This lesson is being piloted (Beta version)

Starting with Data

Overview

Teaching: 50 min
Exercises: 30 min
Questions
  • What is a data.frame?

  • How can I read a complete csv file into R?

  • How can I get basic summary information about my dataset?

  • How can I change the way R treats strings in my dataset?

  • Why would I want strings to be treated differently?

  • How are dates represented in R and how can I change the format?

Objectives
  • Describe what a data frame is.

  • Load external data from a .csv file into a data frame.

  • Summarize the contents of a data frame.

  • Describe the difference between a factor and a string.

  • Convert between strings and factors.

  • Reorder and rename factors.

  • Change how character strings are handled in a data frame.

  • Examine and change date formats.

Presentation of the SAFI Data

SAFI (Studying African Farmer-Led Irrigation) is a study looking at farming and irrigation methods in Tanzania and Mozambique. The survey data was collected through interviews conducted between November 2016 and June 2017. For this lesson, we will be using a subset of the available data. For information about the full teaching dataset used in other lessons in this workshop, see the dataset description.

We will be using a subset of the cleaned version of the dataset that was produced through cleaning in OpenRefine. Each row holds information for a single interview respondent, and the columns represent:

column_name description
key_id Added to provide a unique Id for each observation. (The InstanceID field does this as well but it is not as convenient to use)
village Village name
interview_date Date of interview
no_membrs How many members in the household?
years_liv How many years have you been living in this village or neighboring village?
respondent_wall_type What type of walls does their house have (from list)
rooms How many rooms in the main house are used for sleeping?
memb_assoc Are you a member of an irrigation association?
affect_conflicts Have you been affected by conflicts with other irrigators in the area?
liv_count Number of livestock owned.
items_owned Which of the following items are owned by the household? (list)
no_meals How many meals do people in your household normally eat in a day?
months_lack_food Indicate which months, In the last 12 months have you faced a situation when you did not have enough food to feed the household?
instanceID Unique identifier for the form data submission

You are going load the data in R’s memory using the function read_csv() from the readr package which is part of the tidyverse. So, before we can use the read_csv() function, we need to load the package. Also, if you recall, the missing data is encoded as “NULL” in the dataset. We’ll tell it to the function, so R will automatically convert all the “NULL” entries in the dataset into NA.

library(tidyverse)
interviews <- read_csv("data/SAFI_clean.csv", na = "NULL")

This statement creates a data frame but doesn’t show any data because, as you might recall, assignments don’t display anything. (Note, however, that read_csv may show informational text about the data frame that is created.) If we want to check that our data has been loaded, we can see the contents of the data frame by typing its name: interviews.

interviews
## Try also
## View(interviews)
## head(interviews)
# A tibble: 131 x 14
   key_ID village interview_date      no_membrs years_liv respondent_wall…
    <dbl> <chr>   <dttm>                  <dbl>     <dbl> <chr>           
 1      1 God     2016-11-17 00:00:00         3         4 muddaub         
 2      1 God     2016-11-17 00:00:00         7         9 muddaub         
 3      3 God     2016-11-17 00:00:00        10        15 burntbricks     
 4      4 God     2016-11-17 00:00:00         7         6 burntbricks     
 5      5 God     2016-11-17 00:00:00         7        40 burntbricks     
 6      6 God     2016-11-17 00:00:00         3         3 muddaub         
 7      7 God     2016-11-17 00:00:00         6        38 muddaub         
 8      8 Chirod… 2016-11-16 00:00:00        12        70 burntbricks     
 9      9 Chirod… 2016-11-16 00:00:00         8         6 burntbricks     
10     10 Chirod… 2016-12-16 00:00:00        12        23 burntbricks     
# … with 121 more rows, and 8 more variables: rooms <dbl>,
#   memb_assoc <chr>, affect_conflicts <chr>, liv_count <dbl>,
#   items_owned <chr>, no_meals <dbl>, months_lack_food <chr>,
#   instanceID <chr>

Note

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. It behaves exactly like read_csv but uses different parameters for the decimal and the field separators. If you are working with another format, they can be both specified by the user. Check out the help for read_csv() by typing ?read_csv to learn more. There is also the read_tsv() for tab-separated data files, and read_delim() allows you to specify more details about the structure of your file.

What are data frames and tibbles?

Data frames are the de facto data structure for tabular data in R, and what we use for data processing, statistics, and plotting.

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.

A data frame can be created by hand, but most commonly they are generated by the functions read_csv() or read_table(); in other words, when importing spreadsheets from your hard drive (or the web).

