Which statistical package?

My research stretches across clinical psychology, behavioural neuroscience and neuropsychology (and now, with a smidge of epidemiology thrown in). Researchers in these fields use different statistical approaches, and reflecting this, different packages. SPSS is common, although the neuroscience contingent (especially the younger researchers) tend to use R. I’m a long-time, disgruntled SPSS user. Disgruntled because it’s often clunky and slow, it’s a pain to produce attractive graphs, and it’s also expensive. (It’s free through most universities, but if I wanted to use it on my own it would be a fairly costly yearly subscription fee.)

Therefore, I’ve been teaching myself R, which has a rather steep learning curve, but is probably the best long-term option. In the meantime, I’ve also trialled other free packages that are easily available, namely PSPP and JASP. (I’ve also dipped a toe into STATA, which seems like a pretty good – paid – program, but haven’t used it enough to talk about it at length.)

R is definitely the most powerful and flexible, and the graphs it produces are very pretty. It’s open-source, and it has a large international user base. New packages for R are always being developed, and support is usually available (although I find that those who ask questions are similar in skill level to me – i.e. novices – , whereas those providing answers are…not. Which often makes the answers hard to understand.) I use R Studio, which provides a nicer environment through which to use R. That being said, it’s not a point-and-click interface at all, so to use R you have to use syntax/coding. There are lots of free web-based tutorials on using R. One of these, which looks good for new users, is provided by The Analysis Factor.

PSPP is an open-source take on SPSS, which looks and feels very similar, and as such it’s a great choice for someone needing relatively basic stats but not wanting to pay for SPSS. Pros: it will read SPSS dataset and syntax files, and syntax is almost identical, so if you’re familiar with SPSS it’s an easy transition. Even if you just need to get some data from SPSS files into something else, this will work. You can also edit data in it, i.e. create new variables, edit values within your variables, etc. Cons: It doesn’t have the full functionality of SPSS (e.g. GLM does not support continuous variables/covariates), and graphs are *very* basic. From memory it’s also a bit fiddly to install, but good instructions are available and it’s definitely worth it for a free “SPSS lite” program.

JASP is a good little program. Pros: it is very clean and simple to use. It reads both csv and SPSS (*.sav) data files, and it does some surprisingly funky stuff like some Bayesian analyses (not that I know much about Bayesian statistics at present). While it only has a limited number of analyses available, it does these well, and produces nice graphs, very easily. Cons: It is all point-and-click, i.e. you can’t use syntax. You also can’t use it to edit data at all. It lacks some more advanced options available in SPSS and R, such as bootstrapping.

For now, until I get better at R and can switch to using it full-time, I am using bits and pieces from all these packages (…as I procrastinate by writing this blog post instead of working on my second paper…).


Happy 2017!

The end of the year was a whirlwind. Most of it was spent on preparing for, and then doing, the Overland Track in Tasmania. This is a hiking track in the Cradle Mountain-Lake St Clair National Park. It was *amazing*, and I won’t lie: getting back to civilisation was kind of hard. (But then, once I was in Hobart, I had a long shower, put on some clean clothes, had some delicious pastries and good coffee, and got over it.) I’m planning to write a separate post about the Overland Track, with more pictures. I enjoyed so much that I am now determined to do more multi-day hikes – Six Foot Track next, in April, and loosely considering the Tour du Mont Blanc in the future (that one has a lot more climbing and descending, and is a wee bit longer).


I got back just before Christmas – some pretty intense shopping took place in the two days before Christmas, and then some pretty intense eating, drinking, lawn games and carol-singing, for the next few days. For (at least?) the past two years I was overseas for Christmas; least year I spent Christmas day flying overseas. So it was nice to have a relatively quiet Christmas and New Year’s Eve, for a change. NYE was spent playing games, making and eating pizza, and watching terrible films with a few dear friends – and it was great.

There’s been a bit of work over the break as well – together with a few colleagues, I’m working on a few chapters for an adolescent mental health book. Two of the three chapters have taken shape now and are with the publisher. I’ve also now received feedback from all my supervisors on the systematic review/meta-analysis that’s kept me busy for the second half of 2016, and I’m going to get it ready for publication in the next couple of weeks. (Daunting! It will be my first first-author publication – eep.)

