PDF is a format created to mimic the typical size paper (A4) on a computer. Although not completely static, it is generally a static format. The format is an anachronism when it comes to computers. There is no particular reason to stick with this format over computer-native formats such as HTML.

Many other journals currently use or experiment with computer-native formats. PubMed for instance by default displays full text articles in HTML, but also have their own experimental PubReader, and allows PDF and EPUB download.

PLOS One (the journal of the article above) also has HTML as default and supports PDF download.

As I see it, non-PDF formats are clearly superior and will become the most common within a decade. Currently, our papers are only available in PDF. In my opinion this is a mistake and we should display them as HTML by default.

Displaying them as HTML by default requires more work by editors who have to insert the manuscripts into Wordpress and make sure they look OK. Perhaps this task could be outsourced to authors in the future as well, but that will require more technical work by the web designers.

Furthermore, HTML is not the end of the evolution of written formats. It is possible to embed code with interactive figures for papers. For instance, R has Shiny to do this.

I am willing to put in some extra work converting submissions to both PDF and HTML when publishing. Or letting authors do it themselves when they have the ability (they will be given a temporary login for the journal Wordpress for posting the paper).

We can work on getting e.g. Shiny to work for authors who wish to use that for visualization of results.

Thoughts?

One can also easily embed visualizations from Google Drive. Here's an example from my blog. http://emilkirkegaard.dk/en/?p=4556

The journal software uses Wordpress as does the blog, so this is already supported.

As indicated above, the emerging standard is to publish as HTML or enhanced HTML as well as PDF. The change would solely be that we also start publishing papers in HTML or eHTML. We will of course continue publishing PDFs for those who desire those.