## Making accessible HTML from LaTeX sources — an additional experiment

Last week I reported on my initial experiments using Pandoc and LaTeXML to convert LaTeX to HTML. Here are links to the PDF produced with pdfLaTeX and the HTML:

If you’re like me, you’ll prefer the LaTeXML version to the Pandoc version, but as I pointed out the LaTeXML version includes CSS to customize the styling and the Pandoc version doesn’t. I did a quick Google search, figured out how to add CSS (and a table of contents) to the HTML output from Pandoc, and found a very nice CSS style to use (from Pascal Hertlief on Github). It’s possible that I’ll fiddle with Pascal’s CSS a bit, but there’s a good chance I won’t change it at all. It makes the HTML look really, really nice:

What I haven’t tried yet is converting LaTeX source that includes PDF figures. Let’s try that now and see how it works.

It took a while to get ImageMagick installed, to write a short Perl script to change all of the references to EPS files into references to PNG files and convert the EPSs to PNGs, but I really like the results. But this gets two of my three “to-dos” out of the way.

• Check CSS styling for Pandoc.
• Show the results to an accessibility expert at UConn and get some feedback on the different approaches.
• See what happens with figures when they’re included in a LaTeX document.

Now I just (just?) need to check with an accessibility expert to confirm that the HTML is accessible. If it is, I’m all set.

By the way, if you’re interested in seeing the Perl script, let me know. It will be posted in the Github archive where I post the LaTeX source for my notes later this fall, but I’d be happy to send you a copy now if you drop me a line.

## Making accessible HTML from LaTeX sources – some initial impressions

Some of you know that I’ve been making notes from my graduate course in Population Genetics available online for nearly 20 years (http://darwin.eeb.uconn.edu/uncommon-ground/eeb348/notes/). What a smaller number of you know is that I use LaTeX to write my notes and pdfLaTeX to produce PDFs from the LaTeX source. So far as I can tell (using ANDI), the PDFs produced in this way provide some elements that aid accessibility, but I am exploring options to produce HTML from the same source that might produce documents that are accessible to more readers. For my first experiment, I used the LaTeX file from 2019 that produced notes on resemblance among relatives. Here are links to three versions of the notes:

Both approaches to producing HTML are straightforward.

For Pandoc:

pandoc --standalone --mathjax -o quant-resemblance-pandoc.html quant-resemblance.tex


For LaTeXML:

latexml --includestyles --dest=quant-resemblance.xml quant-resemblance.tex
latexmlpost --dest=quant-resemblance-latexml.html quant-resemblance.xml


With the default options, I like the look of the LaTeXML version better, but it also includes CSS customizations and the Pandoc version doesn’t. It’s probably possible to include customized CSS with Pandoc, but I haven’t had a chance to investigate that yet. I also haven’t had a chance to consult anyone who knows how to judge accessibility of documents. When I’ve had a chance to do that. I’ll return with a report. (Don’t hold your breath. I am a dean, so I don’t have a lot of time on my hands.)

Here’s my to-do list, so that I don’t forget:

• Check CSS styling for Pandoc.
• Show the results to an accessibility expert at UConn and get some feedback on the different approaches.
• See what happens with figures when they’re included in a LaTeX document.

If you have additional questions, let me know, and I’ll add them to the list.

## The Mindset List for the Class of 2022

20 years ago Ron Nief, emeritus Director of Public Affairs, at Beloit College created the Mindset List. Every August since then the Beloit Mindset List has been a feature of higher education in the US. It’s been maligned (http://www.beloitmindlessness.com/2018/08/19/more-of-the-same/,http://www.beloitmindlessness.com/2018/08/21/here-we-go-again/) and it’s been parodied (https://www.theonion.com/a-look-at-the-class-of-2019-1819592320), but as I wrote a couple of years ago “I always get a kick out of looking it over. It reminds me of how old I am.”

I’m a couple of years older now than I was a couple of years ago, and I still get a kick out of looking the list over. Here are a few of the items that I found especially striking:1

• Among the iconic figures never alive in their lifetime are Victor Borge, Charles Schulz, and the original Obi-Wan Kenobi Alec Guinness. That last one really hurts. I remember seeing the original in a movie theater.
• They have grown up afraid that a shooting could happen at their school, too.
• Presidential candidates winning the popular vote and then losing the election are not unusual.
• There has never been an Enron.

1. The comments in bold italic are my commentary.

## This is a spam conference if I ever saw one

In my Spam folder this morning…

Dear Dr. Kent E Holsinger ,

Greetings from  WCEOGPE-2018.

