Research Platform Services Blog
Month
By Dejan Jotanovic & Nic La Mela
2016 was a big year for Research Platforms Training Service. We saw the rise of a bigger, more established Research Bazaar conference in February. We opened training to our other core services, namely high performance computing and cloud computing. We saw our training team grow larger and nourish as the importance of ‘pedagogy over technology’ became central to our mission. 2016 also saw the introduction of our (very short but sweet) feedback form, noting where our training could improve and offering a way to congratulate the brilliant work of our Research Community Coordinators (who all deserve the most massive round of digital applause).
But what would a ResBaz blogpost be without data? Here’s the ResBaz Training Campaign 2017 by the numbers.
Faculty Representation
We had a total number of 1443 researchers attend our events in 2016. The above pie graph denotes the breakdown per faculty. Strong representation is seen from Medicine, Dentistry & Health Sciences, Science & Engineering. This was to be expected. Digital tools and computer software have always been foundational to the research exhibited from these faculties.
Arts had the fourth highest level of representation. Again, this wasn’t too surprising. Kim Doyle & her fantastic team of ‘data web wizards’ have made engaging the digital humanities cohort at unimelb a high priority this year through collaborations with the Library and Academic Services. Engaging HASS (Humanities, Arts & Social Sciences) is a difficult task. The language around ‘digital apps & tools’ can be intimidating to students who live and breath discourse, Foucault and social constructionism. Our aim for 2017 is to strengthen our ties with Arts and look for more equal representation to that of the STEM faculties. We have a wonderful array of tools to help our wordsmiths: Python’s Natural Language Toolkit, for example, acts like one giant control+F button. You can read more here in Kim’s blogpost. Don’t forget: words are data, too!
Another big focus of 2017 will be to engage the less represented University faculties: VCA/MCA (though have you met Emilie?), MGSE, Vet & Agriculture, Business & Economics, Architecture & Design, and Law. Our engagement strategy is two-fold: collaborate with faculty services and student leaders at higher levels and organise events (think our Research Tools Speed Dating sessions) specific for their students, and hire Research Community Coordinators from these faculties to develop their own communities.
Attendee Feedback
This year we asked all of our attendees to fill out a two-question feedback form about our training services. The first question asks, “How likely are you to recommend this training to a friend or colleague?”, with 0 indicating not at all likely, and 10 indicating extremely likely. The second question was qualitative, “If there is something you could change about the training what would it be?”. This question helped us shape and adapt the workshops.
We’ve run 104 events in 2016 (so far!) - varying considerably in size and shape (from ResBaz to humble meet-ups) - and have accumulated a mean qualitative score of 8.5! THIS IS AN ASTOUNDING ACHIEVEMENT! But again, not surprising. Our team of ResComs are a multi-talented hard-working diverse bunch of students who have worked extremely hard to strengthen their communities and enhance the digital literacy of others around them.
We’ve really focused intently on pedagogy this year. What’s pedagogy? It’s the way you learn. When looking at curriculum design, it’s less about the what and more about the how. How do we deliver dynamic interactive and fun workshops? To help, we hired an educational psychologist, Dr Christina Tuke Flanders, to assist our ResComs. Check out these blog-posts she assisted in: teaching tips for training.
We aim to continue this work through 2017. The restructuring of ResBaz 2017 will ensure that more students are exposed and have the opportunity to engage with our tools and services - as well as other University research services. Innovative and collaborative events such as Data Storytelling, MEDevice & the 3D Med Seminar will continue to grow and expand. More communities will snowball. More data will be collected. But none of this could be made possible without the fervour and relentless dedication of our Research Community Coordinators. Thank you, deeply.
Product Managers - Training & Engagement
Dejan Jotanovic & Nicole La Mela
by Nikki Rubinstein & Dr Christina Tuke Flanders
Last week Nikki took us through the power of Peer and Problem Based Learning techniques. In the last blog post of the series we are wrapping up by explaining the value of Assessment and Reflection in training. This is the icing on the cake and once this is a regular part of your training you can claim to be a real champion in the training room. For the final time in this series, over to Nikki…
Assessment of student understanding
How do we know if our teaching is successful? Ask the students! It’s important to gauge what students have learnt from our teaching in order to inform us of what’s working and what needs work. This can be done using either summative or formative assessments. Summative assessments are administered at the end of a course, such as an exam. Formative assessments are administered throughout the course, and can take the forms of questions or challenges that cover key concepts.
