​by Losia Lagisz

If you are conducting systematic literature searches you are very likely to run searchers in online databases. How well these searches capture relevant literature?

In our recent paper (Foo et al. 2021) we explained the systematic review process, from question formulation to screening the retrieved records, but we only briefly mentioned the need for checking the performance of database searches. There is very little practical guidance available on how to do this and there is also some confusion about the relevant terminology.

To fill this gap, I will explain what benchmarking is and how it can be done using Scopus database search as an example. There are some more complicated ways of benchmarking, esp. in computational projects, but I leave them for another time, as usually simple benchmarking will be sufficient (unless you get a very picky manuscript reviewer).

Why Scopus?
Scopus has a broad and interdisciplinary coverage, user-friendly interface with advanced search functionality. For these reasons, Scopus is our database of choice for performing mains searches. We also use Web of Science (Web of Knowledge), which is quite similar, and techniques presented in this blog will apply there too, with minor modifications.

What is benchmarking?
Its main function is to check if your search is able to find relevant papers indexed (i.e. available as records) in a given database. You do not know in advance all the relevant records in the database until you check ALL of the records there against your inclusion criteria (and this is obviously impossible). So, checking is usually done against a pre-determined set of relevant publications. We call this set "banchmarks" or "benchmarking set", but other names used for these are "validation set" or "test set".

How to get a benchmarking set of papers?
We would usually collect relevant papers from various sources - relevant reviews on the topic, Google Scholar, ConnectedPapers, CiteHero, etc. We pick a set of minimum 10 papers, and collect their full references (bibliographic records), including DOI.

How to quickly benchmark in Scopus?
I use an example based on our recent protocol of a systematic map (Vendl et al. 2021 - accepted preprint link). The benchmark set we used consists of 10 papers.

All steps are performed on Scopus using "Advanced document search", which allows us to use complex custom search strings but also has a useful feature of tracking history of recent searches (as a table at the bottom of the search page).
​
Here is the process in seven simple steps, with screenshots:

1.
Find your benchmark papers on Scopus using a search string made of paper's doi (search strings based on titles are longer and less accurate):

2.
​This should find all benchmark papers that are indexed in the database (unless associated doi is wrong, which sometimes happens). If some papers do not get picked up, search for them individually using title, then author or citing papers, get their "correct" doi or other identification code. In the example, all benchmark papers were found:

7.
When the number of returned record equals the number of papers in the benchmarking set (as in this example) - all benchmark papers were found by the search string being validated. If the number is less - some benchmark papers were not found. Although you do not have to aim for 100% search string sensitivity, it is desirable to be able to locate most of the benchmark papers, so carefully revise your string and benchmark it again.

Advantages of benchmarking using online database:

• quick and accurate, because databases use their internal records IDs to check overlaps of the lists of references, rather than trying to match titles
• easily works with searches that bring up very large numbers of references - no need to download large files with all the records (there are usually limits on downloads - 2,000 records fro Scopus, 1,000 for WoS, per download file)
• displays your search history, you can then export/copy as documentation of your benchmarking process (add your comments to this).

Much of the advice is quite long-term focussed (house buying, families etc) but there are some really simple and valuable tips that I think anyone at any stage of their life can implement. Here are some that I recommend:
 
1)  Get a bank account with no fees (including ATM fees and annual fees). I bank with ING, which is also the bank that the Barefoot Investor recommends. Their Everyday account has zero fees, including international ATMs. This was great when travel was possible because you can withdraw cash in the local currency and not get hit with any overpriced fees.
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2)  Get a high interest savings account. Interest rates are very low at the moment, but you might as well choose one that has the highest rates possible. The ING Everyday account comes connected to a savings account which currently has one of the highest interest rates in Australia. They also have a great initiative called ‘everyday round-up’ which is a good way to save on top of regular payments. Basically, it rounds up every transaction you make to the nearest dollar (or $5) and transfers the difference into your savings. For example, a $3.50 coffee becomes $4 and 50 cents goes into your savings. This may not sound like much, but it adds up pretty quickly if you’re like me and buy way too many coffees (or wines in a pre-pandemic world), and you barely, if at all, notice that you’re transferring anything to your savings.