On behalf of the Organizing committee, we are delighted to invite you to be a speaker at 3rd World Congress & Expo on Oil, Gas & Petroleum EngineeringWCEOGPE-2018) on April 16-17, 2018 which will be held in Dubai, UAE which brings well versed scrutinizers at one place. It provides a platform to have open discussions, knowledge sharing and interactive sessions with field experts. WCEOGPE-2018 will focus on the theme Pioneering Revolutionary Technologies in Oil, Gas & Petroleum Industries .

This is our humble request to join us in the WCEOGPE-2018 to up-skill your next generations to protect and continue our valuable innovations.

For questions about topics, registration or other enquiries, please do not hesitate to contact me.  I will be happy to go into further details regarding any concerns you might have.

Best regards,
Rohith Rao
WCEOGPE Summit-2018
P: +91-779-979-0002
E: WCEOGPE-2018@scientificfederation.com

If you don’t want to receive any further e-mail from WCOEGPE Summit-2018, please revert back with a subject Unsubscribe.

Are there people who accept these invitations? Who in their right mind would invite me to a meeting on oil, gas, and petroleum engineering?

## 2017 Graduate Commencement Ceremonies @UConn

The University of Connecticut celebrated its 138th Commencement exercises last weekend.1 The Graduate School now confers so many degrees that we have two ceremonies, a ceremony for recipients of master’s degrees on Saturday afternoon and a ceremony for recipients of doctoral degrees on Monday evening. Stuart Rothenburg, who received his

Stuart Rothenburg, who received his PhD in Political Science from UConn, addressed the graduating class at the master’s ceremony. If you’d like to see his remarks, follow the link below, click on “Graduate School Ceremony: Masters Candidates, May 6, 2017”, and then click on “Commencement Address” at the left.

I addressed the graduating class at the doctoral ceremony on behalf of Elizabeth Jockusch, this year’s winner of the Edward C. Marth Award for Mentorship, and Takiyah Harper-Shipman was our student speaker. If you’d like to see my remarks, follow the link below, click on “Graduate School Ceremony: Doctoral Candidates, May 8, 2017”,  and then click on “Welcome Remarks” at the left. After a brief welcome from Interim Provost Jeremy Teitelbaum, you’ll see me. If you’d like to see Takiyah’s remarks, click on “Commencement Address” instead. If for some reason you’d like to read my remarks, keep scrolling down (or click through if you’re on the home page).

University of Connecticut Commencement Ceremonies 2017 (from Total Webcasting)

## On the importance of openness in scholarship

I was recently looking something up in Evernote, and I ran across a post by Eric Rauchway on Crooked Timber from July 2013. The post concerns the American Historical Association/s proposed recommendation for an embargo on dissertations. The AHA adopted a Statement on Policies Regarding the Option to Embargo Completed PhD Dissertations on 19 July 2013. It begins

The American Historical Association strongly encourages graduate programs and university libraries to adopt a policy that allows the embargoing of completed history PhD dissertations in digital form for as many as six years.

There was a lot of debate about the wisdom of dissertation embargoes before and after the statement was announced. Rauchway finished his post with a comment that all of us should think about.

When we find ourselves trying to make scholarship less readily available – however good our intentions – we should probably ask ourselves if we can solve our problems some other way.

## 3-minute thesis @UConn @U21News

In 2008, the University of Queensland started the 3-minute thesis competition, in which advanced doctoral students are challenged to summarize their dissertation research for a non-specialist audience in three minutes. As they put it on the 3-MT website,

An 80,000 word thesis would take 9 hours to present.

Their time limit… 3 minutes

UConn has sponsored a local 3-minute thesis competition since the fall of 2013. Each year we send a video recording of the winner of our local competition to a “virtual” competition sponsored by Universitas 21. Judges in the international competition award a first prize and a highly commended prize. In addition, visitors to the U21 website can vote for their favorite presentation, with the presentation receiving the highest number of votes being given the Peoples Choice award. More than 3400 votes were cast in this year’s competition, and I’m delighted to report that Islam Mosa, a PhD student in Chemistry at UConn, is the 2016 People’s Choice award winner. Take three minutes of your time and watch his presentation below. You will be inspired.

## You get what you measure

Last December I saw a fascinating talk by Julie Posselt.1 She described work deriving from her PhD dissertation in which she sat in on meetings of doctoral admissions committees in a variety of disciplines at several different (and anonymous) elite private and public research university. She described how overreliance on “cut points” for GPA, GRE scores, or both led to admissions decisions that favored applicants from relatively privileged backgrounds. Even though the faculty making those decisions were almost uniformly committed to ensuring that they admitted doctoral students from a wide variety of backgrounds, the pool of admitted students was far less diverse than the pool of applicants. As she put it in a piece for Inside Higher Ed earlier this year: “Despite their good intentions to increase diversity, broadly defined, admissions work was laced with conventions — often rooted in inherited or outdated assumptions — that made it especially hard for students from underrepresented backgrounds to gain access.”