In teaching R, I find formative assessments are more useful. They allow me to assess student understanding online and adjust my teaching accordingly. The Socrative app (http://www.socrative.com/) and Kahoot (https://kahoot.it/#/) are some methods that facilitates online feedback. This feedback is important both for students and trainers. Students learn better if they feel a sense of empowerment over their learning and are give measures of success. Moreover, online feedback can help you adapt your curriculum to the needs of the students.
Reflection
Teaching can be tiring and emotionally draining. Talking to other trainers and helpers can be a good way to vent frustrations as well as celebrate successes. This debriefing is important to ensure that you don’t implode from frustration or burnout from over-exertion.
This year ResComs have had the opportunity to use the services of a Training Consultant to debrief after delivering training. This is an opportunity to reflect upon what is working well and problem solve what needs to be changed.
I asked Emilie Walsh, ResCom for CAD, what were the benefits of using a Training Consultant to debrief: "Reflecting on my teaching with Christina has been extremely valuable: to sit down and go through the training, breaking it down into logical sequences, finding some key sentences to get the attention of the audience, all of this has really improved my teaching. What I really like is that we focus on what is positive, what actually works in your training. Putting words on what is really engaging your audience is the best way to reproduce this in future teaching situation.“
Emilie reflecting on her ResPitch in the Colab at University of Melbourne
Can you see how these techniques could translate to the courses that you are teaching? If you would like to know more about different teaching styles, you can contact Dr Christina Tuke Flanders (drtukeflanders@gmail.com). You can also just drop by CoLab (Room 101, Frank Tate Building) for a drink and a chat. Or alternatively, come to one of our training sessions (http://melbourne.resbaz.edu.au/catalogue) and experience these teaching techniques first-hand! And finally, if you have any other teaching tips that weren’t covered in this article (or would just like to teach me something), please get in contact (nikkir@student.unimelb.edu.au), because I would love to hear from you!
Reproducible research. Digital literacy. Pedagogy. Community of support. Open access. Diversity.
We’ve used plenty of phrases and keywords to describe the Research Bazaar since 2014. ResBaz launched as a community of likeminded researchers looking to improve their colleagues’ and friends’ literacy in digital tools and skills. A campaign was birthed, curriculums were created, free researcher-to-researcher was delivered. And finally, a conference constructed as an amalgamation of the campaign and community.
But there is no end-point or final destination to ResBaz. It’s a process. It’s adaptive. Malleable. ResBaz 2017 will be your starting point - your induction, kickstarter, igniting point - to our community for the year to come. Think of the conference as your roadmap to research for 2017.
What to expect at ResBaz?
Tools / Services / Skills
You’ll leave ResBaz 2017 with knowledge of which digital tools and services you’ll need for the year to come. We’ve changed the format of ResBaz this year to give you more choice and engage your curiosity. One difficulty we all encounter is knowing which tools are the right fit for your research. Learning can also be exhausting and time-consuming, so our ‘ResPitches’ are designed to give you tasters for the menu of tools we have on offer. You’ll meet the ResComs (research community coordinators) who run the trainings for the year and they’ll help you navigate your digital roadmap. You’ll also have the opportunity to directly sign up for workshops scheduled for the weeks following the conference.
But digital tools are just part of the journey. This year we’ll also be engaging other University research services to better prepare you for the course ahead. We’ll have activities around data management and storage, cloud computing, library services (etc.) and a number of ‘electives’ aimed at more ‘generalist’ research skills (hacking a CV, hacking a journal article, the science of data visualisation, transitioning into the workforce).
