Starting with data

Learning Objectives

Loading the survey data

We are investigating the animal species diversity and weights found within plots at our study site. The dataset is stored as a comma separated value (CSV) file. Each row holds information for a single animal, and the columns represent:

Column Description
record_id Unique id for the observation
month month of observation
day day of observation
year year of observation
plot_id ID of a particular plot
species_id 2-letter code
sex sex of animal (“M”, “F”)
hindfoot_length length of the hindfoot in mm
weight weight of the animal in grams
genus genus of animal
species species of animal
taxon e.g. Rodent, Reptile, Bird, Rabbit
plot_type type of plot

Downloading the data

We are going to use the R function download.file() to download the CSV file that contains the survey data from Figshare, and we will use read_csv() to load the content of the CSV file into R.

Inside the download.file command, the first entry is a character string with the source URL (“https://ndownloader.figshare.com/files/2292169”). This source URL downloads a CSV file from figshare. The text after the comma (“data_raw/portal_data_joined.csv”) is the destination of the file on your local machine. You’ll need to have a folder on your machine called “data_raw” where you’ll download the file. So this command downloads a file from Figshare, names it “portal_data_joined.csv” and adds it to a preexisting folder named “data_raw”.

download.file(url = "https://ndownloader.figshare.com/files/2292169",
              destfile = "data_raw/portal_data_joined.csv")

Installing the tidyverse package

The file has now been downloaded to the destination you specified, but R has not yet loaded the data from the file into memory. To do this, we can use the read_csv() function from the tidyverse package.

Packages in R are basically sets of additional functions that let you do more stuff. The functions we’ve been using so far, like round(), sqrt(), or c(), come built into R; packages give you access to additional 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.

To install the tidyverse package, 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)

Reading the data into R

Now we can use the functions from the tidyverse package. Let’s use read_csv() to read the data into a data frame (we will learn more about data frames later):

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

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 its data type. 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.

read_csv() assumes that fields are delineated by commas, however, in several countries, the comma is used as a decimal separator and the semicolon (;) is used as a field delineator. If you want to read in this type of files in R, you can use the read_csv2() function. There is also the read_tsv() for tab separated data files and read_delim() for less common formats. Check out the help for read_csv() by typing ?read_csv to learn more.

Inspecting the data

We can see the contents of the first few lines of the data by typing its name: surveys. By default, this will show show you as many rows and columns of the data as fit on your screen. If you wanted to the first 50 rows, you could type print(surveys, n = 50)

We can also extract the first few lines of this data using the function head():

head(surveys)

#> # A tibble: 6 x 13
#>   record_id month   day  year plot_id species_id sex   hindfoot_length
#>       <dbl> <dbl> <dbl> <dbl>   <dbl> <chr>      <chr>           <dbl>
#> 1         1     7    16  1977       2 NL         M                  32
#> 2        72     8    19  1977       2 NL         M                  31
#> 3       224     9    13  1977       2 NL         <NA>               NA
#> 4       266    10    16  1977       2 NL         <NA>               NA
#> 5       349    11    12  1977       2 NL         <NA>               NA
#> 6       363    11    12  1977       2 NL         <NA>               NA
#> # … with 5 more variables: weight <dbl>, genus <chr>, species <chr>,
#> #   taxa <chr>, plot_type <chr>

Unlike the print() function, head() returns the extracted data. You could use it to assign the first 100 rows of surveys to an object using surveys_sample <- head(surveys, 100). This can be useful if you want to try out complex computations on a subset of your data before you apply them to the whole data set. There is a similar function that lets you extract the last few lines of the data set. It is called (you might have guessed it) tail().

To open the dataset in RStudio’s Data Viewer, use the view() function:

view(surveys)

Data Frames

What are data frames?

When we loaded the data into R, it got stored as an object of class tibble, which is a special kind of data frame (the difference is not important for our purposes, but you can learn more about tibbles here). Data frames are the de facto data structure for most tabular data, and what we use for statistics and plotting. Data frames can be created by hand, but most commonly they are generated by functions like read_csv(); in other words, when importing spreadsheets from your hard drive or the web.

A data frame is the representation of data in the format of a table where the columns are vectors that all have the same length. Because columns are vectors, each column must contain a single type of data (e.g., characters, integers, factors). For example, here is a figure depicting a data frame comprising a numeric, a character, and a logical vector.

We can see this also when inspecting the structure of a data frame with the function str():

str(surveys)

Inspecting data frames

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. Let’s try them out!

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

Challenge

Based on the output of str(surveys), can you answer the following questions?

