How fractals helped my students to master package development in R

Last semester I taught an R programming at MIMUW. My lectures are project oriented, the second project was related to package development. The idea was straightforward: each team of students shall create a package that produces IFS fractals (based on iterated function systems). Each package shall have two generic functions: create() and plot(), documentation and vignette. Fractals shall be implemented with the use of S3 or S4 classes.

I have students with different backgrounds. Mostly statistics, but some are from physics, psychology or biology. I was a bit unsure how they will deal with concepts like iterated contractions.
After all results exceeded my expectations.

Guess what is happening with students engagement when their packages start producing nice plots. Their need/hunger for more leads to beautiful things.

This team got interested in nonlinear transformations. They manage to create Apollonian Gasket generator and much more. See their vignette and package here.

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This team got interested in probabilistic mixtures of two fractals. They developed a Shiny app that mixes two sets of contractions with given mixture proportions. Here is a mixture of Sierpinski gasket and a tree. Find out their vignette here.

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This team got interested in random fractals. They developed fractal generator that draws parameters of each contraction. In result they get beautiful random shapes like these. Here is their vignette.

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And these two teams got interested in different ways of fractal colouring. Vignettes of Team 1 and Team 2

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After all it turns out that fractals are very addictive!
Use it with care ;-)

DALEX: how would you explain this prediction?

Last week I wrote about single variable explainers implemented in the DALEX package. They are useful to plot relation between a model output and a single variable.

But sometimes we are more focused on a single model prediction. If our model predicts possible drug response for a patient, we really need to know which factors drive the model prediction for a particular patient. For linear models it is relatively easy as the structure of the model is additive. In 2017 we have developed breakDown package for lm/glm models.

But how to explain/decompose/approximate predictions for any black box model?
There are several approaches. The (probably) most known is LIME with great examples for image and text data. There is an R port lime developed by Thomas Pedersen. In collaboration with Mateusz Staniak we developed live package, similar approach, easy to use with models created by mlr package.
The other technique that can be used here are Shapley values which use attribution theory/game theory to attribute effects of different variables for a single prediction.

Recently we have developed a yet another approach (paper under preparation, implemented in the breakDown version 0.4) that works in a model agnostic way (here you can check how to use it for caret models). You can play with it via the single_prediction() function in the DALEX package.
Such decomposition is useful for many reasons mentioned in papers listed above (deeper understanding, validation, trust, etc).
And, what is really extra about the DALEX package, you can compare contributions of different models on the same scale.

Let’s train three models (glm / gradient boosting model and random forest model) to predict quality of wine. These models are very different in structure. In the figure below, for a single wine, we compare predictions calculated by these models. For this single wine, for all models the most influential variable is the alcohol concentration as the wine has much higher concentration than average. Then pH and sulphates take second and third positions in all three models. Looks like models have some agreement even if they structure is very different.


If you want to learn more about DALEX package and decompositions for model predictions please consult following cheatsheet or the DALEX website.

If you want to learn more about explainers in general, join our DALEX Invasion!
Find our DALEX workshops at SER (Warsaw, April 2018), ERUM (Budapest, May 2018), WhyR (Wroclaw, June 2018) or UseR (Brisbane, July 2018).


DALEX: understand a black box model – conditional responses for a single variable

Black-box models, like random forest model or gradient boosting model, are commonly used in predictive modelling due to their elasticity and high accuracy. The problem is, that it is hard to understand how a single variable affects model predictions.

As a remedy one can use excellent tools like pdp package (Brandon Greenwell, pdp: An R Package for Constructing Partial Dependence Plots, The R Journal 9(2017)) or ALEPlot package (Apley, Dan. Visualizing the Effects of Predictor Variables in Black Box Supervised Learning Models (2016)).
Now one can use the DALEX package to not only plot a conditional model response but also superimpose responses from different models to better understand differences between models.

