bookdown | Thought splinters

Physik Libre: A bookdown project

Wed, 05 Jun 2019 00:00:00 +0000

The article is an interview with Michael Rundel. Michael is a teacher at a grammar school in Vienna/Austria and teaches physics, computer science, and media design. He talks about his experiences with bookdown in writing Physik Libre ( https://physikbuch.schule/), a new textbook on physics. His project is a practical implementation of cross-media publishing with bookdown, which I had described in my 7-part German tutorial on my other blog Gedankensplitter.

Status of the following interview

This article is an interview with Michael Rundel. Michael is a teacher at a grammar school in Vienna/Austria and teaches physics, computer science, and media design. He talks about his experiences with blogdown in writing Physik Libre ( https://physikbuch.schule/), a new textbook on physics. His project is a practical implementation of cross-media publishing with bookdown, which I had described by in my 7-part German tutorial on my other blog Gedankensplitter.

Michael Rundel (CC-BY Michael Rundel)

The interview took place two years ago, but I didn’t find until now the time to translate it into English and to publish the article in this weblog. I asked the questions in German via email and translated the text with the help of Google Translate, dict.cc, and thesarus.com. Where it was useful, I have links provided the first time the concept or software was mentioned. Subsequently, I have these same notions marked as red text. I edited the article with the premium version of Grammarly. If you are a native English speaker, I would be happy to know about the mistakes in grammar or other language issues. Please use the Edit Page button on the top right corner to provide improvement via a pull request to my GitHub repository.

I’ve gotten to know Michael during one of my talks about the free software environment for statistical computing and graphics R at Danube University Krems. In this talk titled “The many faces of R,” I demonstrated to (mostly computer science) teachers the many different use cases of R, driven by special R packages like bookdown. When people wanted to see a practical demonstration for school purposes, Michael came to the front and presented Physik Libre. I was delighted not only to have a school-based example but also to find a colleague near my hometown who is also working with bookdown.

Why another physics book?

Question: There are so many physics books why write one more?

There is already a very long tradition of Open Education Resources (OER) in the US. A couple of years ago I found English free physics books for study and teaching (for example Physics for K-12 (Sunil Kumar Singh), People’s Physics Book, CK-12 Physics - Intermediate, …). In German-speaking countries, there was something like that not yet. In the meantime, I have found with Physikunterricht Online an exciting project in the German-speaking area. But in my opinion it does not go far enough: There are more possibilities for interactive usage nowadays. And I want to build the most state-of-the-art physics book available for students.

We can see many extremely positive developments in recent years: web technologies have matured, projects like Gitbook allow you to create documents with minimal effort, we now have a variety of free program tools and Creative Commons licensed more than 1.1 billion media available on different websites and repositories for educational purposes available , and collaborative platforms like GitHub, GitLab or Bitbucket are no longer used exclusively by programmers.

Physik Libre as “Proof of Concept”

With Physik Libre I want to show what is possible today with the latest technology using the example of a physics book for the secondary school. It is a proof of concept – if you will. The last few years of Linux have shaped me, I’m afraid. The following points are important to me personally for the implementation of the project:

Page of ‘Physik Libre’ on a smartphone

Device-independent (Smart TV, PC, notebook, tablet, smartphone, e-book reader, print)
Operating system independent (web browser, ePub reader, PDF reader)
Free Standards (HTML, JS, CSS, ePub, PDF)
Free Licenses (CC-BY-SA 4.0, GPL 2)
Free Software supporting online publications like bookdown, GitBook, R, pandoc, LaTeX, LyX, Inkscape, etc., sharing all their material on free accessible repositories (GitHub / Gitlab / Bitbucket)
Free access and respect for privacy (no accounts, no registration, no tracking)
Contemporary (full-text search, sharing function, etc.) multilingual approach.

Question: What was the origin of your idea to write an online book?

Since my students days in the 1990ties, I have tinkered with web technology. Although I was always impressed what is achievable by combining HTML+JavaScript I never dreamed of the possibility of building full applications like Google maps or tinkercad by using pure web technologies.

