Lump groups together and create “other” category with forcats package

Packages we will need:

library(tidyverse)
library(forcats)
library(tidytext)
library(ggthemes)
library(democracyData)
library(magrittr)

For this blog, we are going to look at the titles of all countries’ heads of state, such as Kings, Presidents, Emirs, Chairman … understandably, there are many many many ways to title the leader of a country.

First, we will download the PACL dataset from the democracyData package.

Click here to read more about this super handy package:

If you want to read more about the variables in this dataset, click the link below to download the codebook by Cheibub et al.

pacl <- redownload_pacl()

We are going to look at the npost variable; this captures the political title of the nominal head of stage. This can be King, President, Sultan et cetera!

pacl %>% 
  count(npost) %>% 
  arrange(desc(n))

If we count the occurence of each title, we can see there are many ways to be called the head of a country!

"president"                         3693
"prime minister"                    2914
"king"                               470
"Chairman of Council of Ministers"   229
"premier"                            169
"chancellor"                         123
"emir"                               117
"chair of Council of Ministers"      111
"head of state"                       90
"sultan"                              67
"chief of government"                 63
"president of the confederation"      63
""                                    44
"chairman of Council of Ministers"    44
"shah"                                33

# ... with 145 more rows

155 groups is a bit difficult to meaningfully compare.

So we can collapse some of the groups together and lump all the titles that occur relatively seldomly – sometimes only once or twice – into an “other” category.

Clueless Movie Tai GIF - Find & Share on GIPHY

First, we use grepl() function to take the word president and chair (chairman, chairwoman, chairperson et cetera) and add them into broader categories.

Also, we use the tolower() function to make all lower case words and there is no confusion over the random capitalisation.

 pacl %<>% 
  mutate(npost = tolower(npost)) %>% 
  mutate(npost = ifelse(grepl("president", npost), "president", npost)) %>% 
  mutate(npost = ifelse(grepl("chair", npost), "chairperson", npost))

Next, we create an "other leader type" with the fct_lump_prop() function.

We specifiy a threshold and if the group appears fewer times in the dataset than this level we set, it is added into the “other” group.

pacl %<>% 
  mutate(regime_prop = fct_lump_prop(npost,
                                   prop = 0.005,
                                   other_level = "Other leader type")) %>% 
  mutate(regime_prop = str_to_title(regime_prop)) 

Now, instead of 155 types of leader titles, we have 10 types and the rest are all bundled into the Other Leader Type category

President            4370
Prime Minister       2945
Chairperson           520
King                  470
Other Leader Type     225
Premier               169
Chancellor            123
Emir                  117
Head Of State          90
Sultan                 67
Chief Of Government    63
The Office Smile GIF - Find & Share on GIPHY

The forcast package has three other ways to lump the variables together.

First, we can quickly look at fct_lump_min().

We can set the min argument to 100 and look at how it condenses the groups together:

pacl %>% 
  mutate(npost = tolower(npost)) %>% 
 
  mutate(post_min = fct_lump_min(npost,
                                   min = 100,
                                   other_level = "Other type")) %>% 
  mutate(post_min = str_to_title(post_min)) %>% 
  count(post_min) %>% 
  arrange(desc(n))
President       4370
Prime Minister  2945
Chairperson      520
King             470
Other Type       445
Premier          169
Chancellor       123
Emir             117

We can see that if the post appears fewer than 100 times, it is now in the Other Type category. In the previous example, Head Of State only appeared 90 times so it didn’t make it.

Next we look at fct_lump_lowfreq().

This function lumps together the least frequent levels. This one makes sure that “other” category remains as the smallest group. We don’t add another numeric argument.

pacl %>% 
  mutate(npost = tolower(npost)) %>% 
  mutate(post_lowfreq  = fct_lump_lowfreq(npost,
                                   other_level = "Other type")) %>% 
  mutate(post_lowfreq = str_to_title(post_lowfreq)) %>% 
  count(post_lowfreq) %>% 
  arrange(desc(n))
President       4370
Prime Minister  2945
Other Type      1844

This one only has three categories and all but president and prime minister are chucked into the Other type category.

Last, we can look at the fct_lump_n() to make sure we have a certain number of groups. We add n = 5 and we create five groups and the rest go to the Other type category.

pacl %>% 
  mutate(npost = tolower(npost)) %>% 
  mutate(post_n  = fct_lump_n(npost,
                                n = 5,
                                other_level = "Other type")) %>% 
  mutate(post_n = str_to_title(post_n)) %>% 
  count(post_n) %>% 
  arrange(desc(n))
President       4370
Prime Minister  2945
Other Type       685
Chairperson      520
King             470
Premier          169
Sums It Up The Office GIF - Find & Share on GIPHY

Next we can make a simple graph counting the different leader titles in free, partly free and not free Freedom House countries. We will use the download_fh() from DemocracyData package again

fh <- download_fh()

We will use the reorder_within() function from tidytext package.

Click here to read the full blog post explaining the function from Julia Silge’s blog.