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Consult the following vignette to learn more about the DALEX package and explainers for a single variable.


if you want to learn more about explainers, join our DALEX Invasion!
Find our DALEX workshops at SER (Warsaw, April 2018), ERUM (Budapest, May 2018), WhyR (Wroclaw, June 2018) or UseR (Brisbane, July 2018).

chRistmas tRees

Year over year, in the last classes before Christmas I ask my students to create a Christmas tree in R.
Classes are about Techniques of data visualisation and usually, at this point, we are discussing interactive graphics and tools like rbokeh, ggiraph, vegalite, googleVis, D3, rCharts or plotly. I like this exercise because with most tools it is easy to create a barchart, but how good must be the tool and the craftsman to handle a christmas tree?

Here is what they did this year (having around 1 hour to finish the task). Knitr scripts.

Update: I am still getting new submissions, feel free to submit yours as well.

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archivist: Boost the reproducibility of your research

A few days ago Journal of Statistical Software has published our article (in collaboration with Marcin Kosiński) archivist: An R Package for Managing, Recording and Restoring Data Analysis Results.

Why should you care? Let’s see.


Would you want to retrieve a ggplot2 object with the plot on the right?
Just call the following line in your R console.


Want to check versions of packages loaded when the plot was created?
Just call


Wishful Thinking?

When people talk about reproducibility, usually they focus on tools like packrat, MRAN, docker or RSuite. These are great tools, that help to manage the execution environment in which analyses are performed. The common belief is that if one is able to replicate the execution environment then the same R source code will produce same results.

And it’s true in most cases, maybe even more than 99% of cases. Except that there are things in the environment that are hard to control or easy to miss. Things like external system libraries or dedicated hardware or user input. No matter what you will copy, you will never know if it was enough to recreate exactly same results in the future. So you can hope that results will be replicated, but do not bet too high.
Even if some result will pop up eventually, how can you check if it’s the same result as previously?

Literate programming is not enough

There are other great tools like knitr, Sweave, Jupiter or others. The advantage of them is that results are rendered as tables or plots in your report. This gives you chance to verify if results obtained now and some time ago are identical.
But what about more complicated results like a random forest with 100k trees created with 100k variables or some deep neural network. It will be hard to verify by eye that results are identical.

So, what can I do?

The safest solution would be to store copies of every object, ever created during the data analysis. All forks, wrong paths, everything. Along with detailed information which functions with what parameters were used to generate each result. Something like the ultimate TimeMachine or GitHub for R objects.

With such detailed information, every analysis would be auditable and replicable.
Right now the full tracking of all created objects is not possible without deep changes in the R interpreter.
The archivist is the light-weight version of such solution.

What can you do with archivist?

Use the saveToRepo() function to store selected R objects in the archivist repository.
Use the addHooksToPrint() function to automatically keep copies of every plot or model or data created with knitr report.
Use the aread() function to share your results with others or with future you. It’s the easiest way to access objects created by a remote shiny application.
Use the asearch() function to browse objects that fit specified search criteria, like class, date of creation, used variables etc.
Use asession() to access session info with detailed information about versions of packages available during the object creation.
Use ahistory() to trace how given object was created.

Lots of function, do you have a cheatsheet?

Yes! It’s here.
If it’s not enough, find more details in the JSS article.

Explain! Explain! Explain!

Predictive modeling is fun. With random forest, xgboost, lightgbm and other elastic models…
Problems start when someone is asking how predictions are calculated.
Well, some black boxes are hard to explain.
And this is why we need good explainers.

In the June Aleksandra Paluszynska defended her master thesis Structure mining and knowledge extraction from random forest. Find the corresponding package randomForestExplainer and its vignette here.

In the September David Foster published a very interesting package xgboostExplainer. Try it to extract useful information from a xgboost model and create waterfall plots that explain variable contributions in predictions. Read more about this package here.

In the October Albert Cheng published lightgbmExplainer. Package with waterfall plots implemented for lightGBM models. Its usage is very similar to the xgboostExplainer package.

Waterfall plots that explain single predictions are great. They are useful also for linear models. So if you are working with lm() or glm() try the brand new breakDown package (hmm, maybe it should be named glmExplainer). It creates graphical explanations for predictions and has such a nice cheatsheet:


Install the package from

Thanks to RStudio for the cheatsheet’s template.

intsvy: PISA for research and PISA for teaching

The Programme for International Student Assessment (PISA) is a worldwide study of 15-year-old school pupils’ scholastic performance in mathematics, science, and reading. Every three years more than 500 000 pupils from 60+ countries are surveyed along with their parents and school representatives. The study yields in more than 1000 variables concerning performance, attitude and context of the pupils that can be cross-analyzed. A lot of data.