3)  Try not to get into debt (i.e., credit cards, overdrafts, loans etc). If you do, make sure you know the terms and conditions on how to avoid being charged interest. Paying interest to a bank worth billions of dollars is the biggest waste of money!

4)  This is a tip from Barefoot investor that I recently set up a couple of months ago and it seems to work really well and keeps me on top of my finances without having to do anything at all. For this, you will need four bank accounts: 2 x everyday accounts and 2 x savings accounts. Here’s what you do:

• Work out all your cost-of-living expenses. This includes rent, insurance, groceries, etc, but doesn’t include coffees, wine, takeaways, or any luxuries. Get your money paid into this everyday account and reserve it especially for ‘cost of living’ (Barefoot suggests that this should be about 60% of your income, but this is obviously income-dependent and is likely to be much more on a PhD stipend).
• Work out how much you need (and can afford) for all those other luxuries you spend in a pay cycle (i.e., for your coffees, weekend activities etc). Set up an automatic payment on payday to go into you second everyday account. This will be your ‘splurge’ account (i.e., the account the waiter thought I was using) and will be the one you use for anything other than cost-of-living.
• Work out how much money you can afford to allocate to savings and divide this between the two savings accounts. One will be a long-term ‘fire-extinguisher’ account and will only be touched in worse case scenarios (i.e., that scary gap between PhD and Postdoc). The other will be your ‘smile’ account that you can spend on something special (a holiday, a new outfit etc). Barefoot suggests that savings should be 30% of your income, but again, this is likely to differ substantially based on income.

 
Following these four steps should get you well on your way to financial stability and good financial practices. Saving can be really hard, depending on your financial situation, but even transferring a small percent of your income each payday will have many benefits, including a greater sense of security in case of emergencies as well as knowing you have an account that is specifically dedicated to making you smile one day!
 
*Mamamia.com.au (2017)

by Samantha Burke

From July 12th to July 14th, many members of I-DEEL attended the first ever SORTEE Conference. You may remember, from Rose’s blog post in February, SORTEE as a society committed to increasing awareness and opportunities to make ecology and evolutionary biology research more open, reliable, and transparent  (see SORTEE.org). This inaugural conference hosted plenaries, presentations, workshops, unconferences, and hackathons all related to providing resources, gathering feedback, and actively pursuing SORTEE’s missions. Its success was reflected by its large attendance with over 700 participants from over 60 countries. It occurred continuously for 48 hours, actively engaging participants across all time zones.

Members of I-DEEL organized many events for the conference:

• Shinichi facilitated an unconference on facilitating pre-registration
• Patrice organized a hackathon for contacting journals to include options for registered reports
• Losia and Sammy facilitated an unconference alongside SORTEE’s Education Outreach Committee to discuss SORTEE member’s perspectives on open science
• Rose and Sammy facilitated an unconference with members of SORTEE’s Executive Committee on SORTEE’s positions on advocacy for initiatives and policies in open science
• Losia, Szymek, and Sammy organized a hackathon for creating infographics to educate others on different topics relating to open, reliable, and transparent research

Many members of I-DEEL attended these events as well as other workshops, unconferences, hackathons, presentations, and plenaries, and learned a great deal about the importance and avenues for conducting open, reproducible, and transparent research. I look forward to the future of SORTEE and how the ideas shared at the conference can shape the future of ecology.

by Losia Lagisz and Shinichi Nakagawa

Have you received and email from GitHub titled “[GitHub] Deprecation Notice“? Or you are still creating a new repositories on GitHub using https links to clone repositories into RStudio and your local computer? If so, it is time to change how you access GitHub from RStudio (and from your computer in general).
 