Why does this happen? Partly it’s because faculty aren’t aware of advice from the Educational Testing Service on how to use GRE scores properly.2 Partly, it’s because there are so many applicants to high-quality doctoral programs that admissions committees often use numerical screens to identify the small number of applicants worthy of close scrutiny.

Athene Donald points out another way in which relying on strict numerical criteria may be harmful to everyone, regardless of what their demographic, economic, social, or cultural background may be. She argues in the context of evaluating academics that in addition to the usual metrics of publication or creative activity and grant dollars (for those in fields where external funding is important), success as an academic should also include “building teams, seeing their students thrive and progress, working with people who sparked them off intellectually and seizing opportunities to try out new things and make new discoveries.”

The challenge, of course, is that you get what you measure. If we only measure publications and grants, that’s what we’ll get. If we want to encourage team building and student support, we have to measure those things and give them as much weight as the things we traditionally measure. If we can’t find numbers with which to measure them, we still need to find ways to assess them, because helping others gain the skills they need is what education is all about.

## Don’t be that dude

Several years ago, Dr. Acclimatrix (@Acclimatrix) published a list of “Handy tips for the male academic.” I just happened to run across it again this morning, and I thought I should pass it along. The advice she offers is as timely now as it was then. As she says:

Gender equality has to be a collaborative venture. If men make up the majority of many departments, editorial boards, search committees, labs and conferences, then men have to be allies in the broader cause of equality, simply because they have more boots on the ground. And, as much as I wish it weren’t so, guys often tend to listen more readily to their fellow guys when it comes to issues like sexism. I’ve also found that there are a lot of guys out there that are supportive, but don’t realize that many of their everyday actions (big and small) perpetuate inequality. So, guys, this post is for you.

The list includes 20 distinct pieces of advice. I’ve tried to follow all of them, but these are the ones I’m working on hardest right now:

3. Don’t talk over your female colleagues.

5. Make sure your department seminars, conference symposia, search committees, and panel discussions have a good gender balance.

6. Pay attention to who organizes the celebrations, gift-giving, or holiday gatherings.

7. Volunteer when someone asks for a note-taker, coffee-run gopher, or lunch order taker at your next meeting.1

15. Don’t leave it to women to do the work of increasing diversity.

19. Know when to listen. (more…)

## Reproducibility is hard

Last year, the Open Science Collaboration published a very important article: Estimating the reproducibility of psychological science. Here’s a key part of the abstract:

We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. There is no single standard for evaluating replication success. Here, we evaluated reproducibility using significance and P values, effect sizes, subjective assessments of replication teams, and meta-analysis of effect sizes. The mean effect size (r) of the replication effects (Mr = 0.197, SD = 0.257) was half the magnitude of the mean effect size of the original effects (Mr = 0.403, SD = 0.188), representing a substantial decline. Ninety-seven percent of original studies had significant results (P < .05). Thirty-six percent of replications had significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.

Since then, reproducibility has gained even more attention than it had before. My students and I have been taking baby steps towards good practice – using Github to share code and data (and versions), using scripts (mostly in R) to manipulate and transform data, and making the code and data freely available as early in the writing process as we can. But there are some important things we don’t do as well as we could – I’ve never tried using Docker to ensure that all versions of the software we use for analysis in a paper are preserved, I’m as bad at writing documentation for what I’m doing as I ever was (but I try to write my code as clearly as possible, so it’s not too hard to figure out what I was doing.

I need to do better, but Lorena Barba (@LorenaABarba) had a article in the “Working Life” section of Science that made me feel a bit better about how far I have to go. Three years ago she posted a manifesto on reproducibility. In her Science piece, she describes how hard it’s been to live up to that pledge. But she concludes with some words to live by:

About 150 years ago, Louis Pasteur demonstrated how experiments can be conducted reproducibly—and the value of doing so. His research had many skeptics at first, but they were persuaded by his claims after they reproduced his results, using the methods he had recorded in keen detail. In computational science, we are still learning to be in his league. My students and I continuously discuss and perfect our standards, and we share our reproducibility practices with our community in the hopes that others will adopt similar ideals. Yes, conducting our research to these standards takes time and effort—and maybe our papers are slower to be published. But they’re less likely to be wrong.

Barba, L.A. 2016. The hard road to reproducibility. Science 354:142 doi: 10.1126/science.354.6308.142
Open Science Collaboration. 2015. Estimating the reproducibility of psychological science. Science 349:aac4716 doi: 10.1126/science.aac4716