In Austria, the current so-called digital schoolbook of today is a PDF document put on the internet. There is much more possible with today’s web technology. Much more!

Question: Could you give me a short overview of the historical development and the different phases of your project?

The idea was roughly born three years ago when I was experimenting with the canvas element, which I was using in my physics applets. This technology helped me to abandon flash applets. Don’t get me wrong! – Flash was a neat tool in its time, and I loved working with it. But it always felt like a workaround, and furthermore, it was proprietary software. At that time (2016), I thought there are all building blocks available to realize such a project with pure web technology.

Cover of the online physics book ‘Physik Libre’

The following months I learned [SVG] (https://en.wikipedia.org/wiki/Scalable_Vector_Graphics) and Inkscape, discovered Markdown and the document converter pandoc, the version control system git and the GitBook project. Summer 2017, I learned about the R package bookdown. The following school year, I have taught a class of 5th grades of Austrian secondary school (second year of the upper school) in physics. So I decided to start the work on the project.

Question: What were your most significant hurdles to overcome in finishing the Physik Libre project successfully??

The biggest challenge for me was time constraints. I managed to finish the project with sleeping sparsely.

Question: Were there some favorable circumstances for the project?

First of all: I would have never had a chance to do such a project if there were not such excellent tools like the Linux software and the combined efforts of the Wikimedia community.
On the technical side: I studied Mathematics and Physics, but I also have acquired some essential programming skills. This knowledge helped me to glue together some parts in the workflow of the book.
And finally on the personal side: First there is the love of my wife and my child. Also, my school principal is so generous as to give me a share of our schools web space for my project.

Question: I noticed that you deliberately do not call your book a textbook. What’s the difference between your physics book and a physics textbook?

A certified textbook always has to be based on the current syllabus and exam regulations. It contains competency-related tasks and guides for teachers. Most of the books websites – at least in the German-speaking countries – are not yet approved by the Ministries of Education. But they play an essential role as a “second opinion.”

In this sense, I understand my physics book project as a “second opinion” for teaching physics to high school students. It tries to explain connections as well as possible – and therefore also with all technically feasible means – for the mathematical level of a high school student.

Question: You have a full teaching commitment and family. How did you come up with the idea to approach such a mammoth project as an individual?

At the beginning of the project, two considerations were crucial.

First, everything - except for the actual writing of the text and the occasional drawing of graphics (where I could not find suitable content on Wikimedia Commons) - should be automated via programs.
The second point is not to view the book as my proprietary, but to view it as a collaborative project. All source files of the project should be hosted on a platform like GitHub or GitLab, thus minimizing the hurdle for other people’s participation in the book and encouraging them to participate –even if they find and correct just a spelling mistake.

But real life is quite different!

Page of ‘Physik Libre’ on a desktop computer

Concerning the first point: Although there are already many excellent free tools such as pandoc and bookdown for the generation of documents and final formats, the devil is in the details. For example, many images from Wikimedia Commons, have wrong dots per inch (DPI entries in the metadata. But this piece of information is essential for printing. If I use, for example, an animated gif picture in the web version, a particular frame must be captured and integrated for the print version.

For all such cases, I had to write programs that automate these tasks.

Reflecting on the second point, I mentioned I have to confess there is still a kind of Wild-West mood in the project: Until now I experiment a lot what is feasible. However, this also means that this additional functionality will change the program. Therefore it is challenging to find collaborators when even I do not know what the final features will be. For fruitful cooperation, one needs to establish a common goal with a framework that is the most salient aspects already consolidated.

I taught the fifth grade in physics last year and tried to write the content in the book in parallel with my lesson preparation so that my current students can benefit from my progress as well. So far, I have mostly succeeded, but it is very time-consuming, especially since I am – unfortunately – not a natural-born author.

Plans with Physik Libre

Question: It sounds that your book is still a work in progress. What are your plans for further developments?