First we add Freedom House data with the inner_join() function

Then we use the fct_lump_n() and choose the top five categories (plus the Other Type category we make)

pacl %<>% 
  inner_join(fh, by = c("cown", "year")) %>% 
  mutate(npost  = fct_lump_n(npost,
                  n = 5,
                  other_level = "Other type")) %>%
  mutate(npost = str_to_title(npost))

Then we group_by the three Freedom House status levels and count the number of each title:

pacl %<>% 
  group_by(status) %>% 
  count(npost) %>% 
  ungroup() %>% 

Using reorder_within(), we order the titles from most to fewest occurences WITHIN each status group:

pacl %<>%
  mutate(npost = reorder_within(npost, n, status)) 

To plot the columns, we use geom_col() and separate them into each Freedom House group, using facet_wrap(). We add scales = "free y" so that we don’t add every title to each group. Without this we would have empty spaces in the Free group for Emir and King. So this step removes a lot of clutter.

pacl_colplot <- pacl %>%
  ggplot(aes(fct_reorder(npost, n), n)) +
  geom_col(aes(fill = npost), show.legend = FALSE) +
  facet_wrap(~status, scales = "free_y") 

Last, I manually added the colors to each group (which now have longer names to reorder them) so that they are consistent across each group. I am sure there is an easier and less messy way to do this but sometimes finding the easier way takes more effort!

We add the scale_x_reordered() function to clean up the names and remove everything from the underscore in the title label.

pacl_colplot + scale_fill_manual(values = c("Prime Minister___F" = "#005f73",
                                "Prime Minister___NF" = "#005f73",
                                "Prime Minister___PF" = "#005f73",
                                
                               "President___F" = "#94d2bd",
                               "President___NF" = "#94d2bd",
                               "President___PF" = "#94d2bd",
                               
                               "Other Type___F" = "#ee9b00",
                               "Other Type___NF" = "#ee9b00",
                               "Other Type___PF" = "#ee9b00",
                               
                               "Chairperson___F" = "#bb3e03",
                               "Chairperson___NF" = "#bb3e03",
                               "Chairperson___PF" = "#bb3e03",
                               
                               "King___F" = "#9b2226",
                               "King___NF" = "#9b2226",
                               "King___PF" = "#9b2226",
                               
                               "Emir___F" = "#001219", 
                               "Emir___NF" = "#001219",
                               "Emir___PF" = "#001219")) +
  scale_x_reordered() +
  coord_flip() + 
  ggthemes::theme_fivethirtyeight() + 
  themes(text = element_size(size = 30))

In case you were curious about the free country that had a chairperson, Nigeria had one for two years.

pacl %>%
  filter(status == "F") %>% 
  filter(npost == "Chairperson") %>% 
  select(Country = pacl_country) %>% 
  knitr::kable("latex") %>%
  kableExtra::kable_classic(font_size = 30)

References

Cheibub, J. A., Gandhi, J., & Vreeland, J. R. (2010). Democracy and dictatorship revisited. Public choice143(1), 67-101.

Download democracy data with democracyData package in R

Packages we will need:

library(democracyData)
library(tidyverse)
library(magrittr)       # for pipes
library(ggstream)       # proportion plots
library(ggthemes)       # nice ggplot themes
library(forcats)        # reorder factor variables
library(ggflags)        # add flags
library(peacesciencer)  # more great polisci data
library(countrycode)    # add ISO codes to countries

This blog will highlight some quick datasets that we can download with this nifty package.

To install the democracyData package, it is best to do this via the github of Xavier Marquez:

remotes::install_github("xmarquez/democracyData", force = TRUE)
library(democracyData)

We can download the dataset from the Democracy and Dictatorship Revisited paper by Cheibub Gandhi and Vreeland (2010) with the redownload_pacl() function. It’s all very simple!

pacl <- redownload_pacl()
Happy Maya Rudolph GIF by PeacockTV - Find & Share on GIPHY

This gives us over 80 variables, with information on things such as regime type, geographical data, the name and age of the leaders, and various democracy variables.

We are going to focus on the different regimes across the years.

The six-fold regime classification Cheibub et al (2010) present is rooted in the dichotomous classification of regimes as democracy and dictatorship introduced in Przeworski et al. (2000). They classify according to various metrics, primarily by examining the way in which governments are removed from power and what constitutes the “inner sanctum” of power for a given regime. Dictatorships can be distinguished according to the characteristics of these inner sanctums. Monarchs rely on family and kin networks along with consultative councils; military rulers confine key potential rivals from the armed forces within juntas; and, civilian dictators usually create a smaller body within a regime party—a political bureau—to coopt potential rivals. Democracies highlight their category, depending on how the power of a given leadership ends

We can change the regime variable from numbers to a factor variables, describing the type of regime that the codebook indicates:

pacl %<>% 
  mutate(regime_name = ifelse(regime == 0, "Parliamentary democracies",
       ifelse(regime == 1, "Mixed democracies",
       ifelse(regime == 2, "Presidential democracies",
       ifelse(regime == 3, "Civilian autocracies",
       ifelse(regime == 4, "Military dictatorships",
       ifelse(regime ==  5,"Royal dictatorships", regime))))))) %>%
  mutate(regime = as.factor(regime)) 

Before we make the graph, we can give traffic light hex colours to the types of democracy. This goes from green (full democracy) to more oranges / reds (autocracies):

regime_palette <- c("Military dictatorships" = "#f94144", 
                    "Civilian autocracies" = "#f3722c", 
                    "Royal dictatorships" =  "#f8961e", 
                    "Mixed democracies" = "#f9c74f", 
                    "Presidential democracies" = "#90be6d", 
                    "Parliamentary democracies" = "#43aa8b")