A tibble is an extension of R data frames used by the tidyverse. When the data is read using read_csv(), it is stored in an object of class tbl_df, tbl, and data.frame. You can see the class of an object with

class(interviews)
[1] "spec_tbl_df" "tbl_df"      "tbl"         "data.frame" 

As a tibble, the type of data included in each column is listed in an abbreviated fashion below the column names. For instance, here key_ID is a column of integers (abbreviated <int>), village is a column of characters (<chr>) and the interview_date is a column in the “date and time” format (<dttm>).

Inspecting data frames

When calling a tbl_df object (like interviews here), there is already a lot of information about our data frame being displayed such as the number of rows, the number of columns, the names of the columns, and as we just saw the class of data stored in each column. However, there are functions to extract this information from data frames. Here is a non-exhaustive list of some of these functions. Let’s try them out!

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

Indexing and subsetting data frames

Our interviews 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)
interviews[1, 1]
# A tibble: 1 x 1
  key_ID
   <dbl>
1      1
## first element in the 6th column (as a vector)
interviews[1, 6]
# A tibble: 1 x 1
  respondent_wall_type
  <chr>               
1 muddaub             
## first column of the data frame (as a vector)
interviews[[1]]
  [1]   1   1   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
 [18]  18  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34
 [35]  35  36  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51
 [52]  52  21  54  55  56  57  58  59  60  61  62  63  64  65  66  67  68
 [69]  69  70  71 127 133 152 153 155 178 177 180 181 182 186 187 195 196
 [86] 197 198 201 202  72  73  76  83  85  89 101 103 102  78  80 104 105
[103] 106 109 110 113 118 125 119 115 108 116 117 144 143 150 159 160 165
[120] 166 167 174 175 189 191 192 126 193 194 199 200
## first column of the data frame (as a data.frame)
interviews[1]
# A tibble: 131 x 1
   key_ID
    <dbl>
 1      1
 2      1
 3      3
 4      4
 5      5
 6      6
 7      7
 8      8
 9      9
10     10
# … with 121 more rows
## first three elements in the 7th column (as a vector)
interviews[1:3, 7]
# A tibble: 3 x 1
  rooms
  <dbl>
1     1
2     1
3     1
## the 3rd row of the data frame (as a data.frame)
interviews[3, ]
# A tibble: 1 x 14
  key_ID village interview_date      no_membrs years_liv respondent_wall…
   <dbl> <chr>   <dttm>                  <dbl>     <dbl> <chr>           
1      3 God     2016-11-17 00:00:00        10        15 burntbricks     
# … with 8 more variables: rooms <dbl>, memb_assoc <chr>,
#   affect_conflicts <chr>, liv_count <dbl>, items_owned <chr>,
#   no_meals <dbl>, months_lack_food <chr>, instanceID <chr>
## equivalent to head_interviews <- head(interviews)
head_interviews <- interviews[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:

interviews[, -1]          # The whole data frame, except the first column
# A tibble: 131 x 13
   village interview_date      no_membrs years_liv respondent_wall… rooms
   <chr>   <dttm>                  <dbl>     <dbl> <chr>            <dbl>
 1 God     2016-11-17 00:00:00         3         4 muddaub              1
 2 God     2016-11-17 00:00:00         7         9 muddaub              1
 3 God     2016-11-17 00:00:00        10        15 burntbricks          1
 4 God     2016-11-17 00:00:00         7         6 burntbricks          1
 5 God     2016-11-17 00:00:00         7        40 burntbricks          1
 6 God     2016-11-17 00:00:00         3         3 muddaub              1
 7 God     2016-11-17 00:00:00         6        38 muddaub              1
 8 Chirod… 2016-11-16 00:00:00        12        70 burntbricks          3
 9 Chirod… 2016-11-16 00:00:00         8         6 burntbricks          1
10 Chirod… 2016-12-16 00:00:00        12        23 burntbricks          5
# … with 121 more rows, and 7 more variables: memb_assoc <chr>,
#   affect_conflicts <chr>, liv_count <dbl>, items_owned <chr>,
#   no_meals <dbl>, months_lack_food <chr>, instanceID <chr>
interviews[-c(7:131), ]   # Equivalent to head(interviews)
# A tibble: 6 x 14
  key_ID village interview_date      no_membrs years_liv respondent_wall…
   <dbl> <chr>   <dttm>                  <dbl>     <dbl> <chr>           
1      1 God     2016-11-17 00:00:00         3         4 muddaub         
2      1 God     2016-11-17 00:00:00         7         9 muddaub         
3      3 God     2016-11-17 00:00:00        10        15 burntbricks     
4      4 God     2016-11-17 00:00:00         7         6 burntbricks     
5      5 God     2016-11-17 00:00:00         7        40 burntbricks     
6      6 God     2016-11-17 00:00:00         3         3 muddaub         
# … with 8 more variables: rooms <dbl>, memb_assoc <chr>,
#   affect_conflicts <chr>, liv_count <dbl>, items_owned <chr>,
#   no_meals <dbl>, months_lack_food <chr>, instanceID <chr>