Answer 

str(surveys)

#> tibble [34,786 × 13] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
#>  $ record_id      : num [1:34786] 1 72 224 266 349 363 435 506 588 661 ...
#>  $ month          : num [1:34786] 7 8 9 10 11 11 12 1 2 3 ...
#>  $ day            : num [1:34786] 16 19 13 16 12 12 10 8 18 11 ...
#>  $ year           : num [1:34786] 1977 1977 1977 1977 1977 ...
#>  $ plot_id        : num [1:34786] 2 2 2 2 2 2 2 2 2 2 ...
#>  $ species_id     : chr [1:34786] "NL" "NL" "NL" "NL" ...
#>  $ sex            : chr [1:34786] "M" "M" NA NA ...
#>  $ hindfoot_length: num [1:34786] 32 31 NA NA NA NA NA NA NA NA ...
#>  $ weight         : num [1:34786] NA NA NA NA NA NA NA NA 218 NA ...
#>  $ genus          : chr [1:34786] "Neotoma" "Neotoma" "Neotoma" "Neotoma" ...
#>  $ species        : chr [1:34786] "albigula" "albigula" "albigula" "albigula" ...
#>  $ taxa           : chr [1:34786] "Rodent" "Rodent" "Rodent" "Rodent" ...
#>  $ plot_type      : chr [1:34786] "Control" "Control" "Control" "Control" ...
#>  - attr(*, "spec")=
#>   .. cols(
#>   ..   record_id = col_double(),
#>   ..   month = col_double(),
#>   ..   day = col_double(),
#>   ..   year = col_double(),
#>   ..   plot_id = col_double(),
#>   ..   species_id = col_character(),
#>   ..   sex = col_character(),
#>   ..   hindfoot_length = col_double(),
#>   ..   weight = col_double(),
#>   ..   genus = col_character(),
#>   ..   species = col_character(),
#>   ..   taxa = col_character(),
#>   ..   plot_type = col_character()
#>   .. )
## * class: data frame
## * how many rows: 34786,  how many columns: 13

Indexing and subsetting data frames

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. However, note that different ways of specifying these coordinates lead to results with different classes.

# first element in the first column of the data frame (as a vector)
surveys[1, 1]   
# first element in the 6th column (as a vector)
surveys[1, 6]   
# first column of the data frame (as a vector)
surveys[, 1]    
# first column of the data frame (as a data.frame)
surveys[1]      
# first three rows of the 6th column (as a vector)
surveys[1:3, 6] 
# the 3rd row of the data frame (as a data.frame)
surveys[3, ]    
# equivalent to head_surveys <- head(surveys)
head_surveys <- surveys[1:6, ]

: is a special function that creates numeric vectors of integers in increasing or decreasing order, test 1:10 and 10:1 for instance.

You can also exclude certain indices of a data frame using the “-” sign:

surveys[, -1]          # The whole data frame, except the first column
surveys[-(7:34786), ] # Equivalent to head(surveys)

Data frames can be subset by calling indices (as shown previously), but also by calling their column names directly:

surveys["species_id"]       # Result is a data.frame
surveys[, "species_id"]     # Result is a vector
surveys[["species_id"]]     # Result is a vector
surveys$species_id          # Result is a vector

In RStudio, you can use the autocompletion feature to get the full and correct names of the columns.

Challenge

  1. Create a data.frame (surveys_200) containing only the data in row 200 of the surveys dataset.

  2. Notice how nrow() gave you the number of rows in a data.frame?

    • Use that number to pull out just that last row in the data frame.
    • Compare that with what you see as the last row using tail() to make sure it’s meeting expectations.
    • Pull out that last row using nrow() instead of the row number.
    • Create a new data frame (surveys_last) from that last row.

  3. Use nrow() to extract the row that is in the middle of the data frame. Store the content of this row in an object named surveys_middle.

  4. Combine nrow() with the - notation above to reproduce the behavior of head(surveys), keeping just the first through 6th rows of the surveys dataset.

Answer 

## 1.
surveys_200 <- surveys[200, ]
## 2.
# Saving `n_rows` to improve readability and reduce duplication
n_rows <- nrow(surveys)
surveys_last <- surveys[n_rows, ]
## 3.
surveys_middle <- surveys[n_rows / 2, ]
## 4.
surveys_head <- surveys[-(7:n_rows), ]

Factors

When we did str(surveys) we saw that several of the columns consist of integers. The columns genus, species, sex, plot_type, … however, are of the class character. Arguably, these columns contain categorical data, that is, they can only take on a limited number of values.

R has a special class for working with categorical data, called factor. Factors are very useful and actually contribute to making R particularly well suited to working with data. So we are going to spend a little time introducing them.

