Category: R

Valerio Gherardi takes us through the concept of k-grams:

The post is structured as follows: we start by giving a succinct theoretical introduction to kk-gram models. Subsequently, we illustrate how to train a kk-gram model in R using kgrams, and explain how to use the standard perplexity metric for model evaluation or tuning. Finally, we use our trained model to generate some random text at different temperatures.

This goes into some depth on the topic and is worth giving a careful read.

Nathaniel Schmucker explains some of the principles of k-means clustering:

k-Means is easy to implement. In R, you can use the function kmeans() to quickly deploy an efficient k-Means algorithm. On datasets of reasonable size (thousands of rows), the kmeans function runs in fractions of a second.

k-Means is easy to interpret (in 2 dimensions). If you have two features of your k-Means analysis (e.g., you are grouping by length and width), the result of the k-Means algorithm can be plotted on an xy-coordinate system to show the extent of each cluster. It’s easy to visually inspect the assignment to see if the k-Means analysis returned a meaningful insight. In more dimensions (e.g., length, width, and height) you will need to either create a 3D plot, summarize your features in a table, or find another alternative to describing your analysis. This loses the intuitive power that a 2D k-Means analysis has in convincing you or your audience that your analysis should be trusted. It’s not to say that your analysis is wrong; it simply takes more mental focus to understand what your analysis says.

The k-Means analysis, however, is not always the best choice. k-Means does well on data that naturally falls into spherical clusters. If your data has a different shape (linear, spiral, etc.), k-Means will force clustering into circles, which can result in outputs that defy human expectations. The algorithm is not wrong; we have fed the algorithm data it was never intended to understand.

There’s a lot of depth in this article which makes it really interesting.

Gary Hutson has a new package for us:

The package aim is to make it easier to convert the outputs of the lists from caret and collapse these down into row-by-row entries, specifically designed for storing the outputs in a database or row by row data frame.

This is something that the CARET library does not have as a default and I have designed this to allow the confusion matrix outputs to be stored in a data frame or database, as many a time we want to track the ML outputs and fits over time to monitor feature slippage and changes in the underlying patterns of the data.

I like the way caret shows the confusion matrix when I’m reviewing result on my own, but I definitely appreciate efforts to make it easier to handle within code—similar to how broom reads linear regression outputs. H/T R-bloggers

Jack Davis explains the concept of polychoric correlation:

In polychoric correlation, we don’t need to know or specify where the boundary between “good” and “very good” is, just that it exists. The distribution of the ordinal responses, along with the assumption that the latent values follow a normal distribution, is enough that the polychor() function in the polycor R package can do that for us. In most practical cases, you don’t even need to know where the cutoffs are, but they are useful for demonstration that the method works.

Polychoric correlation estimates the correlation between such latent variables as if you actually knew what those values were. In the examples given, we start with the latent variables and use cutoffs to set them into bins, and then use polychoric on the artificially binned data. In any practical use case, the latent data would be invisible to you, and the cutoffs would be determined by whoever designed the survey.

Read on for a demonstration of the process in R.