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

interviews["village"]       # Result is a data frame
interviews[, "village"]     # Result is a data frame
interviews[["village"]]     # Result is a vector
interviews$village          # Result is a vector

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

Exercise

  1. Create a data frame (interviews_100) containing only the data in row 100 of the interviews 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 (interviews_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 interviews_middle.

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

Solution

## 1.
interviews_100 <- interviews[100, ]
## 2.
# Saving `n_rows` to improve readability and reduce duplication
n_rows <- nrow(interviews)
interviews_last <- interviews[n_rows, ]
## 3.
interviews_middle <- interviews[n_rows / 2, ]
## 4.
interviews_head <- interviews[-(7:n_rows), ]

Factors

R has a special data class, called factor, to deal with categorical data that you may encounter when creating plots or doing statistical analyses. 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.

Factors represent categorical data. They 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.

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:

respondent_floor_type <- factor(c("earth", "cement", "cement", "earth"))

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

levels(respondent_floor_type)
[1] "cement" "earth" 
nlevels(respondent_floor_type)
[1] 2

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 respondent_floor_type vector would be:

respondent_floor_type # current order
[1] earth  cement cement earth 
Levels: cement earth
respondent_floor_type <- factor(respondent_floor_type, levels = c("earth", "cement"))
respondent_floor_type # after re-ordering
[1] earth  cement cement earth 
Levels: earth cement

In R’s memory, these factors are represented by integers (1, 2), but are more informative than integers because factors are self describing: "cement", "earth" is more descriptive than 1, and 2. Which one is “earth”? 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. It also makes renaming levels easier. Let’s say we made a mistake and need to recode “cement” to “brick”.

levels(respondent_floor_type)
[1] "earth"  "cement"
levels(respondent_floor_type)[2] <- "brick"
levels(respondent_floor_type)
[1] "earth" "brick"
respondent_floor_type
[1] earth brick brick earth
Levels: earth brick

Converting factors

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

as.character(respondent_floor_type)
[1] "earth" "brick" "brick" "earth"

Converting factors where the levels appear as numbers (such as concentration levels, or years) to a numeric vector 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...
[1] 3 2 1 4 3
as.numeric(as.character(year_fct))       # Works...
[1] 1990 1983 1977 1998 1990
as.numeric(levels(year_fct))[year_fct]   # The recommended way.
[1] 1990 1983 1977 1998 1990

Notice that in the recommended 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 extract the memb_assoc column from our data frame, convert it into a factor, and use it to look at the number of interview respondents who were or were not members of an irrigation association:

## create a vector from the data frame column "memb_assoc"
memb_assoc <- interviews$memb_assoc
## convert it into a factor
memb_assoc <- as.factor(memb_assoc)
## let's see what it looks like
memb_assoc
  [1] <NA> yes  <NA> <NA> <NA> <NA> no   yes  no   no   <NA> yes  no   <NA>
 [15] yes  <NA> <NA> <NA> <NA> <NA> no   <NA> <NA> no   no   no   <NA> no  
 [29] yes  <NA> <NA> yes  no   yes  yes  yes  <NA> yes  <NA> yes  <NA> no  
 [43] no   <NA> no   no   yes  <NA> <NA> yes  <NA> no   yes  no   <NA> yes 
 [57] no   no   <NA> no   yes  <NA> <NA> <NA> no   yes  no   no   no   no  
 [71] yes  <NA> no   yes  <NA> <NA> yes  no   no   yes  no   no   yes  no  
 [85] yes  no   no   <NA> yes  yes  yes  yes  yes  no   no   no   no   yes 
 [99] no   no   yes  yes  no   <NA> no   no   <NA> no   no   <NA> no   <NA>
[113] <NA> no   no   no   no   yes  no   no   no   no   no   no   no   no  
[127] no   no   no   yes  <NA>
Levels: no yes
## bar plot of the number of interview respondents who were
## members of irrigation association:
plot(memb_assoc)

plot of chunk factor-plot-default-order

Looking at the plot compared to the output of the vector, we can see that n addition to “no”s and “yes”s, there are about some respondents for which the information about whether they were part of an irrigation association hasn’t been recorded, and encoded as missing data. They do not appear on the plot. Let’s encode them differently so they can counted and visualized in our plot.