From August 13, 2021, using a password with GitHub will no longer work and token (or SSH key) authentication will be used for GitHub operations (if you are already using two-factor authentication for GotHub, you do not need to change anything). You can read official information about this change here: https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ .

It may seem quite daunting to go through all the details and options. So, below we present two main ways of switching to SSH when using GiTHUB with RStudio. First, setting public SSH key(pair) for your computer. Second, switching remote URLs from HTTPS to SSH for your existing repositories.
​

​Note: This set up needs to be done for each of computers (and accounts) you are using to access GitHub, i.e. each computer (account) should have its own SSH key. More detailed description of SSH and alternative ways of setting up and troubleshooting are available from: https://happygitwithr.com/ssh-keys.html.

1.1. Open RStudio and go to Preferences from the top menu. [for all Windows users, it is Tools -> Global Options (?)]

1.2. Options box appears. Press on GIV/SVN icon in the left side menu.

1.3. Press the "Create SSH Key..." button.

​1.4. Enter Passphrase and Confirm it (optional). Press "Create" button.

1.8. Press "New SSH Key" green button.

1.9. In Title box, type e.g. name of your current computer. In Key box, paste your public key copied from RStudio. Press on "Add SSH key" green button below. Confirm access change by entering your GitHub password (if prompted).

.
1.10. You should get an email from [GitHub] notifying you that a new public key was added to your account
1.11. Restart RStudio.
1.12. From now, when creating a new repository in GitHub use SSH code to create connect your project to your GitHub account (see https://happygitwithr.com/rstudio-git-github.html, just use SSH not https).

2.1. For each repository: open related R project in RStudio. Display current url link used to fetch and push to GotHub for this project by entering in the Terminal pane:
​
git remote -v

You should get output similar to this (with your own USERNAME/REPONAME, where USERNAME is your GitHub username and REPONAME is the name of your GitHub repository):
​
origin https://github.com/USERNAME/REPONAME.git (fetch)
origin https://github.com/USERNAME/REPOSITORY.git (push)

This output shows what sort of url link you are currently using to connect to GitHub.

2.3. Verify that the remote URL has changed by repeating the code from step 2.1.:

git remote -v 

The output should look like this:

origin git@github.com:USERNAME/REPOSITORY.git (fetch)
origin git@github.com:USERNAME/REPOSITORY.git (push)

2.4. In RStudio Git pane, try pulling and pushing to GitHub (first time, you will get a message that new key was permanently added).
 
If this approach does not work, the simple way around is to delete a local project folder from your computer and cloning it from GitHub using SSH. If you have any files and sub-folders that are not tracked by git within that folder, remember to store/archive these elsewhere before deleting the folder.
 
You can read more about managing remote repositories using git via Terminal here: 
https://docs.github.com/en/get-started/getting-started-with-git/managing-remote-repositories

By Patrice Pottier

In a recent tweet, Sir Richard Evans shared the acceptance rates in the Journal of Contemporary History. Besides the low acceptance rate, a comment raised a public debate: the main reason for rejection was “poor English”. Tweeter users from all over the world highly criticised his opinion, highlighting that non-native English speakers are thus disadvantaged in the academic publication process, and that solutions exist to limit this bias.  

​Yet, Evans was not convinced, posting a second provoking tweet suggesting that “authors whose English is poor don’t of course realise it’s poor, otherwise they would have corrected it.”  Unsurprisingly, this second tweet generated another set of critics over Evans’ opinions.

Although I do not share his opinions, these tweets highlight a sad reality – publishing is hard, and it may be even harder for those whose English is not their primary language. Although Evans focuses on Contemporary History, I believe this applies to all fields in academia.  

In this assay, I share my journey at learning English and the language-related difficulties I faced in academia. The purpose of this assay is not to criticise Evans’ views directly, but to show a different perspective to his argument.