I have already implemented solutions for most of the technical issues I have encountered. But these program snippets are not very elegant, and there may be a more straightforward answer - after all, I am not a professional programmer.

One problem I am still struggling with is the same-origin policy concept, which limits the embedding of content from other web sites. So far, I have not found a satisfactory solution to this problem.

Besides, much work needs to be done on the documentation before I want to release the project on Github or GitLab.

Thank you, Michael, for this interview!

What is obvious, and for whom?

Tue, 17 Oct 2017 00:00:00 +0000

In the last few weeks, I tried to work with bookdown, an R package developed by Yihui Xie. This program is/was for me much harder to understand, unlike blogdown by the same author. In blogdown, I could even – after some initial problems – write a tutorial which even the developer applauded :sweat_smile:.

But with bookdown, it was different: Not only that I misunderstood some program functions but more importantly, I could not adequately report my problems in one case, I did not communicate vital information in the other case I did not look at the right place where my question was explicitly addressed. It is not a surprise that Yihui Xie got angry with me and even wrote a blog post about the incident. He gave me the advice:

Please do not make these assumptions when filing issues

Be aware: This is a somewhat theoretical/philosophical discussion.

For me, as a professional educator, this is a fundamental question. Where to start with explanations and where to stop? Should I provide just the information to solve the problem, or should I give some background information? What kind of advice should I give to prevent similar issues in the future? These are examples of questions I have to consider as a teacher all the time. But this time, I am on the other side of this communication exchange - I am the learner and student, and I am the one who has to ask the expert.

Yihui Xie is not blaming me as a user, as he wrote in his last paragraph of the mentioned blog post. You can see his positive attitude in the post on The Minimal Reproducible Example Paradox where he is complaining that many users do not provide a minimal reproducible example or do not know how to produce one. He comes to a somewhat depressing conclusion:

How many times have I reminded a user of posting a minimal, self-contained, and reproducible example (reprex)? Probably 500 times. How many times do I think I will still need to remind users of this? Perhaps 5000 times.

But again: This is a typical situation we have in education as well. We are explaining the same thing over and over but — to different people, students, learners, classes, etc. Even if we explicitly mention common errors and misunderstandings, some learners will always commit these mistakes. When we describe operations you should not undertake, you can be sure there are one or two who will follow precisely these wrong paths.

Tacit knowledge and language games

So what? Are people dumb? Do they deliberately ignore advice? I don’t think so, but instead, there is a gap which cannot be overcome only with linguistic means. It is also a question of transferring tacit knowledge’ to use a notion introduced by Michael Polanyi:

I shall reconsider human knowledge by starting from the fact that {{< hl >}}we know more than we can tell{{< /hl >}}.(Polanyi 2009)

Many philosophers (e.g., Søren Kirkegaard, Ludwig Wittgenstein, Gregory Bateson, Susan Langer, Jürgen Habermas, Nelson Goodman, to name a few) have reflected about the limitation of linguistic expressions. Wittgenstein, for example, has pointed out that we cannot explain the meaning of every word or sentence because we have to use language with other words and sentences. It is an endless regress that we cannot solve with language alone. We have to share a common ground, and we have to know how “to play the language game.” Following some quotes to give you a flavor of the argument:

One has already to know (or be able to do) something to be capable of asking a thing’s name. But what does one have to know? (Philosophical Investigations 30) … When one shows someone the king in chess and says: “This is the king,” this does not tell him the use of this piece-unless he already knows the rules of the game up to this last point. (31) … Someone coming into a strange country will sometimes learn the language of the inhabitants from ostensive definitions that they give him; and he will often have to ‘guess’ the meaning of these definitions; and will guess sometimes right, sometimes wrong. (Wittgenstein 1961)

To use a famous philosophical example (Quine 1960): If I point to a white rabbit and say in my foreign language, “Gavagai!” you have to guess the meaning. Do I say, “There is a rabbit!” or “Look at the nice white color!” So even an ostensive definition is under-determined and does not help to choose the right interpretation and to solve the ambiguity of meaning in our speech acts.

