L3: Dplyr and Basic Visualization

Bogdan G. Popescu

bogdan.popescu@johncabot.edu

John Cabot University

Background

Dplyr and Basic Visualization

Today, we’ll learn how to:

Load and inspect real-world datasets
Clean and prepare data for analysis
Use dplyr to group and summarize values
Join datasets using a common key
Create and customize scatterplots using ggplot2

Using R

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Using R

Then type:

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Using R

Opening the File

We first remove what we had previously

# Remove all objects from memory
rm(list = ls())

Opening a File

Download the following datasets from Dropbox:

Place them in your working directory or folder.

Opening the File

To get the file path we simply go to the relevant folder

# This opens a file dialog to select your file
file_path <- file.choose()
file_path

Opening the File

Once we have the path, we can now read the files:

# Defining Paths
file_path <- "/Users/bgpopescu/Library/CloudStorage/Dropbox/john_cabot/teaching/research_workshop/lecture7/data/"
# Use file.path() to construct full path
life_expectancy_df <- read.csv(file.path(file_path, "life-expectancy.csv"))
urbanization_df <- read.csv(file.path(file_path, "share-of-population-urban.csv"))

What We Want to Do

Explanation

These are our datasets

Measures of Central Tendency

When we collect data, we often want to summarize it with a single number.
Measures of central tendency tell us what a “typical” or “central” value looks like.

What Are Measures of Central Tendency?

Mean: the arithmetic average
Median: the middle value
(and also the mode: the most frequent value — used less often in quantitative analysis)

What We Want to Do

Explanation

These are our datasets

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Explanation

This is what this looks like in code:

library(dplyr)
life_expectancy_df2 <- life_expectancy_df %>%
  dplyr::group_by(Code) %>%
  dplyr::summarize(life_exp_mean=mean(Life.expectancy.at.birth..historical.))

Note that %>% is called a pipe operator.
It allows you you “pipe” an object forward to a function.

You may also sometimes encounter the |> sign.
It has the same role.

library(dplyr)
life_expectancy_df2 <- life_expectancy_df |>
  dplyr::group_by(Code) |>
  dplyr::summarize(life_exp_mean=mean(Life.expectancy.at.birth..historical.))

What We Want to Do

Explanation

You could also write:

library(dplyr)
life_expectancy_df2 <- life_expectancy_df %>%
  group_by(Code) %>%
  summarize(life_exp_mean=mean(Life.expectancy.at.birth..historical.))

instead of:

library(dplyr)
life_expectancy_df2 <- life_expectancy_df %>%
  dplyr::group_by(Code) %>%
  dplyr::summarize(life_exp_mean=mean(Life.expectancy.at.birth..historical.))

The reason for including dplyr:: is because other libraries have functions like group_by.

Not including the library name can lead to unexpected behavior.

What We Want to Do

Explanation

Finally, we can also write this, if we have NAs:

library(dplyr)
life_expectancy_df2 <- life_expectancy_df%>%
  dplyr::group_by(Code)%>%
  dplyr::summarize(life_exp_mean=mean(Life.expectancy.at.birth..historical., na.rm=TRUE))

This allows us to ignore the NA values that might exist within a variable.

For simplicity, we will not include the na.rm=TRUE code.

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Explanation

Calculating Mean

The mean describes the average value of a variable.

It is calculated as:

\[ \bar{x} = \frac{x_1 + x_2 + \dots + x_n}{n} = \frac{\sum x_i}{n} \]

The mean uses all values in the dataset or in a group

Note: \(\sum x_i\) is the sigma summation notation

Calculating Mean

Not resistant to outliers

Extreme values can pull the mean up or down
Example:
Dataset = [10, 11, 12, 13, 100]
Mean = 29.2 (misleading!)

Great for symmetric distributions, less reliable for skewed ones
One extreme value (100) drastically raises the mean, even though most values are in the low teens.

Calculating Mean

In your case, we can calculate the mean for all the values in life expectancy

mean(life_expectancy_df$Life.expectancy.at.birth..historical., na.rm=TRUE)

[1] 61.78467

Central Tendency: Median

The median is the middle value in a dataset ordered from smallest to largest.
It splits the dataset into two equal halves.

