Visualizing obesity across United States by using data from Wikipedia

June 16, 2016
By

(This article was first published on DataScience+, and kindly contributed to R-bloggers)

In this post I will show how to collect from a webpage and to analyze or visualize in R. For this task I will use the rvest package and will get the data from Wikipedia. I got the idea to write this post from Fisseha Berhane.

I will gain access to the prevalence of obesity in United States from Wikipedia page, then I will plot it in the map. Lets begin with loading the required packages.

## LOAD THE PACKAGES ####
library(rvest)
library(ggplot2)
library(dplyr)
library(scales)

After I loaded the packages in R, will upload the data. As I mention before, I will download the data from Wikipedia.

## LOAD THE DATA ####
obesity = read_html("https://en.wikipedia.org/wiki/Obesity_in_the_United_States")

obesity = obesity %>%
     html_nodes("table") %>%
     .[[1]]%>%
     html_table(fill=T)

The first line of code is calling the data from Wikipedia and the second line of codes is transforming the table that we are interested into dataframe in R.

Now lets check how our date looks alike.

head(obesity)
  State and District of Columbia Obese adults Overweight (incl. obese) adults
1                        Alabama        30.1%                           65.4%
2                         Alaska        27.3%                           64.5%
3                        Arizona        23.3%                           59.5%
4                       Arkansas        28.1%                           64.7%
5                     California        23.1%                           59.4%
6                       Colorado        21.0%                           55.0%
  Obese children and adolescents Obesity rank
1                          16.7%            3
2                          11.1%           14
3                          12.2%           40
4                          16.4%            9
5                          13.2%           41
6                           9.9%           51

The dataframe looks good, now we need to clean it from making ready to plot.

## CLEAN THE DATA ####
str(obesity)
'data.frame':	51 obs. of  5 variables:
 $ State and District of Columbia : chr  "Alabama" "Alaska" "Arizona" "Arkansas" ...
 $ Obese adults                   : chr  "30.1%" "27.3%" "23.3%" "28.1%" ...
 $ Overweight (incl. obese) adults: chr  "65.4%" "64.5%" "59.5%" "64.7%" ...
 $ Obese children and adolescents : chr  "16.7%" "11.1%" "12.2%" "16.4%" ...
 $ Obesity rank                   : int  3 14 40 9 41 51 49 43 22 39 ...

# remove the % and make the data numeric
for(i in 2:4){
     obesity[,i] = gsub("%", "", obesity[,i])
     obesity[,i] = as.numeric(obesity[,i])
}

# check data again
str(obesity)
'data.frame':	51 obs. of  5 variables:
 $ State and District of Columbia : chr  "Alabama" "Alaska" "Arizona" "Arkansas" ...
 $ Obese adults                   : num  30.1 27.3 23.3 28.1 23.1 21 20.8 22.1 25.9 23.3 ...
 $ Overweight (incl. obese) adults: num  65.4 64.5 59.5 64.7 59.4 55 58.7 55 63.9 60.8 ...
 $ Obese children and adolescents : num  16.7 11.1 12.2 16.4 13.2 9.9 12.3 14.8 22.8 14.4 ...
 $ Obesity rank                   : int  3 14 40 9 41 51 49 43 22 39 ...

Now we will fix the names of variables by removing the spaces

names(obesity)
[1] "State and District of Columbia"  "Obese adults"                   
[3] "Overweight (incl. obese) adults" "Obese children and adolescents" 
[5] "Obesity rank"

names(obesity) = make.names(names(obesity))
names(obesity)
[1] "State.and.District.of.Columbia"  "Obese.adults"                   
[3] "Overweight..incl..obese..adults" "Obese.children.and.adolescents" 
[5] "Obesity.rank"

Our data looks good. Its time to load the map data

# load the map data
states = map_data("state")
str(states)
'data.frame':	15537 obs. of  6 variables:
 $ long     : num  -87.5 -87.5 -87.5 -87.5 -87.6 ...
 $ lat      : num  30.4 30.4 30.4 30.3 30.3 ...
 $ group    : num  1 1 1 1 1 1 1 1 1 1 ...
 $ order    : int  1 2 3 4 5 6 7 8 9 10 ...
 $ region   : chr  "alabama" "alabama" "alabama" "alabama" ...
 $ subregion: chr  NA NA NA NA ...

We will merge two datasets (obesity and states) by region, therefore we need first to create new variable (region) in obesity dataset.

# create a new variable name for state
obesity$region = tolower(obesity$State.and.District.of.Columbia)

Now we will merge the datasets.

states = merge(states, obesity, by="region", all.x=T)
str(states)
'data.frame':	15537 obs. of  11 variables:
 $ region                         : chr  "alabama" "alabama" "alabama" "alabama" ...
 $ long                           : num  -87.5 -87.5 -87.5 -87.5 -87.6 ...
 $ lat                            : num  30.4 30.4 30.4 30.3 30.3 ...
 $ group                          : num  1 1 1 1 1 1 1 1 1 1 ...
 $ order                          : int  1 2 3 4 5 6 7 8 9 10 ...
 $ subregion                      : chr  NA NA NA NA ...
 $ State.and.District.of.Columbia : chr  "Alabama" "Alabama" "Alabama" "Alabama" ...
 $ Obese.adults                   : num  30.1 30.1 30.1 30.1 30.1 30.1 30.1 30.1 30.1 30.1 ...
 $ Overweight..incl..obese..adults: num  65.4 65.4 65.4 65.4 65.4 65.4 65.4 65.4 65.4 65.4 ...
 $ Obese.children.and.adolescents : num  16.7 16.7 16.7 16.7 16.7 16.7 16.7 16.7 16.7 16.7 ...
 $ Obesity.rank                   : int  3 3 3 3 3 3 3 3 3 3 ...

Plot the data

Finally we will plot the prevalence of obesity in adults.

## MAKE THE PLOT ####

# adults
ggplot(states, aes(x = long, y = lat, group = group, fill = Obese.adults)) + 
     geom_polygon(color = "white") +
     scale_fill_gradient(name = "Percent", low = "#feceda", high = "#c81f49", guide = "colorbar", na.value="black", breaks = pretty_breaks(n = 5)) +
     labs(title="Prevalence of Obesity in Adults") +
     coord_map()

Here is the plot in adults:
adults

Similarly, we can plot the prevalence of obesity in children.

# children
ggplot(states, aes(x = long, y = lat, group = group, fill = Obese.adults)) + 
     geom_polygon(color = "white") +
     scale_fill_gradient(name = "Percent", low = "#feceda", high = "#c81f49", guide = "colorbar", na.value="black", breaks = pretty_breaks(n = 5)) +
     labs(title="Prevalence of Obesity in Adults") +
     coord_map()

Here is the plot in children:
children

If you like to show the name of State in the map use the code below to create a new dataset.

statenames = states %>% 
     group_by(region) %>%
     summarise(
          long = mean(range(long)), 
          lat = mean(range(lat)), 
          group = mean(group), 
          Obese.adults = mean(Obese.adults), 
          Obese.children.and.adolescents = mean(Obese.children.and.adolescents)
 )

After you add this code to ggplot code above

geom_text(data=statenames, aes(x = long, y = lat, label = region), size=3)

That’s all. I hope you learned something useful today.

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