We will use count() to count the number of countries in each regime type and create a variable n

pacl %>% 
  mutate(regime_name = as.factor(regime_name)) %>% 
  mutate(regime_name = fct_relevel(regime_name, 
 levels = c("Parliamentary democracies", 
           "Presidential democracies",
           "Mixed democracies",
           "Royal dictatorships",
           "Civilian autocracies",
           "Military dictatorships"))) %>% 
  group_by(year, un_continent_name) %>% 
  filter(!is.na(regime_name)) %>% 
  count(regime_name) %>% 
  ungroup() %>%  
  filter(un_continent_name != "") %>%
  filter(un_continent_name != "Oceania") -> pacl_count
Cant Handle It Kristen Wiig GIF by Saturday Night Live - Find & Share on GIPHY

We have all the variables we need.

We can now graph the count variables across different regions.

pacl_count %>% 
  ggplot(aes(x = year, y = n, 
             groups = regime_name, 
             fill = regime_name)) +
  ggstream::geom_stream(type = "proportion") + 
  facet_wrap(~un_continent_name) + 
  scale_fill_manual(values = regime_palette) + 
  ggthemes::theme_fivethirtyeight() + 
  theme(legend.title = element_blank(),
        text = element_text(size = 30)) 

I added the title and source header / footer section on canva.com to finish the graph.

Of course, the Cheibub et al (2010) dataset is not the only one that covers types of regimes.

Curtis Bell in 2016 developed the Rulers, Elections, and Irregular Governance Dataset (REIGN) dataset.

This describes political conditions in every country (including tenures and personal characteristics of world leaders, the types of political institutions and political regimes in effect, election outcomes and election announcements, and irregular events like coups)

Again, to download this dataset with the democracyData package, it is very simple:

reign <- download_reign()
Saturday Night Live Happy Dance GIF - Find & Share on GIPHY

I want to compare North and South Korea since their independence from Japan and see the changes in regimes and democracy scores over the years.

Next, we can easily download Freedom House or Polity 5 scores.

The Freedom House Scores default dataset ranges from 1972 to 2020, covering around 195 countries (depending on the year)

fh <- download_fh()

Alternatively, we can look at Polity Scores. This default dataset countains around 190 ish countries (again depending on the year and the number of countries in existance at that time) and covers a far longer range of years; from 1880 to 2018.

polityiv <- redownload_polityIV()

Alternatively, to download democracy scores, we can also use the peacesciencer dataset. Click here to read more about this package:

democracy_scores <- peacesciencer::create_stateyears() %>% 
  add_gwcode_to_cow() %>%
  add_democracy() 

With inner_join() we can merge these two datasets together:

reign %>% 
  select(ccode = cown, everything()) %>% 
  inner_join(democracy_scores, by = c("year", "ccode")) -> reign_demo

We next choose the years and countries for our plot.

Also, for the geom_flag() we will need the country name to be lower case ISO code. Click here to read more about the ggflags package.

reign_demo %>% 
    filter(year > 1945) %>% 
    mutate(gwf_regimetype = str_to_title(gwf_regimetype)) %>% 
    mutate(iso2c_lower = tolower(countrycode::countrycode(reign_country, "country.name", "iso2c"))) %>% 
filter(reign_country == "Korea North" | reign_country == "Korea South") -> korea_reign

We may to use specific hex colours for our graphs. I always prefer these deeper colours, rather than the pastel defaults that ggplot uses. I take them from coolors.co website!

korea_palette <- c("Military" = "#5f0f40",
                   "Party-Personal" = "#9a031e",
                   "Personal" = "#fb8b24",
                   "Presidential" = "#2a9d8f",
                   "Parliamentary" = "#1e6091")

We will add a flag to the start of the graph, so we create a mini dataset that only has the democracy scores for the first year in the dataset.

  korea_start <- korea_reign %>%
    group_by(reign_country) %>% 
    slice(which.min(year)) %>% 
    ungroup() 

Next we plot the graph

korea_reign %>% 
 ggplot(aes(x = year, y = v2x_polyarchy, groups = reign_country))  +
    geom_line(aes(color = gwf_regimetype), 
         size = 7, alpha = 0.7, show.legend = FALSE) +
    geom_point(aes(color = gwf_regimetype), size = 7, alpha = 0.7) +
    ggflags::geom_flag(data = korea_start, 
       aes(y = v2x_polyarchy, x = 1945, country = iso2c_lower), 
           size = 20) -> korea_plot

And then work on the aesthetics of the plot:

korea_plot + ggthemes::theme_fivethirtyeight() + 
    ggtitle("Electoral democracy on Korean Peninsula") +
    labs(subtitle = "Sources: Teorell et al. (2019) and Curtis (2016)") +
    xlab("Year") + 
    ylab("Democracy Scores") + 
    theme(plot.title = element_text(face = "bold"),
      axis.ticks = element_blank(),
      legend.box.background = element_blank(),
      legend.title = element_blank(),
      legend.text = element_text(size = 40),
      text = element_text(size = 30)) +
    scale_color_manual(values = korea_palette) + 
    scale_x_continuous(breaks = round(seq(min(korea_reign$year), max(korea_reign$year), by = 5),1))

While North Korea has been consistently ruled by the Kim dynasty, South Korea has gone through various types of government and varying levels of democracy!