Community
ResBaz has, and always will be, about meeting like-minded people regardless of career stage or research area. Realising that what binds you together as researchers is your unwavering pursuit of discovery and challenge is one of the most enriching aspects of the conference. Why is this important? Because research can also be lonely. Chances are that regardless of passion, you’ll all encounter similar missteps and barriers. Sharing your stories and experiences, fostering a sense of camaraderie and mentorship, those moments are what makes the journey so much more worthwhile. ResBaz is the catalyst for such community.
You’ll make friends and you’ll meet your future colleagues. You’ll find pockets of opportunity for collaboration. And you’ll greet the faces of those key players whose services and skills will come in handy as the year develops. You’ll find your roadmap quickly populated.
Employment
Our ResBaz team at Research Platforms is rapidly shifting and expanding. Our employment strategy is to recruit research students from the University to help us develop communities, workshops and curriculum around digital tools. These are the ResComs. As ResComs reach the end of their education (whether Masters or PhD), they leave our team (but not our hearts) with an extensive array of skills and experience. After ResBaz 2016 we hired four new ResComs directly from the community!
And after ResBaz 2017 we expect to hire many more. The role of ResCom is perfectly suited around existing work commitments and is extremely flexible (~ 8-12 hours per week). You’ll have the chance to develop a community, organise events, work on curriculum, sharpen your teaching/training skills and work in a diverse fast-paced multi-talented team! Interested? Come along to ResBaz and tap us on the shoulder for more information.
My #ResFamily! The people behind #ResBazMelb ❤ #ResBaz pic.twitter.com/BpZl6PCQp1
— Dejan (@heyDejan)
February 5, 2016
Creativity
As you’ve surely heard before, ResBaz operates more like a festival than a conference. Much of the activity happens under a large bedouin tent. Some attendees choose to camp on South Lawn. We’ve had yoga. Mindfulness workshops. A chai tea station. Roaming masseuses. A MakerSpace. NerdNite. Opportunities for attendees to give ‘lightning talks’ on their research. And many more creative ventures.
ResBaz is therefore also an opportunity to try something new - whether it’s a new tool, relaxation technique or type of cuisine (the catering is always excellent). It’s a chance to get creative. To meet new people. Broaden horizons. Set goals. ResBaz is open, diverse and supportive. It’ll be the beginnings of your roadmap to research for 2017.
Halfway through my PhD candidature in linguistics at Melbourne Uni, I was introduced by Fiona to the ResPlat family. One of their aims, I was told, was to train researchers across the university in emerging tools and methods for doing better, more reproducible research. A specific target of this agenda was the Humanities and Social Sciences, who, let’s admit, sometimes lag behind a little when it comes to engagement with digital tools and methods.
My thesis was about corpus linguistics—that is, using computers to locate patterns in large collections of written text. Because of this, Fiona asked me if I could come on board and help out, teaching Python to researchers around the university, but with extra focus on those from the humanities. A key issue among corpus linguists, however, is that many don’t really know how to code. A more common workflow is to load text files into graphical tools, which provide interesting, but in many senses limited, windows into natural language data. The expertise is more in the interpretation of results than in the generation of them.
My confession is that at the time, this was me. I ran decade-old software, and pressed the ‘Keywords’ button to get a list of words that were 'key’ in the texts. I described and tried to explain the meaning behind whatever output the tool gave me—but the process was leaving me with doubts. When there were problems, could I fix them at their source? If someone gave me a new set of texts, or if I updated the old set, would I have to start all all over again? Was what I doing transparent and reproducible? And though it was all very interesting, was I really doing research that I could respect?
Regardless of how things were going in Thesisland, with only the most basic knowledge of shell scripting and Python under my belt, in December of 2014, I was invited on board with ResPlat, and was quickly apprenticed (read: hazed) in. While being an instructor was a key part of the job, really, I was a student at the same time. We were running the first ResBaz in February, and I was supposed to revise the course materials for “Text analysis with Python”. Uh oh.