One proposal which could serve as an avenue of escape for this gap or paradox is to invent a special kind of notational system. Common examples to demonstrate this strategy is chess notation or musical notation. I believe that a minimal reproductive example or to deliver the sessionInfo() is also a kind of notational system. But the problem is the same: One has to learn this (new) language to use it correctly.

Many different layers

The malice of the situation is the assumption that from the fact that we are using the same (English) words and sentences that we communicate the same meaning and understand to each other. The expert believes that (s)he has expressed every necessary information and so the novice in asking a question. – And this is mostly correct – from his/her point of view or understanding.¹

I have reflected why for me, using bookdown was so much more complicated than blogdown. I started several months ago with bookdown, but I gave up and started another trial after I had some success with blogdown. This sequence seems weird as it appears that for Yihui Xie, the situation was inverse.²

I think there are different reasons:

Blogdown was written together with Amber Thomas and Alison Presmanes Hill. It was an excellent inventive and successful strategy to integrate authors who can provide the perspective of the user side. In the blogdown book, there are some beneficial chapters about action strategies. They give, on the one hand, practical tips and contain, on the other hand, some (technical) simplification. We, educationalists, call this method “pedagogical reduction”). I refer to chapters like A quick example or A recommended workflow.
The success in working with blogdown is more straight and comes in smaller bits and pieces. You write a sentence with Markdown in your blog, and you can see the result immediately. It seems - at least for laypeople like me - that in blogdown, there are not so many hidden conversion processes as this appears to be the case in bookdown. Bookdown, by definition, provides the means for cross-media publishing resulting in three different products (website, PDF, and ePub), all three with their underlying structure and rules.

The importance of mental models

But there is one common point why both blogdown and bookdown are intrinsically difficult to understand for novices: Many different layers of software are working together to produce the result. I am not sure if I am even able to enumerate these different layers correctly: There is

the used hardware,
the operating system,
R with all its various packages,
the programming and writing environment RStudio,
Rmarkdown using pandoc,
knitr,
blogdown or bookdown,
the used theme,
with needs for adoption CSS knowledge,
git and GitHub,
and last but not least, Netlify.

All of these different tools work on top of each other and/or together. And all of these different levels have their complexities, laws, functions, manuals, commands, etc.

As long as everything works fine, there is no need to understand the different parts and their interaction and/or synergy. But when something breaks down, then a shift of focus occurs, or as Heidegger says, the worldliness becomes obvious, changing tool usage from “ready-to-hand” to “present-at-hand”(Heidegger 2008). In “ready-to-hand” awareness, you are using tools to fulfill their purpose (to write a blog post); in a breakdown (= “ready-to-hand” awareness), you get consciousness of the complexities inside your tools machinery.³

But here comes now the problem: As users, we are only experts in “ready-to-hand” awareness, and we have no clue about the functionality inside the black box. We can only report some weird behavior about some experienced phenomenon from the “ready-to-hand” perspective. We, laypersons, have constructed a mental model about the functionality of our tools, and we are reporting about the problems with the underlying implicit assumptions of our mental model. The mental model functions as a world view: We see all the different objects, people, etc., under a particular perspective guided by our underlying tacit assumptions.

After the breakdown, we should question our mental model, but this is very difficult: Our worldview has worked successfully so far. One will not change the world view with just one different fact. The same happens with scientific theories: One other point is a challenge to elaborate on the theory, improve it, and incorporate the anomaly into the argument. Maybe the problem lies in the reluctant fact itself (e.g., the software has a bug, or the author misreported the effect).