References

Cheibub, J. A., Gandhi, J., & Vreeland, J. R. (2010). . Public choice143(1), 67-101.

Przeworski, A., Alvarez, R. M., Alvarez, M. E., Cheibub, J. A., Limongi, F., & Neto, F. P. L. (2000). Democracy and development: Political institutions and well-being in the world, 1950-1990 (No. 3). Cambridge University Press.

Exploratory Data Analysis and Descriptive Statistics for Political Science Research in R

Packages we will use:

library(tidyverse)      # of course
library(ggridges)       # density plots
library(GGally)         # correlation matrics
library(stargazer)      # tables
library(knitr)          # more tables stuff
library(kableExtra)     # more and more tables
library(ggrepel)        # spread out labels
library(ggstream)       # streamplots
library(bbplot)         # pretty themes
library(ggthemes)       # more pretty themes
library(ggside)         # stack plots side by side
library(forcats)        # reorder factor levels

Before jumping into any inferentional statistical analysis, it is helpful for us to get to know our data. For me, that always means plotting and visualising the data and looking at the spread, the mean, distribution and outliers in the dataset.

Before we plot anything, a simple package that creates tables in the stargazer package. We can examine descriptive statistics of the variables in one table.

Click here to read this practically exhaustive cheat sheet for the stargazer package by Jake Russ. I refer to it at least once a week.

I want to summarise a few of the stats, so I write into the summary.stat() argument the number of observations, the mean, median and standard deviation.

The kbl() and kable_classic() will change the look of the table in R (or if you want to copy and paste the code into latex with the type = "latex" argument).

In HTML, they do not appear.

Seth Meyers Ok GIF by Late Night with Seth Meyers - Find & Share on GIPHY

To find out more about the knitr kable tables, click here to read the cheatsheet by Hao Zhu.

Choose the variables you want, put them into a data.frame and feed them into the stargazer() function

stargazer(my_df_summary, 
          covariate.labels = c("Corruption index",
                               "Civil society strength", 
                               'Rule of Law score',
                               "Physical Integerity Score",
                               "GDP growth"),
          summary.stat = c("n", "mean", "median", "sd"), 
          type = "html") %>% 
  kbl() %>% 
  kable_classic(full_width = F, html_font = "Times", font_size = 25)
StatisticNMeanMedianSt. Dev.
Corruption index1790.4770.5190.304
Civil society strength1790.6700.8050.287
Rule of Law score1737.4517.0004.745
Physical Integerity Score1790.6960.8070.284
GDP growth1630.0190.0200.032

Next, we can create a barchart to look at the different levels of variables across categories. We can look at the different regime types (from complete autocracy to liberal democracy) across the six geographical regions in 2018 with the geom_bar().

my_df %>% 
  filter(year == 2018) %>%
  ggplot() +
  geom_bar(aes(as.factor(region),
               fill = as.factor(regime)),
           color = "white", size = 2.5) -> my_barplot

And we can add more theme changes

my_barplot + bbplot::bbc_style() + 
  theme(legend.key.size = unit(2.5, 'cm'),
        legend.text = element_text(size = 15),
        text = element_text(size = 15)) +
  scale_fill_manual(values = c("#9a031e","#00a896","#e36414","#0f4c5c")) + 
  scale_color_manual(values = c("#9a031e","#00a896","#e36414","#0f4c5c")) 

This type of graph also tells us that Sub-Saharan Africa has the highest number of countries and the Middle East and North African (MENA) has the fewest countries.

However, if we want to look at each group and their absolute percentages, we change one line: we add geom_bar(position = "fill"). For example we can see more clearly that over 50% of Post-Soviet countries are democracies ( orange = electoral and blue = liberal democracy) as of 2018.

We can also check out the density plot of democracy levels (as a numeric level) across the six regions in 2018.

With these types of graphs, we can examine characteristics of the variables, such as whether there is a large spread or normal distribution of democracy across each region.

my_df %>% 
  filter(year == 2018) %>%
  ggplot(aes(x = democracy_score, y = region, fill = regime)) +
  geom_density_ridges(color = "white", size = 2, alpha = 0.9, scale = 2) -> my_density_plot

And change the graph theme:

my_density_plot + bbplot::bbc_style() + 
  theme(legend.key.size = unit(2.5, 'cm')) +
  scale_fill_manual(values = c("#9a031e","#00a896","#e36414","#0f4c5c")) + 
  scale_color_manual(values = c("#9a031e","#00a896","#e36414","#0f4c5c")) 

Click here to read more about the ggridges package and click here to read their CRAN PDF.

Next, we can also check out Pearson’s correlations of some of the variables in our dataset. We can make these plots with the GGally package.