If the number of observations is odd:
- Median = middle number
- Example:
  Data = [1, 3, 7] → Median = 3

If the number of observations is even:
- Median = average of the two middle values
- Example:
  Data = [1, 3, 5, 7] → Median = ( = 4)

Central Tendency: Median

Resistant to outliers:

Unlike the mean, the median is not pulled by extreme values.
Example:
Data = [1, 3, 5, 7, 100] →
Median = 5, while Mean = 23.2

Calculating Median

In your case, we can calculate the median for all the values in life expectancy

median(life_expectancy_df$Life.expectancy.at.birth..historical., na.rm=TRUE)

[1] 64.3

Measures of Dispersion

Intro

Central tendency tells us the center of a distribution…
But what about spread?

Why Dispersion Matters

Two datasets can have the same mean but very different variability
Measures of dispersion tell us how spread out the values are

Measures of Dispersion

Common Measures

Range:
\[\text{Range} = \text{Max} - \text{Min}\]

Variance:
\[s^2 = \frac{1}{n - 1} \sum_{i=1}^{n} (x_i - \bar{x})^2\]

where:
- \(y_i\) stands for the ith value
- \(\bar{x}\) is the population mean of the variable
- n - is the population size

Measures of Dispersion

Common Measures

Standard Deviation:
\[s = \sqrt{s^2}\] (Gives average distance from the mean)

Calculating Range

In your case, we can calculate the range for all the values in life expectancy

min_max <- range(life_expectancy_df$Life.expectancy.at.birth..historical., na.rm=TRUE)
print(min_max)

[1] 12.0 86.5

This means that the minimum value of life expectancy is 12

min_max[1]

[1] 12

This means that the maximum value of life expectancy is 86.5

min_max[2]

[1] 86.5

range_value <- min_max[2] - min_max[1]
print(range_value)

[1] 74.5

Calculating Range

range_value <- min_max[2] - min_max[1]
print(range_value)

[1] 74.5

Thus, the difference is 74.5.

Calculating Variance

This is how we calculate the variance

var(life_expectancy_df$Life.expectancy.at.birth..historical., na.rm=TRUE)

[1] 167.3311

This is how we calculate the standard deviation

sd(life_expectancy_df$Life.expectancy.at.birth..historical., na.rm=TRUE)

[1] 12.93565

sqrt(var(life_expectancy_df$Life.expectancy.at.birth..historical., na.rm=TRUE))

[1] 12.93565

What We Want to Do

Recap Dplyr Functions: `group_by` and `summarize`

Doing it

1. Calculating Average by Country Code

This is what this looks like in code for life_expectancy_df2:

library(dplyr)
life_expectancy_df2 <- life_expectancy_df%>%
  dplyr::group_by(Code)%>%
  dplyr::summarize(life_exp_mean=mean(Life.expectancy.at.birth..historical.))

This is what this looks like in code for urbanization_df2:

urbanization_df2 <- urbanization_df%>%
  dplyr::group_by(Code)%>%
  dplyr::summarize(urb_mean=mean(Urban.population....of.total.population.))

Doing it

2. Inspect the first entries

This is how we inspect the first entries for life_expectancy_df2:

head(life_expectancy_df2, n=3)

This corresponds to the first three entries of the dataframe:

Doing it

2. Inspect the first entries

This is how we inspect the first entries for life_expectancy_df2:

head(life_expectancy_df2, n=3)

This corresponds to the first three entries of the dataframe:

Doing it

2. Inspect the first entries

This is how we inspect the first entries for urbanization_df2:

head(urbanization_df2, n=3)

This corresponds to the first three entries of the dataframe:

Doing it

2. Inspect the first entries

This is how we inspect the first entries for urbanization_df2:

head(urbanization_df2, n=3)

This corresponds to the first three entries of the dataframe:

Doing it

2. Inspect the first entries

We notice the country codes.

unique(life_expectancy_df2$Code)

