Tag Archives: R-bloggers

Clustered standard errors with R

In many scenarios, data are structured in groups or clusters, e.g. pupils within classes (within schools), survey respondents within countries or, for longitudinal surveys, survey answers per subject. Simply ignoring this structure will likely lead to spuriously low standard errors, i.e. a misleadingly precise estimate of our coefficients. This in turn leads to overly-narrow confidence intervals, overly-low p-values and possibly wrong conclusions.

Clustered standard errors are a common way to deal with this problem. Unlike Stata, R doesn’t have built-in functionality to estimate clustered standard errors. There are several packages though that add this functionality and this article will introduce three of them, explaining how they can be used and what their advantages and disadvantages are. Before that, I will outline the theory behind (clustered) standard errors for linear regression. The last section is used for a performance comparison between the three presented packages. If you’re already familiar with the concept of clustered standard errors, you may skip to the hands-on part right away.

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Simplifying geospatial features in R with sf and rmapshaper

When working with geospatial data, memory consumption and computation time can become quite a problem, since these datasets are often very large. You may have very granular, high resolution data although that isn’t really necessary for your use-case, for example when plotting small scale maps or when applying calculations at a spatial level for which lower granularity is sufficient. In such scenarios, it’s best to first simplify the geospatial features (the sets of points, lines and polygons that represent geographic entities) in your data. By simplify I mean that we generally reduce the amount of information that is used to represent these features, i.e. we remove complete features (e.g. small islands), we join features (e.g. we combine several overlapping or adjacent features) or we reduce the complexity of features (e.g. we remove vertices or holes in a feature). Since applying these operations comes with information loss you should be very careful about how much you simplify and if this in some way biases you results.

In R, we can apply this sort of simplification with a few functions from the packages sf and, for some special cases explained below, rmapshaper. In the following, I will show how to apply them and what the effects of their parameters are. The data and source code are available on GitHub.

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Developing a complex R Shiny app – the good, the bad and the ugly

Together with Clara Bicalho (UC Berkeley) and Sisi Huang (WZB), I recently developed a web application that acts as a convenient interface to the DeclareDesign R package and its repository of research designs, DesignLibrary. This web application, which we called DeclareDesign Wizard, allows users to investigate and customize research designs in their web browser. We used R Shiny for implementing it and since this was my first large Shiny project, I wanted to reflect a bit on the development process and tell in which parts Shiny shone, and in which it didn’t.

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A Twitter network of members of the 19th German Bundestag – part II

This is the second part about my project that deals with the Twitter network of members of the Bundestag. After getting the necessary data, which was explained in part 1, we will now focus on creating a network graph with links between the representatives’ Twitter accounts for exploratory network analysis.

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A Twitter network of members of the 19th German Bundestag – part I

For the R tutorial that I gave at the WZB in the previous semester, I gave an introduction on how to query web APIs – specifically the Twitter API – and automated data extraction from websites (i.e. web scraping). I showed an example that combined both of these techniques for the goal of getting data about the Twitter activities of members of the current (19th) German Bundestag, which is the federal German parliament. The focus was especially on the question “who follows who” on Twitter. I thought it’s a nice little project showing how to use the Twitter API, do web scraping, combine the collected data and do some exploratory network analysis – all within the R environment. So I decided to polish the code a little bit, put in on GitHub and wrote two blog posts. The first part, i.e. this part, is all about getting the data.

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Zooming in on maps with sf and ggplot2

When working with geo-spatial data in R, I usually use the sf package for manipulating spatial data as Simple Features objects and ggplot2 with geom_sf for visualizing these data. One thing that comes up regularly is “zooming in” on a certain region of interest, i.e. displaying a certain map detail. There are several ways to do so. Three common options are:

  • selecting only certain areas of interest from the spatial dataset (e.g. only certain countries / continent(s) / etc.)
  • cropping the geometries in the spatial dataset using sf_crop()
  • restricting the display window via coord_sf()

I will show the advantages and disadvantages of these options and especially focus on how to zoom in on a certain point of interest at a specific “zoom level”. We will see how to calculate the coordinates of the display window or “bounding box” around this zoom point.

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Three ways of visualizing a graph on a map

When visualizing a network with nodes that refer to a geographic place, it is often useful to put these nodes on a map and draw the connections (edges) between them. By this, we can directly see the geographic distribution of nodes and their connections in our network. This is different to a traditional network plot, where the placement of the nodes depends on the layout algorithm that is used (which may for example form clusters of strongly interconnected nodes).

In this blog post, I’ll present three ways of visualizing network graphs on a map using R with the packages igraph, ggplot2 and optionally ggraph. Several properties of our graph should be visualized along with the positions on the map and the connections between them. Specifically, the size of a node on the map should reflect its degree, the width of an edge between two nodes should represent the weight (strength) of this connection (since we can’t use proximity to illustrate the strength of a connection when we place the nodes on a map), and the color of an edge should illustrate the type of connection (some categorical variable, e.g. a type of treaty between two international partners).

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Visualizing graphs with overlapping node groups

I recently came across some data about multilateral agreements, which needed to be visualized as network plots. This data had some peculiarities that made it more difficult to create a plot that was easy to understand. First, the nodes in the graph were organized in groups but each node could belong to multiple groups or to no group at all. Second, there was one “super node” that was connected to all other nodes (while “normal” nodes were only connected within their group). This made it difficult to find the right layout that showed the connections between the nodes as well as the group memberships. However, digging a little deeper into the R packages igraph and ggraph it is possible to get satisfying results in such a scenario.

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Creating a “balloon plot” as alternative to a heat map with ggplot2

Heat maps are great to compare observations with lots of variables (which must be comparable in terms of unit, domain, etc.). In some cases however, traditional heat maps might not suffice, for example when you want to compare multiple groups of observations. One solution is to use facets. Another solution, which I want to explain here, is to make a “ballon plot” with a fixed grid of rows and columns.

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Parallel Coordinate Plots for Discrete and Categorical Data in R — A Comparison

Parallel Coordinate Plots are useful to visualize multivariate data. R provides several packages/functions to draw Parallel Coordinate Plots (PCPs):

In this post I will compare these approaches using a randomly generated data set with three discrete variables.

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