The ggpairs() argument shows a scatterplot, a density plot and correlation matrix.

my_df %>%
  filter(year == 2018) %>%
  select(regime, 
         corruption, 
         civ_soc, 
         rule_law, 
         physical, 
         gdp_growth) %>% 
  ggpairs(columns = 2:5, 
          ggplot2::aes(colour = as.factor(regime), 
          alpha = 0.9)) + 
  bbplot::bbc_style() +
  scale_fill_manual(values = c("#9a031e","#00a896","#e36414","#0f4c5c")) + 
  scale_color_manual(values = c("#9a031e","#00a896","#e36414","#0f4c5c"))

Click here to read more about the GGally package and click here to read their CRAN PDF.

We can use the ggside package to stack graphs together into one plot.

There are a few arguments to add when we choose where we want to place each graph.

For example, geom_xsideboxplot(aes(y = freedom_house), orientation = "y") places a boxplot for the three Freedom House democracy levels on the top of the graph, running across the x axis. If we wanted the boxplot along the y axis we would write geom_ysideboxplot(). We add orientation = "y" to indicate the direction of the boxplots.

Next we indiciate how big we want each graph to be in the panel with theme(ggside.panel.scale = .5) argument. This makes the scatterplot take up half and the boxplot the other half. If we write .3, the scatterplot takes up 70% and the boxplot takes up the remainning 30%. Last we indicade scale_xsidey_discrete() so the graph doesn’t think it is a continuous variable.

We add Darjeeling Limited color palette from the Wes Anderson movie.

Click here to learn about adding Wes Anderson theme colour palettes to graphs and plots.

my_df %>%
 filter(year == 2018) %>% 
 filter(!is.na(fh_number)) %>% 
  mutate(freedom_house = ifelse(fh_number == 1, "Free", 
         ifelse(fh_number == 2, "Partly Free", "Not Free"))) %>%
  mutate(freedom_house = forcats::fct_relevel(freedom_house, "Not Free", "Partly Free", "Free")) %>% 
ggplot(aes(x = freedom_from_torture, y = corruption_level, colour = as.factor(freedom_house))) + 
  geom_point(size = 4.5, alpha = 0.9) +
  geom_smooth(method = "lm", color ="#1d3557", alpha = 0.4) +  
  geom_xsideboxplot(aes(y = freedom_house), orientation = "y", size = 2) +
  theme(ggside.panel.scale = .3) +
  scale_xsidey_discrete() +
  bbplot::bbc_style() + 
  facet_wrap(~region) + 
  scale_color_manual(values= wes_palette("Darjeeling1", n = 3))

The next plot will look how variables change over time.

We can check out if there are changes in the volume and proportion of a variable across time with the geom_stream(type = "ridge") from the ggstream package.

In this instance, we will compare urban populations across regions from 1800s to today.

my_df %>% 
  group_by(region, year) %>% 
  summarise(mean_urbanization = mean(urban_population_percentage, na.rm = TRUE)) %>% 
  ggplot(aes(x = year, y = mean_urbanization, fill = region)) +
  geom_stream(type = "ridge") -> my_streamplot

And add the theme changes

  my_streamplot + ggthemes::theme_pander() + 
  theme(
legend.title = element_blank(),
        legend.position = "bottom",
        legend.text = element_text(size = 25),
        axis.text.x = element_text(size = 25),
        axis.title.y = element_blank(),
        axis.title.x = element_blank()) +
  scale_fill_manual(values = c("#001219",
                               "#0a9396",
                               "#e9d8a6",
                               "#ee9b00", 
                               "#ca6702",
                               "#ae2012")) 

Click here to read more about the ggstream package and click here to read their CRAN PDF.

We can also look at interquartile ranges and spread across variables.

We will look at the urbanization rate across the different regions. The variable is calculated as the ratio of urban population to total country population.

Before, we will create a hex color vector so we are not copying and pasting the colours too many times.

my_palette <- c("#1d3557",
                "#0a9396",
                "#e9d8a6",
                "#ee9b00", 
                "#ca6702",
                "#ae2012")

We use the facet_wrap(~year) so we can separate the three years and compare them.

my_df %>% 
  filter(year == 1980 | year == 1990 | year == 2000)  %>% 
  ggplot(mapping = aes(x = region, 
                       y = urban_population_percentage, 
                       fill = region)) +
  geom_jitter(aes(color = region),
              size = 3, alpha = 0.5, width = 0.15) +
  geom_boxplot(alpha = 0.5) + facet_wrap(~year) + 
  scale_fill_manual(values = my_palette) +
  scale_color_manual(values = my_palette) + 
  coord_flip() + 
  bbplot::bbc_style()

If we want to look more closely at one year and print out the country names for the countries that are outliers in the graph, we can run the following function and find the outliers int he dataset for the year 1990:

is_outlier <- function(x) {
  return(x < quantile(x, 0.25) - 1.5 * IQR(x) | x > quantile(x, 0.75) + 1.5 * IQR(x))
}

We can then choose one year and create a binary variable with the function

my_df_90 <- my_df %>% 
  filter(year == 1990) %>% 
  filter(!is.na(urban_population_percentage))

my_df_90$my_outliers <- is_outlier(my_df_90$urban_population_percentage)

And we plot the graph:

my_df_90 %>% 
  ggplot(mapping = aes(x = region, y = urban_population_percentage, fill = region)) +
  geom_jitter(aes(color = region), size = 3, alpha = 0.5, width = 0.15) +
  geom_boxplot(alpha = 0.5) +
  geom_text_repel(data = my_df_90[which(my_df_90$my_outliers == TRUE),],
            aes(label = country_name), size = 5) + 
  scale_fill_manual(values = my_palette) +
  scale_color_manual(values = my_palette) + 
  coord_flip() + 
  bbplot::bbc_style() 

In the next blog post, we will look at t-tests, ANOVAs (and their non-parametric alternatives) to see if the difference in means / medians is statistically significant and meaningful for the underlying population.