I am a white male who grew up in France, a highly developed country. English is taught at school from a young age, which provides an environment to learn and progress in English. France is a touristic country, and English is sometimes the only way to communicate with tourists. Travelling, if one’s economic situation is suitable, is also relatively easy within Europe, and English is once again, the gold standard for communicating in other countries. All the above reasons combined, one may expect French people to have a high proficiency in English, but the reality is different. Learning a new language is hard, and, although the reader of this assay may have learned a new language relatively easily, this does not apply to everyone. Financial barriers are also major constraints for travelling in English-speaking countries, which is the most efficient way at learning English.

Now, can you imagine how hard it would be to learn English when you grow up in a country where English is not the primary language, is not or hardly taught, with a difficult economic situation, and limited travelling opportunities? I cannot. I am deeply privileged by the country I was born in, the opportunities I had to travel, the fantastic pedagogy of my English-teachers, the similarities between English and French, and my learning facilities. I cannot imagine how hard it would be to learn English without these privileges. Yet, even with these privileges, I faced major barriers when I had to use English during my studies in Biological Sciences.

All my undergraduate studies and experiences of the natural world were taught in French. When I had to use English for academic purposes – I had to learn everything again. All the scientific terms, things as simple as the name of common animals – everything had to be translated. Fortunately, French has a Latin origin, which facilitate the translation. Still, this represents a major challenge that, I believe, many have faced when learning a new language and applying it to their studies.

At the end of my master’s degree, I had the unmatched opportunity to travel to the United States for six months. That was it. That was my opportunity at getting better in English - but I was terrified. I was terrified by my proficiency in English at the time, and how hard it would be to communicate my thoughts. Worse, I thought I would not be able to understand others. Hence, I prepared for my trip. Again, my privileges living in France allowed me to have a personal computer on which I could watch countless videos to improve my English. This “training” was helpful and I felt confident that, although not perfect, my English would be good enough to be understood and understand others.  

The reality was different. My first few weeks in the States showed me how unprepared I was. Even though I worked hard to learn English, I was not quite there yet. I could understand most of the conversations, but it required a high level of concentration. I could not understand most jokes, which made me feel socially awkward, and my communication skills were lagging. My flow of words was probably halved relative to French, and I would sometimes get stuck – unable to communicate what I intended to. Communication with your supervisors and peers is a crucial part of academic work. We generate ideas, discuss them with others, challenge them. We also raise issues and solve complicated problems. All of this represent a substantial part of a job in academia. Difficulties to communicate not only slow down the progress on those parts, but also delay progress on others. Again, I was privileged to be surrounded by supervisors and peers who were compassionate and supportive. I cannot imagine how hard it would be to navigate in such environment without support.

Besides oral communication, I quickly faced another barrier that relates to Evans’ tweets – writing. Writing in another language is exceptionally hard. Again, all my previous trainings were done in French and I did not know how to write in English. Academic writing also relies on references from the literature, which are mostly in English and require extra reading time. Eventually, I produced a piece I am proud of. Yet, I would have produced the same piece in significantly less time, and perhaps of higher quality in my native language.

Slowly, but surely, my English got better. I now have been communicating in English daily for nearly two years and most of my personal and professional writing is done in English. Yet, I still face some issues. In my view, the most troublesome is how different my personality is in English vs. French. I realised that there are some things one cannot translate from a language to the other, some things need to be adjusted more deeply. It is an ongoing challenge that needs to be acknowledged.

In summary, privileges can shape our success at learning a new language. Given that academia is English-centred, people whose English is their secondary language are disadvantaged in many ways, both at the professional and personal level. Facing language barriers not only slow one’s progress in the workplace, but also act as a burden on mood, well-being, and confidence – which may easily feedback on working performance. For every part of an academic journey, language barriers add an extra layer of difficulty and stress. The extent to which these barriers will act on one’s feelings is variable, but some factors like the economic situation of the country or family of origin, the geographical situation, or the similarities with the primary language, are non-exhaustive examples that are important to acknowledge.

