rstats – Page 2 – R Functions and Packages for Political Science Analysis

Packages we will need:

library(sandwich)
library(stargazer)
library(lmtest)

If our OLS model demonstrates high level of heteroskedasticity (i.e. when the error term of our model is not randomly distributed across observations and there is a discernible pattern in the error variance), we run into problems.

Why? Because this means OLS will use sub-optimal estimators based on incorrect assumptions and the standard errors computed using these flawed least square estimators are more likely to be under-valued.

Since standard errors are necessary to compute our t – statistic and arrive at our p – value, these inaccurate standard errors are a problem.

Click here to check for heteroskedasticity in your model with the lmtest package.

To correct for heteroskedastcity in your model, you need the sandwich package and the lmtest package to employ the vcocHC argument.

Gordon Ramsey Idiot GIF - Find & Share on GIPHY

First, let’s fit a simple OLS regression.

summary(free_express_model <- lm(freedom_expression ~ free_elections + deliberative_index, data = data_1990))

We can see that there is a small star beside the main dependent variable of interest! Success!

Happy So Excited GIF - Find & Share on GIPHY

We have significance.

Thus, we could say that the more free and fair the elections a country has, this increases the mean freedom of expression index score for that country.

This ties in with a very minimalist understanding of democracy. If a country has elections and the populace can voice their choice of leadership, this will help set the scene for a more open society.

However, it is naive to look only at the p – value of any given coefficient in a regression output. If we run some diagnostic analyses and look at the relationship graphically, we may need to re-examine this seemingly significant relationship.

Can we trust the 0.087 standard error score that our OLS regression calculated? Is it based on sound assumptions?

Worried Its Always Sunny In Philadelphia GIF by HULU - Find & Share on GIPHY

First let’s look at the residuals. Can we assume that the variance of error is equal across all observations?

If we examine the residuals (the first graph), we see that there is actually a tapered fan-like pattern in the error variance. As we move across the x axis, the variance along the y axis gets continually smaller and smaller.

The error does not look random.

Panicking Oh No GIF by HULU - Find & Share on GIPHY

Let’s run a Breush-Pagan test (from the lmtest package) to check our suspicion of heteroskedasticity.

lmtest::bptest(free_exp_model)

We can reject the null hypothesis that the error variance is homoskedastic.

So the model does suffer from heteroskedasticty. We cannot trust those stars in the regression output!

Season 1 Omg GIF by Friends - Find & Share on GIPHY

In order to fix this and make our p-values more accuarate, we need to install the sandwich package to feed in the vcovHC adjustment into the coeftest() function.

vcovHC stands for variance covariance Heteroskedasticity Consistent.

With the stargazer package (which prints out all the models in one table), we can compare the free_exp_model alone with no adjustment, then four different variations of the vcovHC adjustment using different formulae (as indicated in the type argument below).

stargazer(free_exp_model,
          coeftest(free_exp_model, vcovHC(free_exp_model, type = "HC0")),
          coeftest(free_exp_model, vcovHC(free_exp_model, type = "HC1")),
          coeftest(free_exp_model, vcovHC(free_exp_model, type = "HC2")),
          coeftest(free_exp_model, vcovHC(free_exp_model, type = "HC3")),
          type = "text")

Looking at the standard error in the (brackets) across the OLS and the coeftest models, we can see that the standard error are all almost double the standard error from the original OLS regression.

There is a tiny difference between the different types of Heteroskedastic Consistent (HC) types.

The significant p – value disappears from the free and fair election variable when we correct with the vcovHC correction.

Season 2 Friends GIF - Find & Share on GIPHY

The actual coefficient stays the same regardless of whether we use no correction or any one of the correction arguments.

Which HC estimator should I use in my vcovHC() function?

The default in the sandwich package is HC3.

STATA users will be familiar with HC1, as it is the default robust standard error correction when you add robust at the end of the regression command.

The difference between them is not very large.

The estimator HC0 was suggested in the econometrics literature by White in 1980 and is justified by asymptotic arguments.

For small sample sizes, the standard errors from HC0 are quite biased, usually downward, and this results in overly liberal inferences in regression models (Bera, Suprayitno & Premaratne, 2002). But with HC0, the bias shrinks as your sample size increases.

The estimator types HC1, HC2 and HC3 were put forward by MacKinnon and White (1985) to improve the performance in small samples.

Long and Ervin (2000) furthermore argue that HC3 provides the best performance in small samples as it gives less weight to influential observations in the model

In our freedom of expression regression, the HC3 estimate was the most conservative with the standard error calculations. however the difference between the approaches did not change the conclusion; ultimately the main independent variable of interest in this analysis – free and fair elections – can explain variance in the dependent variable – freedom of expression – does not find evidence in the model.

Click here to read an article by Hayes and Cai (2007) which discusses the matrix formulae and empirical differences between the different calculation approaches taken by the different types. Unfortunately it is all ancient Greek to me.

References

Bera, A. K., Suprayitno, T., & Premaratne, G. (2002). On some heteroskedasticity-robust estimators of variance–covariance matrix of the least-squares estimators. Journal of Statistical Planning and Inference, 108(1-2), 121-136.

Hayes, A. F., & Cai, L. (2007). Using heteroskedasticity-consistent standard error estimators in OLS regression: An introduction and software implementation. Behavior research methods, 39(4), 709-722.