Bo Burnham What GIF - Find & Share on GIPHY

Building a dataset for political science analysis in R, PART 2

Packages we will need

library(tidyverse)
library(peacesciencer)
library(countrycode)
library(bbplot)

The main workhorse of this blog is the peacesciencer package by Stephen Miller!

The package will create both dyad datasets and state datasets with all sovereign countries.

Thank you Mr Miller!

There are heaps of options and variables to add.

Go to the page to read about them all in detail.

Here is a short list from the package description of all the key variables that can be quickly added:

We create the dyad dataset with the create_dyadyears() function. A dyad-year dataset focuses on information about the relationship between two countries (such as whether the two countries are at war, how much they trade together, whether they are geographically contiguous et cetera).

In the literature, the study of interstate conflict has adopted a heavy focus on dyads as a unit of analysis.

Alternatively, if we want just state-year data like in the previous blog post, we use the function create_stateyears()

We can add the variables with type D to the create_dyadyears() function and we can add the variables with type S to the create_stateyears() !

Focusing on the create_dyadyears() function, the arguments we can include are directed and mry.

The directed argument indicates whether we want directed or non-directed dyad relationship.

In a directed analysis, data include two observations (i.e. two rows) per dyad per year (such as one for USA – Russia and another row for Russia – USA), but in a nondirected analysis, we include only one observation (one row) per dyad per year.

The mry argument indicates whether they want to extend the data to the most recently concluded calendar year – i.e. 2020 – or not (i.e. until the data was last available).

dyad_df <- create_dyadyears(directed = FALSE, mry = TRUE) %>%
  add_atop_alliance() %>%  
  add_nmc() %>%
  add_cow_trade() %>% 
  add_creg_fractionalization() 

I added dyadic variables for the

You can follow these links to check out the codebooks if you want more information about descriptions about each variable and how the data were collected!

The code comes with the COW code but I like adding the actual names also!

dyad_df$country_1 <- countrycode(dyad_df$ccode1, "cown", "country.name")

With this dataframe, we can plot the CINC data of the top three superpowers, just looking at any variable that has a 1 at the end and only looking at the corresponding country_1!

According to our pals over at le Wikipedia, the Composite Index of National Capability (CINC) is a statistical measure of national power created by J. David Singer for the Correlates of War project in 1963. It uses an average of percentages of world totals in six different components (such as coal consumption, military expenditure and population). The components represent demographic, economic, and military strength

First, let’s choose some nice hex colors

pal <- c("China" = "#DE2910",
         "United States" = "#3C3B6E", 
         "Russia" = "#FFD900")

And then create the plot

dyad_df %>% 
 filter(country_1 == "Russia" | 
          country_1 == "United States" | 
          country_1 == "China") %>% 
  ggplot(aes(x = year, y = cinc1, group = as.factor(country_1))) +
  geom_line(aes(color = country_1)) +
  geom_line(aes(color = country_1), size = 2, alpha = 0.8) + 
  scale_color_manual(values =  pal) +
  bbplot::bbc_style()

In PART 3, we will merge together our data with our variables from PART 1, look at some descriptive statistics and run some panel data regression analysis with our different variables!

Graph linear model plots with sjPlots in R

This blog post will look at the plot_model() function from the sjPlot package. This plot can help simply visualise the coefficients in a model.

Packages we need:

library(sjPlot)
library(kable)

We can look at variables that are related to citizens’ access to public services.

This dependent variable measures equal access access to basic public services, such as access to security, primary education, clean water, and healthcare and whether they are distributed equally or unequally according to socioeconomic position.

Higher scores indicate a more equal society.

I will throw some variables into the model and see what relationships are statistically significant.

The variables in the model are

  • level of judicial constraint on the executive branch,
  • freedom of information (such as freedom of speech and uncensored media),
  • level of democracy,
  • level of regime corruption and
  • strength of civil society.

So first, we run a simple linear regression model with the lm() function:

summary(my_model <- lm(social_access ~ judicial_constraint +
        freedom_information +
        democracy_score + 
        regime_corruption +
        civil_society_strength, 
        data = df))

We can use knitr package to produce a nice table or the regression coefficients with kable().

I write out the independent variable names in the caption argument

I also choose the four number columns in the col.names argument. These numbers are:

  • beta coefficient,
  • standard error,
  • t-score
  • p-value

I can choose how many decimals I want for each number columns with the digits argument.