Rather than filtering the writing performance of English vs. non-English native speakers, providing an environment where everyone can thrive would be more profitable. In a world where some inequalities are finally brought to light, it appears crucial to me to acknowledge our privileges, learn from other’s experience, and embrace, rather than excluding, diversity in academia and beyond.

by Hamza Anwer
As an undergraduate, I used to be fascinated reading journal articles. Seeing not only the amount of effort that went into doing science but also the writing and publishing for the world to see. There would have been a lot going on behind the scenes. It was something I aspired to do but even then, I knew it was going to be a long tough climb.

I started my PhD feeling a little overwhelmed. Looking up at the mountain I had to conquer, I started the climb with a monkey on my back, constantly reminding me that publishing was something I had not yet achieved despite completing my Honours.

I always had pride in my persistence. As an athlete, and competitive one at that, I always set myself goals with an end goal in sight: to win. Prior to winning my first football championship, I had played in several others…and lost. It made the feeling of victory that much sweeter. I had got the monkey off my back. My next championship victory followed not long after. It was a recipe I believed in: conquer the initial climb, enjoy the view at the top, and everything else will follow so as long as you continue to work hard.

Fast forward to the final year of my PhD. Not only had I made great strides in my climb, but the weight of that monkey on my back was getting lighter. I had learnt to carry it with me not as a burden, but as a reminder. Learning the ins and outs of what was required to plan my research, conduct it, write, and publish for the first time was exciting and something I will always value. It was not without challenges, however.

Working as part of a team, we first had to rigorously plan out the experiment and conduct it successfully. Following, we had to plan the analysis and put together reproducible code to ensure transparency. Writing up the manuscript seemed simple enough once we had mapped out our narrative and goals, however it took many sets of eyes and edits to ensure it was a worthy document to submit. Following submission, I was warned there was a decent chance at being rejected, however we received the manuscript back with positive comments, although a lot needed to be changed for it to be considered for publication. Putting together the reply for the editor was very time consuming but we knew it made our manuscript much stronger. After submitting with our edits, I had received a reply about a month later that it had been accepted for publication and was available online on my birthday, a pleasant surprise. Something I need to stress is that while this is my first published paper as first author, I could not have gotten here without the support of my lab members and supervisors who were with me every step of the way.

For now, that monkey is gone, but not forgotten.

My first published paper as first author is on measuring zebrafish anxiety with a new efficient assay that can better detect between-individual differences. Check it out here.

by Rose O'Dea

Peruse the website of the Inter-Disciplinary Ecology and Evolution Lab, and you will read that one of Shinichi’s mottos for this group is ‘Think like a scientist and act like one too.’ The way you interpret this motto probably depends on the way you conceptualise a scientist.
 
Perhaps you picture a scientist as someone one who uses critical thinking and rigorous methods to advance human understanding of the way the universe works. This idealised scientist works hard to form reasoned conclusions, trying to avoid the many cognitive biases and logical fallacies that they know they are susceptible to. They are intellectually humble, honest, and value constructive criticism from their peers. They do not hold tightly onto their beliefs, for they are always seeking disconfirming evidence. They are skeptical of authority and anecdote. Nullius in verba — take nobody’s word for it.
 
Or perhaps you have seen how scientists work.
 
Here at I-DEEL we think fondly of that ideal scientist. But our recent lab discussions have focussed on the messy reality of science in practice.
 
For lab meetings we’ve been reading* stories of scientists behaving badly: chasing metrics over answers, using sloppy or unvalidated methods, and ignoring inconvenient evidence. In our idealised vision of science, errors would be quickly caught and corrected. In reality, too many errors go unchecked, and too few rewards are offered for finding them. All this results in a lot of published research that is unreliable and cannot be reproduced.
 
It doesn’t have to be this way. Most scientists want to produce reliable work. They just need the training and the incentives to do so.
 
That’s why, over the last year, myself and other members of I-DEEL have been helping to from the Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology. ‘SORTEE’ was launched last December, as a community-driven effort to improve the way ecological and evolutionary research is done and change the way researchers are evaluated.
 
