Learning to use HPC clusters, R Markdown & GitHub pages

I had just spent the last 3 weeks or so trying to figure out how to use R on the university’s HPC clusters, and thought it would be helpful to produce a guide to help other beginners as well. I wrote it using R Markdown, since I thought I might as well learn how to write in R Markdown better at the same time.

To turn it from a R Markdown (rmd) file to something others can see, I had several options, as pdf or as html. I could convert it to a pdf, and either share it with the lab or put it up somewhere online. The conversion to pdf produced problems with image placement (the images would be placed somewhere else from where I wanted them to be, so that things would fit nicely on the pages). I didn’t want to learn the hack (incorporating some LaTeX formatting etc.) so I thought I could just leave it as a local html which opens on my browser and then use ‘Save as PDF’ to turn it to a pdf. That removed some formatting and didn’t look very nice either.

I found out I could use the RWordpress package to publish the html file rendered to my WordPress site, which I tried (and actually published briefly for about 20 hours before I took it down from this site). Apart from broken image links which I had to fix manually by uploading my images to the media gallery here, it worked quite alright. The formatting wasn’t as nice perhaps, especially the bits with the code, but it worked.

Then I thought about it a bit more and decided perhaps I should learn how to publish it on my GitHub, because then it’ll be easier to make changes to the code and have the website all synced to changes. So I did! I’m quite pleased to have learned this now, it’s been quite fun writing in markdown language and mastering git a bit more. Here’s the guide if you’re interested. 

The next stage of academia: embarking on a PhD

Since 2017, I have fallen out of the habit of announcing life events/my movements on social media, yet somehow I still feel a need to announce/document my starting a Doctor of Philosophy programme this October at the University of Sheffield’s Department of Animal and Plant Sciences. It’s been a fairly long and considered process, since graduating from my bachelor’s in 2015. It took me 2 months of a voluntary/self-searched research internship at the University of Queensland, a year-long master’s programme at Imperial College London, 15 months research associate job at Nanyang Technological University and another year of intense reading/learning and 9 applications* to finally land myself a PhD (with a scholarship).

I had struggled with the question – to do a PhD or not – the whole time, questioning my motivations for wanting to do a PhD (prestige/reputation? trying to keep on par with my peers from similar educational backgrounds who have already finished/are in the midst of doing their PhD?), my level of commitment knowing what the graduate environment could be like (been reading PHD Comics since finishing GCE ‘A’ levels… though I’m aware the environment in the USA can be quite different to elsewhere), and most importantly, what topic I would want to spend the next 3-5 years of my life working on. The four years I had spent since my bachelor’s was formative in shaping the kind of research experience/academic mentor/environment I would like to have, and realising that I do thoroughly enjoy the research process and being part of the academic community. But I think the key question on what research is worth me spending those years on (and somebody paying me to do it) was really only answered after I attended the summer school on degrowth and environmental justice last July.

Doing a PhD is usually seen as the start of an academic career, culminating in a professorship, and I’ve seen enough criticisms of academia to know that I didn’t want to work on something with no “direct relevance” to reality and to be accused of being in an “ivory tower”. Engaging with political ecology and environmental justice literature also brought into focus many of the political and economic realities faced by those impacted by conservation measures, which are often times overlooked by researchers or perpetuated through conservation interventions. There’s still a lot to learn and think about (and work towards), but for my PhD thesis, I am intending to examine telecoupled links of protected areas in Colombia, Colombia because the lab that I will be joining (Prof David Edwards lab) has a good number of links there that I can tap on. I am sure this will be refined and evolve as I start the PhD process, but I’m really psyched to use the telecoupling framework to look at how distant actors and flows affect local systems.

I’m also really excited about starting the PhD in Sheffield. I had applied to do the undergraduate degree in the Animal and Plant Sciences department 9 years ago (I took a gap year after completing my A levels), and I’m pleased to be able to finally experience being there. Not to mention all the climbing!!

*Coming back to the process of applying for PhDs, I think the main advice I can give is to apply to many and hope for the best (and also make sure you apply to labs you think you’ll fit in/professors whom you can work with). I had applied for 9 programmes from universities across Europe (including the UK), some of which were funded (the European programmes) and others which I had to separately apply for scholarship funding. I was offered a place in Vienna, but declined as I wasn’t prepared to move there (I was being hopefully optimistic when I applied and did not expect to get anywhere near the final selection of candidates, since I did not think my previous research experience fitted what I would be doing. But I really liked the topic that was being investigated, which was hidden emissions of forest transitions). I obtained offers of placement from most of the UK universities I applied to, but unfortunately did not manage to secure any funding. I was all ready to give up ever securing a PhD (scholarship) and so any hopes for an academic career, when an email advertisement forwarded by my previous supervisor A/P Janice Lee at NTU appeared in my inbox. I applied, got interviewed, and was offered the PhD scholarship (all within two weeks in July!) so you know, anything is possible. They say start applying early, but sometimes opportunities arise at the last minute…