And lastly, to make the table, I can set the type to "html". This way, I can copy and paste it into my blog post directly.

my_model %>% 
tidy() %>%
kable(caption = "Access to public services by socio-economic position.", 
col.names = c("Predictor", "B", "SE", "t", "p"),
digits = c(0, 2, 3, 2, 3), "html")
Access to public services by socio-economic position
Predictor B SE t p
(Intercept) 1.98 0.380 5.21 0.000
Judicial constraints -0.03 0.485 -0.06 0.956
Freedom information -0.60 0.860 -0.70 0.485
Democracy Score 2.61 0.807 3.24 0.001
Regime Corruption -2.75 0.381 -7.22 0.000
Civil Society Strength -1.67 0.771 -2.17 0.032
Kristin Cavallari GIF by E! - Find & Share on GIPHY

Higher democracy scores are significantly and positively related to equal access to public services for different socio-economic groups.

There is no statistically significant relationship between judicial constraint on the executive.

But we can also graphically show the coefficients in a plot with the sjPlot package.

There are many different arguments you can add to change the colors of bars, the size of the font or the thickness of the lines.

p <-  plot_model(my_model, 
      line.size = 8, 
      show.values = TRUE,
      colors = "Set1",
      vline.color = "#d62828",
      axis.labels = c("Civil Society Strength",  "Regime Corruption", "Democracy Score", "Freedom information", "Judicial constraints"), title = "Equal access to public services distributed by socio-economic position")

p + theme_sjplot(base_size = 20)

So how can we interpret this graph?

If a bar goes across the vertical red line, the coefficient is not significant. The further the bar is from the line, the higher the t-score and the more significant the coefficient!

Create a correlation matrix with GGally package in R

We can create very informative correlation matrix graphs with one function.

Packages we will need:

library(GGally)
library(bbplot) #for pretty themes

First, choose some nice hex colors.

my_palette <- c("#005D8F", "#F2A202")
Happy Friends GIF by netflixlat - Find & Share on GIPHY

Next, we can go create a dichotomous factor variable and divide the continuous “freedom from torture scale” variable into either above the median or below the median score. It’s a crude measurement but it serves to highlight trends.

Blue means the country enjoys high freedom from torture. Yellow means the county suffers from low freedom from torture and people are more likely to be tortured by their government.

Then we feed our variables into the ggpairs() function from the GGally package.

I use the columnLabels to label the graphs with their full names and the mapping argument to choose my own color palette.

I add the bbc_style() format to the corr_matrix object because I like the font and size of this theme. And voila, we have our basic correlation matrix (Figure 1).

corr_matrix <- vdem90 %>% 
  dplyr::mutate(
    freedom_torture = ifelse(torture >= 0.65, "High", "Low"),
    freedom_torture = as.factor(freedom_t))
  dplyr::select(freedom_torture, civil_lib, class_eq) %>% 
  ggpairs(columnLabels = c('Freedom from Torture', 'Civil Liberties', 'Class Equality'), 
    mapping = ggplot2::aes(colour = freedom_torture)) +
  scale_fill_manual(values = my_palette) +
  scale_color_manual(values = my_palette)

corr_matrix + bbplot::bbc_style()
Figure 1.
Excited Season 4 GIF by Friends - Find & Share on GIPHY

First off, in Figure 2 we can see the centre plots in the diagonal are the distribution plots of each variable in the matrix

Figure 2.

In Figure 3, we can look at the box plot for the ‘civil liberties index’ score for both high (blue) and low (yellow) ‘freedom from torture’ categories.

The median civil liberties score for countries in the high ‘freedom from torture’ countries is far higher than in countries with low ‘freedom from torture’ (i.e. citizens in these countries are more likely to suffer from state torture). The spread / variance is also far great in states with more torture.

Figure 3.

In Figur 4, we can focus below the diagonal and see the scatterplot between the two continuous variables – civil liberties index score and class equality index scores.

We see that there is a positive relationship between civil liberties and class equality. It looks like a slightly U shaped, quadratic relationship but a clear relationship trend is not very clear with the countries with higher torture prevalence (yellow) showing more randomness than the countries with high freedom from torture scores (blue).

Saying that, however, there are a few errant blue points as outliers to the trend in the plot.

The correlation score is also provided between the two categorical variables and the correlation score between civil liberties and class equality scores is 0.52.

Examining at the scatterplot, if we looked only at countries with high freedom from torture, this correlation score could be higher!

Figure 4.

Excited Season 4 GIF by Friends - Find & Share on GIPHY

Analyse Pseudo-R2, VIF scores and robust standard errors for generalised linear models in R

This blog post will look at a simple function from the jtools package that can give us two different pseudo R2 scores, VIF score and robust standard errors for our GLM models in R

Packages we need:

library(jtools)
library(tidyverse)

From the Varieties of Democracy dataset, we can examine the v2regendtype variable, which codes how a country’s governing regime ends.

It turns out that 1994 was a very coup-prone year. Many regimes ended due to either military or non-military coups.