Work is already underway to hold a virtual SORTEE meeting later this year, and you can join the growing community of nearly 500 SORTEE members by going to https://www.sortee.org/join/.
 
This brings us back to the moto ‘Think like a scientist and act like one too.’ I asked Shinichi why he chose this motto for his lab at the University of Otago, and what he originally meant by it. The answer? He wanted to capture the leap that students take when they first join a research lab: they go from memorising facts prescribed in textbooks, to generating and testing their own ideas, and finding answers to unsolved problems.
 
Now, I-DEEL is trying to use those skills to bring the messy reality of science in practice a little closer to our ideals.

*Recent lab meeting readings:
 
Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope, And Wastes Billions
By Richard Harris
https://richardharriswrites.com/
 
The Matter of Facts: Skepticism, Persuasion, and Evidence in Science
By Gareth Leng and Rhodri Ivor Leng
https://www.penguin.com.au/books/the-matter-of-facts-9780262043885
 
The Art of Statistics: Learning from Data
By David Spiegelhalter
https://www.penguin.com.au/books/the-art-of-statistics-9780241258767

Hanging on to the Edges:Essays on Science, Society and the Academic Life
By Daniel Nettle
https://www.openbookpublishers.com/product/842
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by Cat Vendl

To Sydney for the whales (well, that was at least one of the reasons)
In 2016, I moved to Sydney to start my PhD at the University of New South Wales. My PhD investigated the airway bacteria in whales and dolphins. Sydney is the perfect place to study whales as every year between June and October thousands of majestic humpback whales roam its coastal waters migrating to and from their breeding grounds. I have always been fascinated by whales and the elegant way they move in the water. The whales and I certainly share the excitement for their fluid habitat.

The dark side of whale research
I was quite curious to learn that the population of currently around 30,000 humpback whales passing by Sydney every year was once severely depleted. In the 1970s and 1980s only a few hundred individuals remained. The culprit was easy to spot as the industrial whaling fleets of the 20th century were infamous. However, the more I learned about the issue the more intrigued I became. It wasn’t ‘just whaling’ that almost wiped out the entire population of east Australian humpback whales. What happened there was a brutal yet surprising event in modern history that a world-leading whale expert once called ‘one of the greatest environmental crimes of the 20th century’. The culprits are long dead, but the memory of their crimes lives on.

The text below was originally published in German in Wissenschaft' (Springer Nature, German version of Scientific American). The photos are reproduced with permission from their current owner.
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References:
Clapham, P. and Ivashchenko, Y., 2009. A whale of a deception. Marine Fisheries Review, 71, pp.44-52.
Clapham, P., Mikhalev, Y., Franklin, W., Paton, D., Baker, C.S., Ivashchenko, Y.V. and Brownell Jr, R.L., 2009. Catches of humpback whales, Megaptera novaeangliae, by the Soviet Union and other nations in the Southern Ocean, 1947–1973.
Ivashchenko, Y.V., Clapham, P.J. and Brownell Jr, R.L., 2011. Soviet illegal whaling: the devil and the details. Marine Fisheries Review, 73, pp.1-19.
Ivashchenko, Y.V. and Clapham, P.J., 2014. Too much is never enough: the cautionary tale of Soviet illegal whaling. Marine Fisheries Review, 76, pp.1-22.
Rocha, R.C., Clapham, P.J. and Ivashchenko, Y.V., 2014. Emptying the oceans: a summary of industrial whaling catches in the 20th century. Marine Fisheries Review, 76, pp.37-48.

by Losia Lagisz

After months of complete or semi-isolation, we were finally able to hold a proper i-deel lab get-together. 

We were super lucky with great wether, food and company and a new fantastic place near the campus – a small, but fancy, park near the new apartments at Newmarket. Some lab members even managed to sneak out to test a giant double super-slide in the playground behind the BBQ spot.

Thanks to Cat and Shinichi for organising, and to everybody for showing up and sharing food, drinks and stories!
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