I have some big life goals for next year, such as getting my registration, getting a Real (albeit part-time, while I continue with the PhD) Job, and training for a half marathon (aiming for the Blackmores Half, in September-ish). But I also have some smaller goals – smaller in scope, but in a way not easier, as they rely on consistency. Some of these are: get up and get into university earlier, which will hopefully go hand in hand with not working as late; go for at least a short run every couple of days; set time aside to do some creative writing, art, and also some game-playing (there are lots of games I want to play, especially through Steam); go rock-climbing more regularly, and try out outdoor climbing.

2016 was a mixed bag for me, and not great, globally (although Chris Hadfield posted a list of some amazing things that happened last year). So here’s to 2017 – I hope this year treats all of us, and the planet, kindly.

Autumn running and research FOMO

It’s a cool, rainy Autumn morning – finally. I’m inside, with the kitty, planning to do some work on the lit review before heading into uni to do more testing, reading and writing once traffic subsides.

Pearl Izumi
Pearl Izumi E:Motion Trail N2 v2. Love the red, black and lime combo.

My body is feeling quite sore, but a good “done lots of things” sore. On Friday I did a short walk/run with a friend around a bay that’s close to uni (very lucky, running by the water – lots of dog-, people- and boat-watching), on Saturday I did the usual parkrun (10 sec slower than my PB, dammit), followed by more home decluttering – the pantry looks lovely and manageable now (although how long will that last?). On Sunday I did some trail running (almost 10k very slowly, I came 3rd last in my age and sex category, but I enjoyed it a lot). I hit the trails in my new shoes for the first time, and they felt very grippy and secure, although more neutral than I’m used to (less arch support) which I’m not 100% sure about.

It’s sinking in that in just over a month I will be going overseas (North America) to present my research at two conferences. I’m still testing participants, which means I won’t have much time to analyse results and think about discussing the findings. (So I’m quietly terrified.) I’ll be spending some time in the US and Canada beyond conferencing. I’m going with a friend, and I think it’ll be fun – apart from becoming enlightened and covering our dear alma mater with glory,  I think we’re going to hit up some haunted/creepy places, catch trains, and trial some fine local fare (especially of the liquid variety).

Conferences are funny things. They make you pay to attend even if you’re a presenter – so, essentially, you are providing the content, and yet you have to pay for the privilege of being there and providing said content. Also, I’ve just found out that one of the two conferences I’m going to won’t be providing lunch this year – outrage!! And yet we do it, because it’s good experience, good “networking” (ugh…) and not least because the university subsidises the attendance of research students and academics.

Lately I’ve had massive research FOMO. My degree is a combined clinical and research degree, and my research as part of this degree will finish in a few months. I’ve been going to quite a few research seminars and colloquia, and I really wish I was sticking around to do more research – I have ideas on how I’d like to continue the research I’m doing, but it involves more experimental work of a kind that my current university is not really equipped for. Also, I don’t want to lose my clinical skills (hard-earned over the past three years), and I do really like clinical work. So the sensible option is to finish, get a job, and then think about coming back for more research later, which is something lots of psychs do. I just have to make my peace with not being able to Do All The Things at the same time…

On blog reading and writing

I really like blogs, and I read a fair few. Apart from friends’ blogs, I mostly read those of other health professionals, health students, scientists or researchers. It helps if they post food pictures, are snappy dressers or creative, or discuss both professional and personal matters. Being in the health field, its tricky discussing the last two due to confidentiality constraints, both concerning patients, and the professional’s life, in the Google-your-healthcare-provider-or-potential-employee age that we live in. I realise, however, that the blogs I enjoy the most are ones that discuss the personal, at least to some extent: reactions to tricky professional situations, travel, self-care, family. So with this in mind, I’ll try injecting a bit more of myself into this (so far, pretty dry) blog.

This week, I felt more like the bug than the windscreen. I didn’t get a job that I had pinned my hopes on and that would have been a really good fit, my research participants all cancelled, there are some family health issues, and exercise (which I use, not just for fitness but also for mood) felt painful and like a chore.