“Hacky Hour/Frantic ResBaz Preparation”First #HackyHour of the year, snacks courtesy of @OKFNau pic.twitter.com/mhtcM5BskU
— Fiona Tweedie (@FCTweedie)
January 15, 2015
Over the summer, I learned and practiced Python in the Jupyter Notebook, and put what I learned right into our lesson materials. It was a beginners’ guide in more than one sense. Lachlan taught me Git with patience and mercy, so that our emerging materials stayed open-source and under version control.
As I learned, it became obvious how I could apply the code to my thesis research. So, I did. I started writing code that could extract the most common nouns from my dataset. Then, I wrote code that counted the number of imperatives. Before long, I was writing a Python module for getting texts annotated with grammatical features, for searching those annotated texts, and for visualising the results. An early version of the module was used during ResBaz, to show how you can progress from a series of text files to an analysis of meaning and pragmatics in Australian political discourse. Today, use of the tool is becoming more widespread. It bridges the divide between corpus and computational linguistics, and addresses some of the misgivings I had about the the methodology of my thesis.
Seems like #challengeaccepted is very quickly becoming our new #ResBaz mantra! Cheers @About_Memory!
— Research Bazaar (@ResBaz)
February 15, 2015
Because of ResBaz, my research improved, and I honed in on what it is that I really enjoy doing. I also learned the terrifying art of teaching while live-coding—a skill that comes in handy all the time, both for teaching and for conference talks. By submission time, the code was, in my eyes, a key contribution of my work. Shortly after, a live demonstration of the module helped me land a postdoc position at the University of Tübingen, working within the European CLARIN (Common Language Resources and Technology Infrastructure) project. Like ResBaz, CLARIN aims to provide researchers, especially from the humanities and social sciences, with access and training in the use of digital resources that underpin more and more modern research. ResBaz showed me not only how important this aim is, but how much fun it can be to work toward. More specifically, my role will involve developing software and creating exemplar projects, using languages (German, Java) that I’m far from fluent in. No worries—ResBaz, via Jee, taught me to say “Challenge accepted”.
ResBaz Germany, Summer 2017. You heard it here first.
Daniel
The second annual 3DMed Seminar was held on the 5th of October, in conjunction with the 3DMed Lab at Austin Health. The event was hugely successful, with over 130 participants from a whole host of different disciplines signing up to attend. The purpose of the event was to facilitate discussions about the disruptive potential of 3D printing in the medical field, and serve as a catalyst for future ideas and as a meeting point for collaboration!
Our #3dmed16 seminar is about to start! @3dmedLab @Austin_Health pic.twitter.com/3W4n7KjFaI
— Research Platforms (@ResPlat)
October 5, 2016
A wonderful turnout for #3dMed16! Join the live stream now at https://t.co/4PJJ2udfjQ pic.twitter.com/RpAzPDs9W1
— Austin 3DMed Lab (@3dmedLab)
October 5, 2016
We were honoured to be joined by a fantastic and diverse list of speakers from variety of different backgrounds. This was in keeping with the #3DMed16 vision of interdisciplinary collaboration, in particular between engineering and medicine, with the shared goal of improving medical research and patient care!
The seminar was kicked out by Dr David Ackland from the University of Melbourne, who took us through a fascinating journey of how he and Prof Peter Lee designed Australia’s first 3D printed titanium jaw, from prototyping to implantation into a patient.
Dr David Ackland, first #3DMed16 speaker! @ResPlat @3dmedLab pic.twitter.com/yXGc7fCp3x
— Jas Coles-Black (@JasamineCB)
October 5, 2016
Next up was Dr Eka Moseshvilli from the Olivia Newton John Cancer Wellness and Research Centre, on how 3D printing can be used to create a perfect fit for imperfect anatomy in cancer patients. Her emphasis was on the power of 3D printing to create personalised tools to save lives.
#3dprinting is the #logical next step for #radiotherapy - use existing #patient #data #3dmed @ResPlat @3dmedLab @JasamineCB @ozvascdoc pic.twitter.com/oEbg4c4Gls
— Vincent Khau (@thevinniek)
October 5, 2016
Dr Ian Chao from Austin Health and Box Hill Hospital blew people away with the 3D printed emergency airway trainers that his team had developed, costing less than $2 a model! This has the potential to revolutionise and democratise medical simulation training, with conventional models costing hundreds to thousands of dollars.