  [1] ""         "ABW"      "AFG"      "AGO"      "AIA"      "ALB"     
  [7] "AND"      "ARE"      "ARG"      "ARM"      "ASM"      "ATG"     
 [13] "AUS"      "AUT"      "AZE"      "BDI"      "BEL"      "BEN"     
 [19] "BES"      "BFA"      "BGD"      "BGR"      "BHR"      "BHS"     
 [25] "BIH"      "BLR"      "BLZ"      "BMU"      "BOL"      "BRA"     
 [31] "BRB"      "BRN"      "BTN"      "BWA"      "CAF"      "CAN"     
 [37] "CHE"      "CHL"      "CHN"      "CIV"      "CMR"      "COD"     
 [43] "COG"      "COK"      "COL"      "COM"      "CPV"      "CRI"     
 [49] "CUB"      "CUW"      "CYM"      "CYP"      "CZE"      "DEU"     
 [55] "DJI"      "DMA"      "DNK"      "DOM"      "DZA"      "ECU"     
 [61] "EGY"      "ERI"      "ESH"      "ESP"      "EST"      "ETH"     
 [67] "FIN"      "FJI"      "FLK"      "FRA"      "FRO"      "FSM"     
 [73] "GAB"      "GBR"      "GEO"      "GGY"      "GHA"      "GIB"     
 [79] "GIN"      "GLP"      "GMB"      "GNB"      "GNQ"      "GRC"     
 [85] "GRD"      "GRL"      "GTM"      "GUF"      "GUM"      "GUY"     
 [91] "HKG"      "HND"      "HRV"      "HTI"      "HUN"      "IDN"     
 [97] "IMN"      "IND"      "IRL"      "IRN"      "IRQ"      "ISL"     
[103] "ISR"      "ITA"      "JAM"      "JEY"      "JOR"      "JPN"     
[109] "KAZ"      "KEN"      "KGZ"      "KHM"      "KIR"      "KNA"     
[115] "KOR"      "KWT"      "LAO"      "LBN"      "LBR"      "LBY"     
[121] "LCA"      "LIE"      "LKA"      "LSO"      "LTU"      "LUX"     
[127] "LVA"      "MAC"      "MAF"      "MAR"      "MCO"      "MDA"     
[133] "MDG"      "MDV"      "MEX"      "MHL"      "MKD"      "MLI"     
[139] "MLT"      "MMR"      "MNE"      "MNG"      "MNP"      "MOZ"     
[145] "MRT"      "MSR"      "MTQ"      "MUS"      "MWI"      "MYS"     
[151] "MYT"      "NAM"      "NCL"      "NER"      "NGA"      "NIC"     
[157] "NIU"      "NLD"      "NOR"      "NPL"      "NRU"      "NZL"     
[163] "OMN"      "OWID_KOS" "OWID_WRL" "PAK"      "PAN"      "PER"     
[169] "PHL"      "PLW"      "PNG"      "POL"      "PRI"      "PRK"     
[175] "PRT"      "PRY"      "PSE"      "PYF"      "QAT"      "REU"     
[181] "ROU"      "RUS"      "RWA"      "SAU"      "SDN"      "SEN"     
[187] "SGP"      "SHN"      "SLB"      "SLE"      "SLV"      "SMR"     
[193] "SOM"      "SPM"      "SRB"      "SSD"      "STP"      "SUR"     
[199] "SVK"      "SVN"      "SWE"      "SWZ"      "SXM"      "SYC"     
[205] "SYR"      "TCA"      "TCD"      "TGO"      "THA"      "TJK"     
[211] "TKL"      "TKM"      "TLS"      "TON"      "TTO"      "TUN"     
[217] "TUR"      "TUV"      "TWN"      "TZA"      "UGA"      "UKR"     
[223] "URY"      "USA"      "UZB"      "VAT"      "VCT"      "VEN"     
[229] "VGB"      "VIR"      "VNM"      "VUT"      "WLF"      "WSM"     
[235] "YEM"      "ZAF"      "ZMB"      "ZWE"

Doing it

2. Inspect the first entries

We notice the country codes.

Doing it

2. Inspect the first entries

We notice the country codes.

Doing it

2. Inspect the first entries

So we have some unusual entries such as:

“”
“OWID_KOS”
“OWID_WRL”.