There are quite a few jobs out there in my field, but I had not realised how stiff the competition is. Not getting this job makes me worry that I won’t get a job, and feel angry at the thought that I’ve spent so many years studying and working hard, and there might not be light at the end of the tunnel. Of course, no one’s promised that there would be a shiny job at the end of the hard slog, but being human* means you assume things such as hard work -> some sort of reward. It’s also especially frustrating when you know that the mental health needs of Australians are far from decreasing, and that all the services you’ve done training with are stretched beyond capacity, with high rates of burn-out for clinicians – and yet there aren’t enough new jobs. (I should mention that I haven’t been applying for heaps of jobs, just very specific part-time ones, since I’m still doing my research. Not to mention that many/most positions are not available for people still finishing their clinical degree, which is fair enough.)

This brings me to the second point: I’m trying to finish my research, and even though I am still really interested in it, I also feel disheartened by the publication cycle and how hard it seems to get my last lot of participants. People are very generous to volunteer their time to participate in studies, and many have already done so for my research. So much goes on “behind the scenes”, before I meet with participants: out of those who contact me to say they’re interested, I end up talking to and screening about 2/3rds. Out of these, maybe half are eligible. Then I have time set aside for assessments, and it sucks when people don’t turn up. Even when they do – there’s a lot of forward and backward emailing, calling, schedule-checking, etc. Of course, there’s no reason for participants to know all this background information. TL;DR – research is really time-intensive and it makes me sad when participants cancel or don’t show up, which happens regularly. (Even so, I’m grateful that so many people have been interested in my research.)

Running, which is my preferred form of exercise, normally helps with life’s bumps and jolts, such as the above. I’ve recently come back from an (amazing!) overseas trip (honeymoon, actually), with some unwelcome residual sinus issues probably made worse by rapid changes in climate and aggressive airplane air conditioning. This has made running painful for the past couple of weeks. Bad breathing -> huge stitches -> sad runner. I’ve powered through: two painful Parkruns, a painful trail-running race, and a painful short run with a friend. I’ve tried to stay mindful, and the beautiful scenery of the trail run helped, but still, not the best outlet. Happy to report that this morning’s Parkrun was relatively-pain free, probably helped by sucking it up and taking some antihistamine medication.

So where to, from here? I’ll apply for other jobs that seem suitable to my stage in training. I’ll keep screening research participants, whether or not they end up coming in. I’ll keep going. And I’ll also see how this personal-and-professional blogging thing goes.


* Really, an instrumentally-conditioned animal.

How long is a piece of string?

Here’s the thing: changing careers is hard. Not just because of the need to pick up completely new skills, and hit the ground running, but also because everyone expects you to be unwaveringly enthusiastic about how you’re going in your new field. You feel a need to prove to everyone that this is not a mistake, that you’ll make it, that this is ‘it’.

So when the going gets hard, there’s still this need to keep smiling, because ‘you chose this’ and ‘if you don’t like it, why don’t you go do something easier’. This week, the going got hard. I’m trying to get my research off the ground, conceptually, and it’s like hitting my head against a brick wall. I have to bring something new to the table, so I had a couple of ideas that I thought would be pretty nifty to look at, and they are – but it turns out they’re also too involved for the scope of my current degree. It’s hard finding the ‘right’ idea: one that’s above all, interesting enough to sustain you throughout the degree, but that will also let you graduate at some point, and that’s also possible given the chronic lack of time. Not too little, not too big. (Hence the title of this post.)

While trying to get my research off the ground, I’m also trying to memorise hundreds of symptoms (plus changes from one diagnostic system to another), trying to learn different therapies and techniques so I can provide adequate treatment in the clinic, make weekly session plans, and prep for upcoming neuropsych assessments that we do throughout the degree. (And this is my ‘mid-year break’ – soon, coursework will start up again.) All these components are pretty much separate. Patients don’t (and shouldn’t have to!) care that you have to do research; the research supervisor doesn’t care that you have to do coursework; the neuropsych supervisor doesn’t care that you’ve had a hard clinical week and don’t feel like writing reports. And exactly zero people care that you also have to work for money. And the admin. Oh, the admin – it never ends, and I’m sure one day it will provide the subject for an absurdist play. So this is where I’m at right now.