Lesson learned

So what the fuss with all these abstract ideas? Where is the practical impact of all these considerations? — I make the case in this article that we should focus separately on two different kinds of explanations:

On the one hand, we users need “ready-to-hand” reasons which are easy to follow even if they are simplified and do not cover all eventualities. We need guidelines, step-by-step (video)-tutorials, etc. Are there shortcuts, tips, and rules of thumb one could follow? And we would need tons of examples! But people who provide this kind of explanation should be aware: This explanation always is under-determined and cannot prevent misunderstandings. Lacking the necessary knowledge, we still have to interpret what “Gavagai!” means.
On the other hand, we users need at the same time “present-to-hand” explanations to build up correct mental models of the inherent complexities and functionalities of the tools. Which software components rely on which other parts? What is the task of component X, and how is it related to the ready-to-hand functionality? But people who provide this kind of explanation should be aware: This level of explication is not a technical one, not directed to other experts. (This is another critical third level of description and documentation, one I will not cover here in this article). So we would need individual formats like diagrams of the interconnectedness and synergistic effects. The result is a kind of multiple representations and would provide additional access to discover the functionality of different parts of the software machinery.⁴
A piece of advice like “Please do not make this assumption when filing issues.” are basic ethical guidelines but not very practical and helpful. We are always using (implicit) assumptions. In stating one proposition, we rely on a set of different assumptions; otherwise, we could not use language and construct meaningful sentences. The problem is to know what assumptions are to test and what assumptions are to rely on.⁵

There is no possibility to examine all belief systems at the same time. The whole book “On Certainty” by Ludwig Wittgenstein Wittgenstein (1975) is full of aphorisms about tacit assumptions we rely on. Our knowledge does not consist of separated propositions but is a system of interconnected views/opinions. I will close this post with some quotes by Wittgenstein to illustrate this point.

§139. Not only rules, but also examples are needed for establishing a practice. Our rules leave loop-holes open, and the practice has to speak for itself."

§142. It is not single axioms that strike me as obvious, it is a system in which consequences and premises give one another mutual support.

§144. The child learns to believe a host of things. I.e. it learns to act according to these beliefs. Bit by bit there forms a system of what is believed, and in that system some things stand unshakeably fast and some are more or less liable to shift. What stands fast does so, not because it is intrinsically obvious or convincing; it is instead held fast by what lies around it.⁶

StackOverflow for instance, is very, very good for “ready-to-hand” explanations but does - as far as I know - a lousy job for building up mental models. Discussions about different but similar software packages, their advantages and disadvantages are forbidden.⁷

References

Heidegger, Martin. 2008. Being and Time. Reprint. New York: Harper Perennial Modern Classics.

Polanyi, Michael. 2009. The Tacit Dimension. University of Chicago Press.

Quine, Willard Van Orman. 1960. Word and Object. The Mit Press.

Wittgenstein, Ludwig. 1961. Philosophical investigations. New York: Macmillan.

———. 1975. On Certainty. Revised ed. Oxford: John Wiley; Sons Ltd.

I could tell some jokes about misunderstandings between Germans and Austrians, both using German as their native language. ↩︎
He said that blogdown was especially complicated to develop, but I cannot find the place at the moment to quote it correctly. ↩︎
For an understandable description of the philosophical concept of ‘breakdown’ read this example on Human-Computer Interaction ↩︎
An essential step for me in understanding the complex template structure of Hugo was to write in every template the sentence: “This here is the template ” and to see what happens in different situations ↩︎
BTW: This is the same conclusion as Yihui Xie has drawn: “To clarify, I’m not blaming this user. I can totally understand it. Many users do the same thing. The problem is that there are so many possibilities for software to screw up, so you have to describe everything clearly to eliminate as many possibilities as possible.”— So we do have the same analysis. Still, I propose (in addition to reflect and report all hidden assumptions) another new long-term strategy (namely helping to build up correct mental models about the complex software dependencies) to prevent similar faults as I have committed. ↩︎
To prevent a possible misunderstanding: I do not think that only or even predominantly software engineers are responsible for the two mentioned explanation levels. Their expertise is to develop programs, document them, and resolve bugs. I just want to point out that there should be more focus on these two levels and that more people should be concerned about providing information on these two levels. ↩︎
At least this is *my* mental model from StackOverflow For instance, the moderator closed my question about the difference between packrat and checkpoint as off-topic. ↩︎