Once created, factors can only contain a pre-defined set of values, known as levels. Factors are stored as integers associated with labels and they can be ordered or unordered. While factors look (and often behave) like character vectors, they are actually treated as integer vectors by R. So you need to be very careful when treating them as strings.

When importing a data frame with read_csv(), the columns that contain text are not automatically coerced (=converted) into the factor data type, but once we have loaded the data we can do the conversion using the factor() function:

surveys$sex <- factor(surveys$sex)

We can see that the conversion has worked by using the summary() function again. This produces a table with the counts for each factor level:

summary(surveys$sex)

By default, R always sorts levels in alphabetical order. For instance, if you have a factor with 2 levels:

sex <- factor(c("male", "female", "female", "male"))

R will assign 1 to the level "female" and 2 to the level "male" (because f comes before m, even though the first element in this vector is "male"). You can see this by using the function levels() and you can find the number of levels using nlevels():

levels(sex)
nlevels(sex)

Sometimes, the order of the factors does not matter, other times you might want to specify the order because it is meaningful (e.g., “low”, “medium”, “high”), it improves your visualization, or it is required by a particular type of analysis. Here, one way to reorder our levels in the sex vector would be:

sex # current order

#> [1] male   female female male  
#> Levels: female male
sex <- factor(sex, levels = c("male", "female"))
sex # after re-ordering

#> [1] male   female female male  
#> Levels: male female

In R’s memory, these factors are represented by integers (1, 2, 3), but are more informative than integers because factors are self describing: "female", "male" is more descriptive than 1, 2. Which one is “male”? You wouldn’t be able to tell just from the integer data. Factors, on the other hand, have this information built in. It is particularly helpful when there are many levels (like the species names in our example dataset).

Challenge

  1. Change the columns taxa and genus in the surveys data frame into a factor.

  2. Using the functions you learned before, can you find out…

    • How many rabbits were observed?
    • How many different genera are in the genus column?
Answer 

surveys$genus <- factor(surveys$genus)
summary(surveys)
nlevels(surveys$genus)
## * how many genera: There are 26 unique genera in the `genus` column.
## * how many rabbts: There are 75 rabbits in the `taxa` column.

Converting factors

If you need to convert a factor to a character vector, you use as.character(x).

as.character(sex)

In some cases, you may have to convert factors where the levels appear as numbers (such as concentration levels or years) to a numeric vector. For instance, in one part of your analysis the years might need to be encoded as factors (e.g., comparing average weights across years) but in another part of your analysis they may need to be stored as numeric values (e.g., doing math operations on the years). This conversion from factor to numeric is a little trickier. The as.numeric() function returns the index values of the factor, not its levels, so it will result in an entirely new (and unwanted in this case) set of numbers. One method to avoid this is to convert factors to characters, and then to numbers.

Another method is to use the levels() function. Compare:

year_fct <- factor(c(1990, 1983, 1977, 1998, 1990))
as.numeric(year_fct)               # Wrong! And there is no warning...
as.numeric(as.character(year_fct)) # Works...
as.numeric(levels(year_fct))[year_fct]    # The recommended way.

Notice that in the levels() approach, three important steps occur:

Renaming factors

When your data is stored as a factor, you can use the plot() function to get a quick glance at the number of observations represented by each factor level. Let’s look at the number of males and females captured over the course of the experiment:

## bar plot of the number of females and males captured during the experiment:
plot(surveys$sex)

Howver, as we saw when we used summary(surveys$sex), there are about 1700 individuals for which the sex information hasn’t been recorded. To show them in the plot, we can turn the missing values into a factor level with the addNA() function. We will also have to give the new factor level a label. We are going to work with a copy of the sex column, so we’re not modifying the working copy of the data frame:

sex <- surveys$sex
levels(sex)

#> [1] "F" "M"
sex <- addNA(sex)
levels(sex)

#> [1] "F" "M" NA
head(sex)

#> [1] M    M    <NA> <NA> <NA> <NA>
#> Levels: F M <NA>
levels(sex)[3] <- "undetermined"
levels(sex)

#> [1] "F"            "M"            "undetermined"
head(sex)

#> [1] M            M            undetermined undetermined undetermined
#> [6] undetermined
#> Levels: F M undetermined

Now we can plot the data again, using plot(sex).