Doing it

2. Inspect the first entries

Which countries do these codes refer to? We can subset the data to find out.

weird_labels <- c("OWID_KOS", "OWID_WRL", "")
weird_countries <- subset(life_expectancy_df2, (Code %in% weird_labels))

Doing it

3. Cleaning our dataset

We can now clean the dataset

weird_labels <- c("OWID_KOS", "OWID_WRL", "")
clean_life_expectancy_df <- subset(life_expectancy_df2, !(Code %in% weird_labels))

Doing it

3. Cleaning our dataset

We can now clean the dataset

head(clean_life_expectancy_df, n=5)

Doing it

3. Cleaning our dataset

Let’s repeat the procedure for the other dataset

weird_labels <- c("OWID_KOS", "OWID_WRL", "")
clean_urbanization_df <- subset(urbanization_df2, !(Code %in% weird_labels))

Doing it

3. Cleaning our dataset

Let’s repeat the procedure for the other dataset

head(clean_urbanization_df, n=5)

Doing it

4. Performing a left join

We will now perform a left join to combine urbanization data with life expectancy data based on Code.

Doing it

4. Performing a left join

We will now perform a left join to combine urbanization data with life expectancy data based on Code.

merged_data <- left_join(clean_life_expectancy_df, clean_urbanization_df, by = c("Code"="Code"))

Doing it

4. Performing a left join

We will now perform a left join to combine urbanization data with life expectancy data based on Code.

merged_data <- left_join(clean_life_expectancy_df, clean_urbanization_df, by = c("Code"="Code"))

Doing it

4. Performing a left join

We will now perform a left join to combine urbanization data with life expectancy data based on Code.

head(merged_data, n=10)

Doing it

5. Getting rid of NAs for urbanization

This is how we remove NA values

merged_data2 <- subset(na.omit(merged_data))
head(merged_data2, n=10)

Doing it

5. Getting rid of NAs for urbanization

How many countries did we drop?

nrow(merged_data) - nrow(merged_data2)

[1] 21

where

nrow(merged_data)

[1] 235

and

nrow(merged_data2)

[1] 214

Doing it

5. Getting rid of NAs for urbanization

How many countries did we drop?

nrow(merged_data) - nrow(merged_data2)

[1] 21

We dropped 21.

Doing it

5. Getting rid of NAs for urbanization

How many countries did we drop?

nrow(merged_data) - nrow(merged_data2)

[1] 21

We dropped 21.

Doing it

5. Getting rid of NAs for urbanization

How many countries did we drop?

nrow(merged_data) - nrow(merged_data2)

[1] 21

We dropped 21.

Doing it

5. Getting rid of NAs for urbanization

What are those countries?

countries_dropped <- merged_data[!complete.cases(merged_data), ]
countries_dropped$Code

 [1] "AIA" "BES" "COK" "ESH" "FLK" "GGY" "GLP" "GUF" "JEY" "MAF" "MSR" "MTQ"
[13] "MYT" "NIU" "REU" "SHN" "SPM" "TKL" "TWN" "VAT" "WLF"

Doing it

5. Getting rid of NAs for urbanization

Let us have a quick look at what these codes mean.

cntries <- subset(life_expectancy_df, Code %in% countries_dropped$Code)
unique(cntries$Entity)

 [1] "Anguilla"                        "Bonaire Sint Eustatius and Saba"
 [3] "Cook Islands"                    "Falkland Islands"               
 [5] "French Guiana"                   "Guadeloupe"                     
 [7] "Guernsey"                        "Jersey"                         
 [9] "Martinique"                      "Mayotte"                        
[11] "Montserrat"                      "Niue"                           
[13] "Reunion"                         "Saint Helena"                   
[15] "Saint Martin (French part)"      "Saint Pierre and Miquelon"      
[17] "Taiwan"                          "Tokelau"                        
[19] "Vatican"                         "Wallis and Futuna"              
[21] "Western Sahara"

Doing it

6. Creating a Scatterplot

ggplot2 is one of the most elegant and most versatile graphing libraries in R

Before we use ggplot we need to install and load the library:

install.packages("ggplot2")

Note: this has to be ggplot2, not ggplot.

Doing it

6.Creating a Scatterplot

Now, you have to load the package

library(ggplot2)

Note: this has to be ggplot2, not ggplot.

Doing it

6.Creating a Scatterplot

library(ggplot2)
fig1 <- ggplot(merged_data2, mapping = aes(x=urb_mean, y=life_exp_mean)) +
  geom_point()
fig1

Doing it

7. Saving our first plot

Within your working folder, create a sub-folder called “graphs”

In this case, the working folder is the folder “lab” which is inside the “week3” folder.

I then created another folder, called “graphs” to keep things organized.

Doing it

7. Saving our first plot

Next copy and paste the life-expectancy.csv from “data” to “graphs”

Doing it