Learning Objectives

Presentation of the Survey Data

We are studying the species and weight of animals caught in plots in our study area. The dataset is stored as a 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
taxa e.g. Rodent, Reptile, Bird, Rabbit
plot_type type of plot

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 into memory (as a data.frame) the content of the CSV file.

To download the data into the data/ subdirectory, do:

download.file("https://ndownloader.figshare.com/files/2292169",
              "data/portal_data_joined.csv")

You are now ready to load the data:

surveys <- read.csv('data/portal_data_joined.csv')

This statement doesn’t produce any output because, as you might recall, assignment doesn’t display anything. If we want to check that our data has been loaded, we can print the variable’s value: surveys.

Wow… that was a lot of output. At least it means the data loaded properly. Let’s check the top (the first 6 lines) of this data.frame using the function head():

head(surveys)
#>   record_id month day year plot_id species_id sex hindfoot_length weight
#> 1         1     7  16 1977       2         NL   M              32     NA
#> 2        72     8  19 1977       2         NL   M              31     NA
#> 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
#>     genus  species   taxa plot_type
#> 1 Neotoma albigula Rodent   Control
#> 2 Neotoma albigula Rodent   Control
#> 3 Neotoma albigula Rodent   Control
#> 4 Neotoma albigula Rodent   Control
#> 5 Neotoma albigula Rodent   Control
#> 6 Neotoma albigula Rodent   Control

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 each column is a vector, they all contain the same type of data. We can see this when inspecting the __str__ucture of a data.frame with the function str():

str(surveys)

Challenge

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

  • What is the class of the object surveys?
  • How many rows and how many columns are in this object?
  • How many species have been recorded during these surveys?

As you can see, many of the columns consist of integers, however, the columns species and sex are of a special class called a factor. Before we learn more about the data.frame class, let’s talk about factors. They are very useful but not necessarily intuitive, and therefore require some attention.

Factors

Factors are used to represent categorical data. Factors can be ordered or unordered, and understanding them is necessary for statistical analysis and for plotting.

Factors are stored as integers, and have labels associated with these unique integers. While factors look (and often behave) like character vectors, they are actually integers under the hood, and you need to be careful when treating them like strings.

Once created, factors can only contain a pre-defined set of values, known as levels. 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 check this by using the function levels(), and check 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”) or it is required by a particular type of analysis. Additionally, specifying the order of the levels allows for level comparison:

food <- factor(c("low", "high", "medium", "high", "low", "medium", "high"))
levels(food)
food <- factor(food, levels=c("low", "medium", "high"))
levels(food)
min(food) ## doesn't work
#> Error in Summary.factor(structure(c(1L, 3L, 2L, 3L, 1L, 2L, 3L), .Label = c("low", : 'min' not meaningful for factors
food <- factor(food, levels=c("low", "medium", "high"), ordered=TRUE)
levels(food)
min(food) ## works!

In R’s memory, these factors are represented by integers (1, 2, 3), but are more informative than integers because factors are self describing: "low", "medium", "high"" is more descriptive than 1, 2, 3. Which is low? 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 in our example data set).

Converting factors

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

Converting factors where the levels appear as numbers (such as concentration levels) to a numeric vector is a little trickier. One method is to convert factors to characters and then numbers. Another method is to use the levels() function. Compare:

f <- factor(c(1, 5, 10, 2))
as.numeric(f)               ## wrong! and there is no warning...
as.numeric(as.character(f)) ## works...
as.numeric(levels(f))[f]    ## The recommended way.

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

  • We obtain all the factor levels using levels(f)
  • We convert these levels to numeric values using as.numeric(levels(f))
  • We then access these numeric values using the underlying integers of the vector f inside the square brackets

Challenge

The function plot() can be used to quickly create a bar plot of a factor. For instance, for the factor exprmt <- factor(c("treat1", "treat2", "treat1", "treat3", "treat1", "control", "treat1", "treat2", "treat3")), the code plot(exprmt) gives you a barplot of the number of observations at each level, as shown below.

  • What determines the order in which the treatments are listed in the plot? (Hint: use str to inspect the factor.)
  • How can you recreate this plot with “control” listed last instead of first?