Anyway, adaptation is a capacity that plays an essential role in evolutionary biology; it is a dynamic process that adapts organisms to their environment, improving their evolutionary fitness. Similarly, but on a different time scale, an individual's acclimatization capacity to a change in its environment enables it to maintain fitness across various environmental conditions. My name is Lorenzo Ricolfi, and, like anyone who has survived these two years of the pandemic, I struggle every day to acclimatize to change.

The COVID-19 pandemic has dramatically upset our habits and daily routines. Moreover, it has presented us with a tough challenge: to cope with dramatic and sudden changes. I lived my life in Italy, studying and working as a researcher at the University of Rome, until January 2020, when I took a plane to Brisbane. Study and work followed each other without a gap year, and I needed a breath of fresh air and an adventure before returning to Italy six months later. It was a good plan.

Well, it never came true. The World Health Organization declared the outbreak a Public Health Emergency of International Concern on the 30th of January 2020, 21 days after my landing in Australia. On the 31st of January, two Chinese tourists in Rome tested positive for the virus, and Italy was the first country in Europe to be affected by the pandemic. A month and a half later, the Italian army vehicles had to transport the dead out of the city of Bergamo as its crematorium struggled to cope. This disaster happened only a week after the World Health Organization officially declared COVID-19 a pandemic. That was the situation.

Australia at that time was in a bubble of its own, far removed from what was happening overseas. I was reading the news on the web, and it all seemed absurdly surreal. Virus? Wheezing and difficulty breathing? Social distancing? Masks? It was hard to assess and assimilate the news with reason and objectivity. And I had to take a decision now and immediately: return to my country or keep staying in Australia. How could I take such a decision lightly?

​There were many factors to consider and the implications too. Italy was in full lockdown, and although I was worried about my loved ones, I decided to stay, not knowing when I would return. I would return when the situation improved and the pandemic had passed. Days turned into weeks and weeks into months, and I began to need work. I held about ten different jobs in the time that followed. I worked as a dishwasher, a waiter, a kitchen hand, a warehouse worker, a driver, a delivery guy and a carpenter. I had never done any of these jobs before in my life. Months turned into years, and I realized that I wasn't coming back anytime soon. Australia closed its borders. There were no more planes in the sky.

Suddenly, my life was completely different, and the sense of nostalgia was strong. If I couldn't go home, I wanted at least to get back to what I was passionate about. I decided to take the English exam necessary to apply for a research project at the university level. I studied and passed the exam with flying colours.

Meanwhile, while surfing the websites of various Australian universities, I found an exciting laboratory at the University of New South Wales in Sydney. As luck would have it, the lab was looking for a PhD student with my background. I immediately got in touch and, after devising a research proposal that matched my interests and the knowledge and skills of the lab, I applied for a scholarship from the Australian government to cover the PhD.

It is now the beginning of April 2022, it has been two years and three months since I landed in Australia, and I started my PhD a couple of months ago. The pandemic situation has improved thanks to vaccines, although the pandemic is not over. And I have still never returned home. Over the last two years, the changes in my life have been massive, but I am thrilled with where they have taken me, even though they were unplanned and presented me with some callous times and challenges.
The point of all of this is that although we constantly try to categorize, order, and simplify reality, it is permeated by the chaos in which change is the engine. We need order and stillness in our environment and minds, but we cannot avoid change. Instead, we must learn to be flexible enough to shape ourselves without breaking or losing our identity. It is a challenging game based on compromise and sometimes on acceptance and letting go.

The pandemic has abruptly put reality before us, where not everything goes as planned. But it also reminded us of one thing: there is nothing wrong with that. Plans in life are necessary, but their implementation is not to achieve a state of happiness. Instead, an idea and a plan can evolve into something completely different. This turning point may initially be seen as a failure, a crack in the wall of our lives. However, it is only after time that we realize that the plan was but one of many steps, rather than the dividing line between success and failure.

by Losia Lagisz
 
Removing duplicated records can be cumbersome. When collating bibliographic records from   multiple literature databases both the total number of records and the proportion of duplicates can be high making manual removal of duplicates extremely time-consuming. Manual resolution of each set of potentially duplicated records is required when using reference managers such as Zotero or EndNote, and especially a screening platform Rayyan (note that deduplication algorithms available in all these are reasonably good at detecting (flagging) duplicating records (exact and non-exact duplicates), but not perfect, so combining different approaches is recommended anyway).
 