Challenge

Answer 

levels(sex)[1:2] <- c("female", "male")
sex <- factor(sex, levels = c("female", "male", "undetermined"))
plot(sex)

Challenge

  1. We have seen how data frames are created when using read_csv(), but they can also be created by hand with the data.frame() function. There are a few mistakes in this hand-crafted data.frame. Can you spot and fix them? Don’t hesitate to experiment!
animal_data <- data.frame(
         animal = c(dog, cat, sea cucumber, sea urchin),
         feel = c("furry", "squishy", "spiny"),
         weight = c(45, 8 1.1, 0.8)
         )

  1. Can you predict the class for each of the columns in the following example? Check your guesses using str(country_climate):

    • Are they what you expected? Why? Why not?
    • What would you need to change to ensure that each column had the accurate data type?
   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)
          )
Answer

  • missing quotations around the names of the animals
  • missing one entry in the feel column (probably for one of the furry animals)
  • missing one comma in the weight column
  • country, climate, temperature, and northern_hemisphere are characters; has_kangaroo is numeric
  • using factor() one could replace character columns with factors columns
  • removing the quotes in temperature and northern_hemisphere and replacing 1 by TRUE in the has_kangaroo column would give what was probably intended

The automatic conversion of data type is sometimes a blessing, sometimes an annoyance. Be aware that it exists, learn the rules, and double check that data you import in R are of the correct type within your data frame. If not, use it to your advantage to detect mistakes that might have been introduced during data entry (for instance, a letter in a column that should only contain numbers).

Learn more in this RStudio tutorial

Formatting dates

One of the most common issues that new (and experienced!) R users have is converting date and time information into a variable that is appropriate and usable during analyses. As a reminder from earlier in this lesson, the best practice for dealing with date data is to ensure that each component of your date is stored as a separate variable. Using str(), We can confirm that our data frame has a separate column for day, month, and year, and that each contains integer values.

str(surveys)

We are going to use the ymd() function from the package lubridate (which belongs to the tidyverse; learn more here). lubridate gets installed as part as the tidyverse installation. When you load the tidyverse (library(tidyverse)), the core packages (the packages used in most data analyses) get loaded. lubridate however does not belong to the core tidyverse, so you have to load it explicitly with library(lubridate)

Start by loading the required package:

library(lubridate)

ymd() takes a vector representing year, month, and day, and converts it to a Date vector. Date is a class of data recognized by R as being a date and can be manipulated as such. The argument that the function requires is flexible, but, as a best practice, is a character vector formatted as “YYYY-MM-DD”.

Let’s create a date object and inspect the structure:

my_date <- ymd("2015-01-01")
str(my_date)

Now let’s paste the year, month, and day separately - we get the same result:

# sep indicates the character to use to separate each component
my_date <- ymd(paste("2015", "1", "1", sep = "-")) 
str(my_date)

Now we apply this function to the surveys dataset. Create a character vector from the year, month, and day columns of surveys using paste():

paste(surveys$year, surveys$month, surveys$day, sep = "-")

This character vector can be used as the argument for ymd():

ymd(paste(surveys$year, surveys$month, surveys$day, sep = "-"))

There is a warning telling us that some dates could not be parsed (understood) by the ymd() function. For these dates, the function has returned NA, which means they are treated as missing values. We will deal with this problem later, but first we add the resulting Date vector to the surveys data frame as a new column called date:

surveys$date <- ymd(paste(surveys$year, surveys$month, surveys$day, sep = "-"))
str(surveys) # notice the new column, with 'date' as the class

Let’s make sure everything worked correctly. One way to inspect the new column is to use summary():

summary(surveys$date)

#>         Min.      1st Qu.       Median         Mean      3rd Qu. 
#> "1977-07-16" "1984-03-12" "1990-07-22" "1990-12-15" "1997-07-29" 
#>         Max.         NA's 
#> "2002-12-31"        "129"

Let’s investigate why some dates could not be parsed.

We can use the functions we saw previously to deal with missing data to identify the rows in our data frame that are failing. If we combine them with what we learned about subsetting data frames earlier, we can extract the columns “year,”month“,”day" from the records that have NA in our new column date. We will also use head() so we don’t clutter the output:

missing_dates <- surveys[is.na(surveys$date), c("year", "month", "day")]

head(missing_dates)

#> # A tibble: 6 x 3
#>    year month   day
#>   <dbl> <dbl> <dbl>
#> 1  2000     9    31
#> 2  2000     4    31
#> 3  2000     4    31
#> 4  2000     4    31
#> 5  2000     4    31
#> 6  2000     9    31

Why did these dates fail to parse? If you had to use these data for your analyses, how would you deal with this situation?

Corrections

If you see mistakes or want to suggest changes, please create an issue on the source repository.

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/datacarpentry/R-ecology-lesson, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".

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