## Let's recreate the vector from the data frame column "memb_assoc"
memb_assoc <- interviews$memb_assoc
## replace the missing data with "undetermined"
memb_assoc[is.na(memb_assoc)] <- "undetermined"
## convert it into a factor
memb_assoc <- as.factor(memb_assoc)
## let's see what it looks like
memb_assoc
  [1] undetermined yes          undetermined undetermined undetermined
  [6] undetermined no           yes          no           no          
 [11] undetermined yes          no           undetermined yes         
 [16] undetermined undetermined undetermined undetermined undetermined
 [21] no           undetermined undetermined no           no          
 [26] no           undetermined no           yes          undetermined
 [31] undetermined yes          no           yes          yes         
 [36] yes          undetermined yes          undetermined yes         
 [41] undetermined no           no           undetermined no          
 [46] no           yes          undetermined undetermined yes         
 [51] undetermined no           yes          no           undetermined
 [56] yes          no           no           undetermined no          
 [61] yes          undetermined undetermined undetermined no          
 [66] yes          no           no           no           no          
 [71] yes          undetermined no           yes          undetermined
 [76] undetermined yes          no           no           yes         
 [81] no           no           yes          no           yes         
 [86] no           no           undetermined yes          yes         
 [91] yes          yes          yes          no           no          
 [96] no           no           yes          no           no          
[101] yes          yes          no           undetermined no          
[106] no           undetermined no           no           undetermined
[111] no           undetermined undetermined no           no          
[116] no           no           yes          no           no          
[121] no           no           no           no           no          
[126] no           no           no           no           yes         
[131] undetermined
Levels: no undetermined yes
## bar plot of the number of interview respondents who were
## members of irrigation association:
plot(memb_assoc)

plot of chunk factor-plot-reorder

Exercise

  • Rename the levels of the factor to have the first letter in uppercase: “No”,”Undetermined”, and “Yes”.

  • Now that we have renamed the factor level to “Undetermined”, can you recreate the barplot such that “Undetermined” is last (after “Yes”)?

Solution

levels(memb_assoc) <- c("No", "Undetermined", "Yes")
memb_assoc <- factor(memb_assoc, levels = c("No", "Yes", "Undetermined"))
plot(memb_assoc)

plot of chunk factor-plot-exercise

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. In our dataset, we have a column interview_date which contains information about the year, month, and day that the interview was conducted. Let’s convert those dates into three separate columns.

str(interviews)

We are going to use the package lubridate (which belongs to the tidyverse; learn more here) to work with dates. 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)

The lubridate function 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 extract our interview_date column and inspect the structure:

dates <- interviews$interview_date
str(dates)
 POSIXct[1:131], format: "2016-11-17" "2016-11-17" "2016-11-17" "2016-11-17" "2016-11-17" ...

When we imported the data in R, read_csv() recognized that this column contained date information. We can now use the day(), month() and year() functions to extract this information from the date, and create new columns in our data frame to store it:

interviews$day <- day(dates)
interviews$month <- month(dates)
interviews$year <- year(dates)
interviews
# A tibble: 131 x 17
   key_ID village interview_date      no_membrs years_liv respondent_wall…
    <dbl> <chr>   <dttm>                  <dbl>     <dbl> <chr>           
 1      1 God     2016-11-17 00:00:00         3         4 muddaub         
 2      1 God     2016-11-17 00:00:00         7         9 muddaub         
 3      3 God     2016-11-17 00:00:00        10        15 burntbricks     
 4      4 God     2016-11-17 00:00:00         7         6 burntbricks     
 5      5 God     2016-11-17 00:00:00         7        40 burntbricks     
 6      6 God     2016-11-17 00:00:00         3         3 muddaub         
 7      7 God     2016-11-17 00:00:00         6        38 muddaub         
 8      8 Chirod… 2016-11-16 00:00:00        12        70 burntbricks     
 9      9 Chirod… 2016-11-16 00:00:00         8         6 burntbricks     
10     10 Chirod… 2016-12-16 00:00:00        12        23 burntbricks     
# … with 121 more rows, and 11 more variables: rooms <dbl>,
#   memb_assoc <chr>, affect_conflicts <chr>, liv_count <dbl>,
#   items_owned <chr>, no_meals <dbl>, months_lack_food <chr>,
#   instanceID <chr>, day <int>, month <dbl>, year <dbl>

Notice the three new columns at the end of our data frame.

Key Points

  • Use read.csv to read tabular data in R.

  • Use factors to represent categorical data in R.