We can extract all the regimes that end due to a coup d’etat in 1994. Click here to read the VDEM codebook on this variable.

vdem_2 <- vdem %>% 
  dplyr::filter(vdem$year == 1994) %>% 
  dplyr::mutate(regime_end = as.numeric(v2regendtype)) %>% 
  dplyr::mutate(coup_binary = ifelse(regime_end == 0 |regime_end ==1 | regime_end == 2, 1, 0))

First we can quickly graph the distribution of coups across different regions in this year:

palette <- c("#228174","#e24d28")

vdem_2$region <- car::recode(vdem_2$e_regionpol_6C, 
    '1 = "Post-Soviet";
     2 = "Latin America";
     3 = "MENA";
     4 = "Africa";
     5 = "West";
     6 = "Asia"')


dist_coup <- vdem_2 %>%
  dplyr::group_by(as.factor(coup_binary), as.factor(region)) %>% 
  dplyr::mutate(count_conflict = length(coup_binary)) %>% 
  ggplot(aes(x = coup_binary, fill = as.factor(coup_binary))) + 
  facet_wrap(~region) +
  geom_bar(stat = "count") +
  scale_fill_manual(values = palette) + 
  labs(title = "Did a regime end with a coup in 1994?",
       fill = "Coup") +
  stat_count(aes(label = count_conflict),
       geom = "text", 
       colour = "black", 
       size = 10, 
       position = position_fill(vjust = 5)

Okay, next on to the modelling.

Happy Season 9 GIF by The Office - Find & Share on GIPHY

With this new binary variable, we run a straightforward logistic regression in R.

To do this in R, we can run a generalised linear model and specify the family argument to be “binomial” :

summary(model_bin_1 <- glm(coup_binary ~ diagonal_accountability + military_control_score,
 family = "binomial", data = vdem_2) 

However some of the key information we want is not printed in the default R summary table.

Help Me New Girl Quotes GIF - Find & Share on GIPHY

This is where the jtools package comes in. It was created by Jacob Long from the University of South Carolina to help create simple summary tables that we can modify in the function. Click here to read the CRAN package PDF.

The summ() function can give us more information about the fit of the binomial model. This function also works with regular OLS lm() type models.

Set the vifs argument to TRUE for a multicollineary check.

summ(model_bin_1, vifs = TRUE)

And we can see there is no problem with multicollinearity with the model; the VIF scores for the two independent variables in this model are well below 5.

Click here to read more about the Variance Inflation Factor and dealing with pesky multicollinearity.

In the above MODEL FIT section, we can see both the Cragg-Uhler (also known as Nagelkerke) and the McFadden Pseudo R2 scores give a measure for the relative model fit. The Cragg-Uhler is just a modification of the Cox and Snell R2.

There is no agreed equivalent to R2 when we run a logistic regression (or other generalized linear models). These two Pseudo measures are just two of the many ways to calculate a Pseudo R2 for logistic regression. Unfortunately, there is no broad consensus on which one is the best metric for a well-fitting model so we can only look at the trends of both scores relative to similar models. Compared to OLS R2 , which has a general rule of thumb (e.g. an R2 over 0.7 is considered a very good model), comparisons between Pseudo R2 are restricted to the same measure within the same data set in order to be at all meaningful to us. However, a McFadden’s Pseudo R2 ranging from 0.3 to 0.4 can loosely indicate a good model fit. So don’t be disheartened if your Pseudo scores seems to be always low.

If we add another continuous variable – judicial corruption score – we can see how this affects the overall fit of the model.

summary(model_bin_2 <- glm(coup_binary ~
     diagonal_accountability + 
     military_control_score + 
     judicial_corruption,
     family = "binomial", 
     data = vdem_2))

And run the summ() function like above:

summ(model_bin_2, vifs = TRUE)

The AIC of the second model is smaller, so this model is considered better. Additionally, both the Pseudo R2 scores are larger! So we can say that the model with the additional judicial corruption variable is a better fitting model.

Season 9 Thank You GIF by The Office - Find & Share on GIPHY

Click here to learn more about the AIC and choosing model variables with a stepwise algorithm function.

stargazer(model_bin, model_bin_2, type = "text")

One additional thing we can specify in the summ() function is the robust argument, which we can use to specify the type of standard errors that we want to correct for.

The assumption of homoskedasticity is does not need to be met in order to run a logistic regression. So I will run a “gaussian” general linear model (i.e. a linear model) to show the impact of changing the robust argument.

We suffer heteroskedasticity when the variance of errors in our model vary (i.e are not consistently random) across observations. It causes inefficient estimators and we cannot trust our p-values.

Click to learn more about checking for and correcting for heteroskedasticity in OLS.

We can set the robust argument to “HC1” This is the default standard error that Stata gives.

Set it to “HC3” to see the default standard error that we get with the sandwich package in R.

Season 6 Netflix GIF by Gilmore Girls  - Find & Share on GIPHY

So run a simple regression to see the relationship between freedom from torture scale and the three independent variables in the model

summary(model_glm1 <- glm(freedom_torture ~ civil_lib + exec_bribe + judicial_corr, data = vdem90, family = "gaussian"))

Now I run the same summ() function but just change the robust argument:

First with no standard error correction. This means the standard errors are calculated with maximum likelihood estimators (MLE). The main problem with MLE is that is assumes normal distribution of the errors in the model.

summ(model_glm1, vifs = TRUE)

Next with the default STATA robust argument:

summ(model_glm1, vifs = TRUE, robust = "HC1")

And last with the default from R’s sandwich package:

summ(model_glm1, vifs = TRUE, robust = "HC3")

If we compare the standard errors in the three models, they are the highest (i.e. most conservative) with HC3 robust correction. Both robust arguments cause a 0.01 increase in the p-value but this is so small that it do not affect the eventual p-value significance level (both under 0.05!)

Season 7 Reaction GIF by The Office - Find & Share on GIPHY