A #3dPrinted $2 emergency surgical airway trainer? I can see @edexam drooling in the audience… 😀#3dMed16 pic.twitter.com/uxSI5Wh83r
— Austin 3DMed Lab (@3dmedLab)
October 5, 2016
We were also treated to a recorded lecture from Dr Steve Pieper from Harvard’s Surgical Planning Laboratory, on some of the inspiring applications of 3D Slicer worldwide! Some of my favourite examples included utilising 3D Slicer for robotic prostatic biopsies, as well as modelling the morphological and phenotypic changes in various lung cancers.
We were also very honoured to have A/Prof Tracie Barber from UNSW come down from Sydney to deliver her talk on using 3D printing in addition to computational fluid dynamics to aid her analysis of blood flow through blood vessels such as fistulas in dialysis patients.
Utterly amazing. 3D ultrasound for #3dprinting to troubleshoot AV fistulas. #Awesome #3dmed16 pic.twitter.com/wdAHWEEDsf
— Andy Buck (@edexam)
October 5, 2016
Dr Raf Ratinam from Monash Health explored the views of
orthopaedic surgeons on complex 3D printed fractures, and provided a
fascinating and instructional overview of how his team were able to achieve
these 3D printed models of their patients’ individual fractured bones.
Dr. Raf Ratinam gives his presentation at #3dMed16 @ResPlat @JasamineCB @3dmedLab @ozvascdoc pic.twitter.com/LB9HbDeLXl
— Vincent Khau (@thevinniek)
October 5, 2016
The symposium was finished strong with Dr Ryan Jefferies, curator of the Harry Brookes Allen Museum of Anatomy and Pathology, on how 3D printing was used to enhance the museum’s exhibits, such as a 3D printed recreation of Ned Kelley’s death mask, bringing a 2000-year-old mummy back to life, and a photorealistic 3D printed lung specimen with tuberculosis!
Some great presentations and 3D printed models on display today at #3dmed16 - Ned Kelly’s death mask, a mummy skull and a diseased lung pic.twitter.com/WImgU9jgU3
— Ben Loveridge @ MIGW (@benloveridge)
October 5, 2016
Thank you to all our participants, for your enthusiasm and for providing such engaging discourse both in the panel discussions as well as in the Twittersphere! You helped make this event the success that it was!
Finally, a big shout out to our sponsors, Konica Minolta and Objective3D, for the delicious afternoon tea and for helping to make this event happen!
In conclusion, we are glad that so many of you found the seminar informative, and most importantly, fun! The feedback we have thus far received has been overwhelmingly positive, and we will without a doubt be holding this event again next year.
If you have any thoughts or feedback about how #3DMed17 can be improved upon, please feel free to email me at jasaminecb@gmail.com, or tweet me @jasaminecb!
We hope to see everyone next year!
Congrats to all for today’s fantastic #3dmed16 symposium at Austin #ResearchFest! @3dmedLab @JasamineCB @ozvascdoc @ResPlat
— Austin Health (@Austin_Health)
October 5, 2016
I guess I am showing my age here: when I was six, one of the best TV shows around was Voltron: Defender of the Universe.
It had everything a six year old could want: robots that looked like lions that joined together to form a giant new robot that had sword fights with space pirates.
The thing is, the TV show would not have worked if it was about just one of the robot lions working by itself. As the first episode explains, the smaller (but still formidable) robot lions were created by fragmenting the larger, almost godlike, Voltron. The giant Voltron, Defender of the Universe, had much greater power than the sum of the leonine components.
Not long ago, I wrote about LaTeX. Certainly LaTeX is fantastic. However, when I try to convince people to give LaTeX a shot, it sometimes feels like I’m trying to get across the virtues of Voltron by selling one of the robot lions in a used car lot.
