance the sex column.

Now that our data set is ready, we can save it as a CSV file in our data folder.

write_csv(surveys_complete, path = "data/surveys_complete.csv")

#> Warning: The `path` argument of `write_csv()` is deprecated as of readr 1.4.0.
#> ℹ Please use the `file` argument instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.

Time for a git commit

Summary of functions in this lesson

read_csv() # load a csv formatted file into R memory
str() # check structure of the object and information about the class, length and content of each column
View() # invoke a spreadsheet-style data viewer
select() # select columns of a data frame
filter() # allows you to select a subset of rows in a data frame
%>% # pipes to select and filter at the same time
mutate() # create new columns based on the values in existing columns
head() # shows the first 6 rows
group_by() # split the data into groups (so that you can apply some analysis to each group)
summarize() # collapses each group into a single-row summary of that group
n() # get the the number of rows in your group
mean() # calculate the mean value of a vector
!is.na() # test if there are no missing values
print() # print values to the console
min() # return the minimum value of a vector
arrange() # arrange rows by variables
desc() # transform a vector into a format that will be sorted in descending order (use in arrange())
count() # counts the total number of records for each category
pivot_wider() # reshape a data frame by a key-value pair across multiple columns (new version of spread())
pivot_longer() # reshape a data frame by collapsing into a key-value pair (new version of gather())
n_distinct() # get a count of unique values
write_csv() # save to a csv formatted file

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Manipulating, analyzing and exporting data with tidyverse

Data Carpentry contributors

Manipulating and analyzing data with dplyr

Learning Objectives

Data Manipulation using `dplyr` and `tidyr`

What are `dplyr` and `tidyr`?

Selecting columns and filtering rows

Pipes

Challenge

Answer

Mutate

Challenge

Answer

Split-apply-combine data analysis and the `summarize()` function

Counting

Challenge

Answer

Answer

Answer

Answer

Answer

Reshaping by pivoting data wider or longer

Pivoting wider

Pivoting longer

Challenge

Answer

Answer

Answer

Answer

Exporting data

Summary of functions in this lesson

Manipulating, analyzing and exporting data with tidyverse

Data Carpentry contributors

Manipulating and analyzing data with dplyr

Learning Objectives

Data Manipulation using dplyr and tidyr

What are dplyr and tidyr?

Selecting columns and filtering rows

Pipes

Challenge

Answer

Mutate

Challenge

Answer

Split-apply-combine data analysis and the summarize() function

Counting

Challenge

Answer

Answer

Answer

Answer

Answer

Reshaping by pivoting data wider or longer

Pivoting wider

Pivoting longer

Challenge

Answer

Answer

Answer

Answer

Exporting data

Summary of functions in this lesson

Data Manipulation using `dplyr` and `tidyr`

What are `dplyr` and `tidyr`?

Split-apply-combine data analysis and the `summarize()` function