Long, J. S., & Ervin, L. H. (2000). Using heteroscedasticity consistent standard errors in the linear regression model. The American Statistician, 54(3), 217-224.

MacKinnon, J. G., & White, H. (1985). Some heteroskedasticity-consistent covariance matrix estimators with improved finite sample properties. Journal of econometrics, 29(3), 305-325.

One core assumption when calculating ordinary least squares regressions is that all the random variables in the model have equal variance around the best fitting line.

Essentially, when we run an OLS, we expect that the error terms have no fan pattern.

Example of homoskedasticiy

So let’s look at an example of this assumption being satisfied. I run a simple regression to see whether there is a relationship between and media censorship and civil society repression in 178 countries in 2010.

ggplot(data_010, aes(media_censorship, civil_society_repression)) 
      + geom_point() + geom_smooth(method = "lm") 
      + geom_text(size = 3, nudge_y = 0.1, aes(label = country))

If we run a simple regression

summary(repression_model <- lm(media_censorship ~ civil_society_repression, data = data_2010))
stargazer(repression_model, type = "text")

This is pretty common sense; a country that represses its citizens in one sphere is more likely to repress in other areas. In this case repressing the media correlates with repressing civil society.

We can plot the residuals of the above model with the autoplot() function from the ggfortify package.

library(ggfortify)
autoplot(repression_model)

Nothing unusual appears to jump out at us with regard to evidence for heteroskedasticity!

In the first Residuals vs Fitted plot, we can see that blue line does not drastically diverge from the dotted line (which indicates residual value = 0).

The third plot Scale-Location shows again that there is no drastic instances of heteroskedasticity. We want to see the blue line relatively horizontal. There is no clear pattern in the distribution of the residual points.

In the Residual vs. Leverage plot (plot number 4), the high leverage observation 19257 is North Korea! A usual suspect when we examine model outliers.

While it is helpful to visually see the residuals plotted out, a more objective test can help us find whether the model is indeed free from heteroskedasticity problems.

For this we need the Breusch-Pagan test for heteroskedasticity from the lmtest package.

install.packages("lmtest)
library(lmtest)
bptest(repression_model)

The default in R is the studentized Breusch-Pagan. However if you add the studentize = FALSE argument, you have the non-studentized version

The null hypothesis of the Breusch-Pagan test is that the variance in the model is homoskedastic.

With our repression_model, we cannot reject the null, so we can say with confidence that there is no major heteroskedasticity issue in our model.

The non-studentized Breusch-Pagan test makes a very big assumption that the error term is from Gaussian distribution. Since this assumption is usually hard to verify, the default bptest() in R “studentizes” the test statistic and provide asymptotically correct significance levels for distributions for error.

Why do we care about heteroskedasticity?

If our model demonstrates high level of heteroskedasticity (i.e. the random variables have non-random variation across observations), we run into problems.

Why?

OLS uses sub-optimal estimators based on incorrect assumptions and

The standard errors computed using these flawed least square estimators are more likely to be under-valued. Since standard errors are necessary to compute our t – statistics and arrive at our p – value, these inaccurate standard errors are a problem.

Example of heteroskedasticity

Let’s look at an example of this homoskedasticity assumption NOT being satisfied.

I run a simple regression to see whether there is a relationship between democracy score and respect for individuals’ private property rights in 178 countries in 2010.

When you are examining democracy as the main dependent variable, heteroskedasticity is a common complaint. This is because all highly democratic countries are all usually quite similar. However, when we look at autocracies, they are all quite different and seem to march to the beat of their own despotic drum. We cannot assume that the random variance across different regime types is equally likely.

First, let’s have a look at the relationship.

prop_graph <- ggplot(vdem2010, aes(v2xcl_prpty, v2x_api)) 
                     + geom_point(size = 3, aes(color = factor(regime_type))) 
                     + geom_smooth(method = "lm")
prop_graph + scale_colour_manual(values = c("#D55E00", "#E69F00", "#009E73", "#56B4E9"))

Next, let’s fit the model to examine the relationship.

summary(property_model <- lm(property_score ~ democracy_score, data = data_2010))
stargazer(property_model, type = "text")

To plot the residuals (and other diagnostic graphs) of the model, we can use the autoplot() function to look at the relationship in the model graphically.

autoplot(property_model)

Graph number 1 plots the residuals against the fitted model and we can see that lower values on the x – axis (fitted values) correspond with greater spread on the y – axis. Lower democracy scores relate to greater error on property rights index scores. Plus the blue line does not lie horizontal and near the dotted line. It appears we have non-random error patterns.

Examining the Scale – Location graph (number 3), we can see that the graph is not horizontal.

Again, interpreting the graph can be an imprecise art. So a more objective approach may be to run the bptest().

bptest(property_model)

Since the p – value is far smaller than 0.05, we can reject the null of homoskedasticity.

Rather, we have evidence that our model suffers from heteroskedasticity. The standard errors in the regression appear smaller than they actually are in reality. This inflates our t – statistic and we cannot trust our p – value.

In the next blog post, we can look at ways to rectify this violation of homoskedasticity and to ensure that our regression output has more accurate standard errors and therefore more accurate p – values.

Click here to use the sandwich package to fix heteroskedasticity in the OLS regression.