OECD prepared manuals and tools for SAS and SPSS that show how to use and analyze this data. What about R? Just a few days ago Journal of Statistical Software published an article ,,intsvy: An R Package for Analyzing International Large-Scale Assessment Data”. It describes the intsvy package and gives instructions on how to download, analyze and visualize data from various international assessments with R. The package was developed by Daniel Caro and me. Daniel prepared various video tutorials on how to use this package; you may find them here:

PISA is intended not only for researchers. It is a great data set also for teachers who may employ it as an infinite source of ideas for projects for students. In this post I am going to describe one such project that I have implemented in my classes in R programming.

I usually plan two or three projects every semester. The objective of my projects is to show what is possible with R. They are not set to verify knowledge nor practice a particular technique for data analysis. This year the first project for R programming class was designed to experience that ,,With R you can create an automated report that summaries various subsets of data in one-page summaries”.
PISA is a great data source for this. Students were asked to write a markdown file that generates a report in the form of one-page summary for every country. To do this well you need to master loops, knitr, dplyr and friends (we are rather focused on tidyverse). Students had a lot of freedom in trying out different things and approaches and finding out what works and how.

This project has finished just a week ago and the results are amazing.
Here you will find a beamer presentation with one-page summary, smart table of contents on every page, and archivist links that allow you to extract each ggplot2 plots and data directly from the report (click to access full report or the R code).


Here you will find one-pagers related to the link between taking extra math and students’ performance for boys and girls separately (click to access full report or the R code).


And here is a presentation with lots of radar plots (click to access full report or the R code).


Find all projects here:

And if you are willing to use PISA data for your students or if you need any help, just let me know.

DIY – cheat sheets

I found recently, that in addition to a great list of cheatsheets designed by RStudio, one can also download a template for new cheatsheets from RStudio Cheat Sheets webpage.
With this template you can design your own cheatsheet, and submit it to the collection of Contributed Cheatsheets (Garrett Grolemund will help to improve the submission if needed).

Working on a new cheatsheet is pretty enjoying. You need to squeeze selected important stuff into a quite small surface like one or two pages.
Lots of fun.
I did it for eurostat and survminer packages (cheatsheets below).
And would love to see one for caret.

How to weigh a dog with a ruler? (looking for translators)

We are working on a series of comic books that introduce statistical thinking and could be used as activity booklets in primary schools. Stories are built around adventures of siblings: Beta (skilled mathematician) and Bit (data hacker).

What is the connection between these comic books and R? All plots are created with ggplot2.

The first story (How to weigh a dog with a ruler?) is translated to English, Polish and Czech. If you would like to help us to translate this story to your native language, just write to me (przemyslaw.biecek at gmail) or create an issue on GitHub. It’s just 8 pages long, translations are available on Creative Commons BY-ND licence.

Click images below to get the comic book:
In English

In Polish

In Czech

The main point of the first story is to find the relation between Height and Weight of different animals and then assess the weight of dinosaur T-Rex based only on the length of its skeleton. A method called Regression by Eye.


PISA 2015 – how to read/process/plot the data with R

Yesterday OECD has published results and data from PISA 2015 study (Programme for International Student Assessment). It’s a very cool study – over 500 000 pupils (15-years old) are examined every 3 years. Raw data is publicly available and one can easily access detailed information about pupil’s academic performance and detailed data from surveys for studetns, parents and school officials (~2 000 variables). Lots of stories to be found.

You can download the dataset in the SPSS format from this webpage. Then use the foreign package to read sav files and intsvy package to calculate aggregates/averages/tables/regression models (for 2015 data you shall use the GitHub version of the package).

Below you will find a short example, how to read the data, calculate weighted averages for genders/countries and plot these results with ggplot2. Here you will find other use cases for the intsvy package.