Likewise, when I try to convince people that R is better than Excel, or Git is better than Dropbox, it is always like selling a beat up old robot lion collecting dust in a used car lot. People get this look in their eye and I can tell what they’re thinking. They’re thinking, what am I going to do with a beat up old robot lion with dust all over it; it can’t destroy fleets of space pirates, it doesn’t even have a sword; what I really need to help me is the legendary Voltron: Defender of my Thesis.
Now, from using these tools in my own work, what I really want to get across is a vision of Voltron, made up of these other tools which in isolation don’t appear obviously superior to what people already feel comfortable with. I mean, a robot lion might be cool, but if you were told you need a bit of training to pilot one, would you really prefer it to the car you already know how to drive?
The purpose of this blog post is to let you know that Voltron does exist; that although the lions by themselves might not attract you at first, you will not be able to deny the benefits of bringing them together to form a greater whole. A greater whole that together can wield a giant sword for annihilating all the space pirates your supervisors and reviewers can throw at you.
Unconvinced? Okay, we shall have a look at each of the lions. Then we will consider what happens when we bring them together.
There are a lot of fancy words that can be used to describe Git. It is:
Forget all that. From now on you should think of Git as the green lion.
The green lion forms the left arm of Voltron. The green lion has the youngest, smartest, smallest and fastest pilot, called Pidge. Git in turn is very fast, a bit technical, and was first developed in 2005, which makes it quite young in computer years.
Pidge’s homeworld was destroyed by nuclear war; likewise Git was born from battle. Once upon a time, people used the excellent BitKeeper software to collaborate on large programming projects. Unfortunately, it was commercial software, and a great war erupted over copyright and licencing issues. Git was created as a free replacement for BitKeeper so that no one had to worry about such matters any more.
There are all sorts of reasons to use Git, such as keeping your work synced between all your machines, and being able to roll back to earlier points in time — but of course you already use Dropbox for all that, right? And it is not like you need to collaborate on large software projects, at least, not at the moment.
That is okay, I am not telling you to stop using Dropbox. Git as a single green lion working by itself is not obviously superior to Dropbox.
What I am asking is, do you just want a single lion, or do you want Voltron? If you want Voltron at your side, then you will need to consider how well Dropbox works with the other lions.
RR is the red lion.
The pilot of the red lion is a charismatic and reckless trickster called Lance.
As the right arm, the red lion holds Voltron’s sword and other armaments.
Likewise when you use R, it can seem a bit tricksy at first,
but it brings in a wide variety of
external packages that can slay just about any type of data problem.
One way to think of R is as a programming language; and it is that.
However, if you haven’t done programming before,
this is perhaps not the most useful way to think of R.
It is possible to do simple things in R without ever having done programming
before.
If you have ever entered a function into a cell in Excel,
that is a way you can think of R.
The difference is that you won’t automatically see all the data
laid out before you in spreadsheet format.
Instead, like a genie in a bottle, R will keep everything tidily
hidden away until you give it commands.
A typical session in R looks something like this:
In addition to having powerful statistical tools, R is able to generate
beautiful graphics such as the following:
Still, you might think, you already can do reasonable things in Excel. The plots might be hard to customise, but you still have your papers accepted by some journals, and publication is all that matters, right? And in Excel you already know your way around all the buttons and options.
Again, I am not asking you to stop using Excel
and I am not trying to say R is always obviously better than Excel.
Instead, what I want you to think about is how much you can trust Excel
to seamlessly work with other tools.
When writing your paper in Word, if you get some new idea for a plot,
can you tell Word to go and re-run your analysis in Excel and have
the new plot automatically inserted at the right place?
(Well, maybe with some time-consuming VBA magic it is at least theoretically possible, but no one would call this seamless.)
LaTeX is the blue lion, Voltron’s right leg, piloted by Princess Allura. Like LaTeX, Allura is the beautiful, strong-willed and principled ruler over a domain with a long history. She welcomes newcomers and helps them acquire full control over Voltron. Like Allura, LaTeX will often seem to demonstrate telepathic powers and will stubbornly resist attempts to make it do things that will not end up looking perfect.
People often try comparing LaTeX to Word. People accustomed to a traditional word processor will be inclined to approach LaTeX with some skepticism. It can seem a little baroque to write everything in plain text scattered through with commands that need converting to a PDF before you can see what the document really looks like.