I started writing this post a few days ago, but wanted to cool off a bit before submitting it. Now, looking back at it, I have to smile a little, because this really is what I want to be doing, and I do generally prefer to keep busy. But, the point is, there most certainly are bad days, and just because something is done by choice, there shouldn’t be an expectation (often self-imposed) of permanent cheerfulness.

How to fail at breaking down a study population into groups

1. Inform the public that you’re doing a study on comparing rates of schizophrenia and other psychoses in immigrants of different ethnic groups in Sweden with the majority population in Sweden (i.e. Swedish-born people with Swedish-born parents).

2. Get funding and obtain a large sample size (N = 1.47 million).

3. Break down the sample size into the following, seemingly random, categories based on country of origin:

A. Sweden
B. Finland
C. Western countries (Norway, Denmark, Iceland, Germany, Great Britain, USA, Canada, Australia, Other Western)
D. Eastern and Southern Europe (Poland, Hungary, Other Eastern Europe, Yugoslavia, Greece, Italy, Other Southern Europe)
E. Non-European (Middle East: Turkey, Iran, Iraq, Other Middle East; Asia: Far East, South Asia; Latin America: Chile, Other Latin America; Africa)

4. Claim that your break-down of the population into these groups is due to the diversity of ethnic backgrounds of immigrants in Sweden, which left you no other option but to create categories based on “similarities in lifestyle and living conditions.”

(4b. Because surely the lifestyle and living conditions of immigrants from Finland is hugely different to that of immigrants from Norway, as opposed to immigrants from Japan, Chile, Iran and The Country of Africa, which are practically like part of the same big happy colourful nation.)

5. Congratulations, you’ve arrived at your destination: FAIL.

Hjern, A., Wicks, S., & Dalman, C. (2004). Social adversity contributes to high morbidity in psychoses in immigrants – A national cohort study in two generations of Swedish residents. Psychological Medicine, 34(6), 1025-1033.

MINI musings

One of the components of the research project I’m currently involved in is collecting mental health information using the Mini International Neuropsychiatric Interview (MINI) Plus 5.01. This is a long-ish structured diagnostic interview for the major Axis 1 psychiatric disorders in DSM-IV and ICD-10, with most of the questions requiring a Y/N answer.

There is so much variety in how the participants I’ve tested approach the MINI, despite its relatively straight-forward structure. Some of the sections are a bit confronting (like the Suicidality section), and while some people take the questions in their stride, others are quite uncomfortable and need a lot of reassurance.

Other participants have a lot of trouble with the formal language of the interview – I know it so well that I can now simplify it and make it sound more casual – more like something that someone would say, rather than something out of a textbook (the MINI is already simplified and made more accessible to the layperson, but some parts still sound very formal). Other participants (quite rightly, in a sense), react negatively to the classifications – I don’t read these out, but some of the participants either ask me or peek at the interview sheets while I’m going through them.

There is a usually some nervous chuckling and I can see how anxious some people get – even at this informal, anonymous, completely voluntary level – about any kind of stain on their character; any kind of implication of pathology, or “strangeness”, or judgement on my behalf. The fear of being seen as an “insane subject” is alive and well.

Then there is the other end of the spectrum – people who almost seem to want to be classified, despite the fact that they are well within “healthy” parameters, as far as the MINI goes.

The MINI has a section on Anorexia Nervosa; this section requires the participant’s height and weight. Interestingly, this seems to be a touchy topic for male as well as female participants. It’s hard not to make comments at this point that reflect my own politics (i.e., you should have the body shape/size/weight you want, if you’re a healthy control), when the participant make disparaging remarks about their own weight, but I don’t feel that’d be professional. It’s a personal issue and I don’t want to add to it. But I also feel that by not responding, it might seem like I’m silently agreeing with negative comments.

Anyway, the variety of responses is really interesting. I love this part of research – talking to people to collect data – as much as I like collecting non-verbal data, and looking at squigly lines on the screen.

1. MINI Plus English Version 5.0 ©1994-2006 Sheehan DV & Lecrubier Y