Once again, this is a matter of focusing on the individual robot lion and forgetting about the power of Voltron. Word is okay for simple tasks, but if you need to kill a horde of space pirates then you will need a robot lion that can play nicely with the rest.
Remember, your thesis advisor is a space pirate.
Your reviewers are all space pirates.
Your thesis is a space ship driven by space pirates who want to kill you.
Do you want to take them all on in a Ford Laser, or do you want Voltron?
At this point, I could belabour the analogy further.
No doubt, the strong golden lion on the left leg, supporting the rest of Voltron, could well be Linux. Likewise, the black lion, forming the torso of Voltron, is the Unix command line, holding all the other lions together.
We can discuss these more in another blog post in future; for the moment let’s go with the three lions discussed so far.
RGit is used by programmers to collaborate, keep a history of work, and distribute backups around between multiple machines. It is especially efficient when working with plain text, which is the usual method for writing programs.
R is a programming language which, like all the others,
stores its commands in plain text files.
Thus it makes sense that if you are working in R,
especially if you need to work on multiple computers or collaborate with
other researchers,
that you would use Git to handle the backing up and sharing of R code.
It is true that you can collaborate on data analysis with other researchers
without using R and Git.
However, by using R with Git:
R and LaTeXOne common way to try doing research is to perform some analysis in Excel, then copy the results into Word or PowerPoint when you want to present the results. Invariably, whatever is pasted needs further massaging since there are always formatting problems. If you also want to number the figures and tables, you can only cross your fingers that everything will update correctly each time there is a change.
Compared to this, if you are working in LaTeX,
you can use tools called Sweave or KnitR to mix in
any R commands you feel like.
Then the outcome of your analysis will appear directly in the final PDF,
including all your plots.
Let’s say you are using KnitR; it is regarded as a bit nicer than Sweave. Then if you need to update your data or change some parameters of your analysis, all you have to do is run KnitR again. This will rebuild your document from scratch, with the new data and settings, ensuring all the plots and their numbering and cross-references are updated automatically
Like R, LaTeX is written in plain text.
For the same reason that you can (and should) use Git with R,
you can also use Git with LaTeX.
Some interesting things have already been written by others on
what this allows and how to do it most effectively:
For example, since Git makes it very easy to create and merge branches, you can have branches for activities like trying out supervisor and reviewer suggestions, or changing the formatting and bibliography style to better suit particular journals. If you are using LaTeX to prepare cover letters or a curriculum vitae when looking for work, you can create a different branch for each different employer.
Overall, use Git with LaTeX if you are working on a complicated document like a thesis or paper and you have any of the following extra requirements:
It is not the only way to do things, but working with Voltron is a good way to do things.
R + LaTeXHopefully you can see where this is going.
By bringing together all of the above points,
you can now imagine a situation where you
are writing a thesis or paper in LaTeX,
with bits of R code through it that will automate your analysis for you.
You always have a copy of this document on any computer where you are currently working, and so do all your collaborators. No one has to rely on a particular external company to keep everything available and safe.
You and all your collaborators are free to experiment with innovative ideas without affecting anyone else’s work. If anything goes wrong anyone can delete their failures without feeling self-conscious. Everyone gets to choose which contributions they share with everyone else.
Furthermore, you don’t even have to switch around between different programs.
Once Voltron is fully formed, the individual lions are no longer noticed.
In particular, there is a program called RStudio
which has built into it not only R,
but also the ability to write documents in LaTeX
and automatically run KnitR on them,
and an interface for Git.
Rstudio is not the only way to form Voltron but it offers a low barrier to entry.
Finally, all these tools are free, open source, and cross-platform. What this means for researchers is that whatever type of computer you are working on, from now and forever into the future, you will be able to install all this software completely without charge. All the tools you use can be audited for correctness, and all your work will be fully reproducible.
If you want to learn more, come and speak to us in Research Platforms. We might start by telling you about the individual lions, but really we want to empower you to awaken your inner Voltron.