Here, I present an efficient workflow in which records from multiple sources (literature databases) are combined in Rayyan (https://rayyan.ai/), then automatically deduplicated using an R script (www.r-project.org), and finally uploaded into Rayyan again for the final round of deduplication and screening. Importantly, apart from Rayyan and R no other software is needed (but, at any stage, you can import/export lists of records into your reference manager to see the records or convert file formats). I assume you are already quite familiar with Rayyan and R.
​ 
The workflow:

​1. Gather the bibliographic files. 

​Download lists of bibliographic references (with abstracts) from databases used to run the literature searches. Most of the time, exporting thema as a .ris file would work best. Rayyan has guidelines for the most commonly used databases on its upload page (see the screenshot below).

2. Upload files into Rayan.
​Create a new project in Rayyan and upload all files into it. This will create a combined list of records.

3. Run deduplication algorithm in Rayan (optional).

This will give you an idea on how many duplicated records you have in the combined set of records (if less <200 you may want to resolve them manually in Rayyan). To run the algorithm, press a “Detect duplicates” button close to the top right corner of the view with the list of combined references in Rayyan.

4. Export combined list of records from Rayan.

​This will create one .csv with all references in the same format. To export the records, press a “Export” button close to the top right corner of the view with the list of combined references in Rayyan. In the pop-up window select “All” and “CSV” format (you can include all the fields listed below these options). Note that Rayyan will send you a link via email to download a compressed file. After decompressing, rename the .csv file to something usable (e.g., "FILENAME.csv") and place it in your R project folder.

5. Upload combined .csv file into R.

Load the R packages needed:
 
library(tidyverse) # https://www.tidyverse.org/
library(synthesisr) # https://CRAN.R-project.org/package=synthesisr
library(revtools) # https://revtools.net/
dat <- read.csv("FILENAME.csv") #load the file
dim(dat) #see the initial number of uploaded references
 
6. Prepare data for deduplication in R.

We will deduplicate by comparing titles. Before doing so, it is good to tidy them up by bring them to the same case, removing extra white spaces and punctuation. We save these “processed” titles in a new column.
 
dat$title2 <- stringr::str_replace_all(dat$title,"[:punct:]","") %>% str_replace_all(.,"[ ]+", " ") %>% tolower() # Removing all punctuation and extra white spaces
 
7. Remove exact title matches in R.

This step uses processed titles to create a new smaller list of references with exact duplicates removed. It will save computational time for the next step (detection of non-exact duplicates).
 
dat2 <- distinct(dat, title2, .keep_all = TRUE) #reduce to records with unique titles
(removes exact duplicates)
 
dim(dat2) #see the new number of records
#View(arrange(dat2, title2)$title2) #an optional visual check - sorted titles
 
8. Deduplicate by fuzzy matching the remaining titles in R.

This step uses string distances to identify likely duplicates - it may take a while for long lists of references.
 
duplicates_string <- synthesisr::find_duplicates(dat2$title2, method = "string_osa", to_lower = TRUE, rm_punctuation = TRUE, threshold = 7)
 
#dim(manual_checks) #number of duplicated records found
#View( review_duplicates(dat2$title2, duplicates_string) # optional visual check of the list of duplicates detected. If needed, you can manually mark some records as unique (not duplicates) by providing their new record number from duplicates_string (duplicates have the same record number), e.g.
#new_duplicates <- synthesisr::override_duplicates(duplicates_string, 34)
 
dat3 <- extract_unique_references(dat2, duplicates_string) #extract unique references (i.e. remove fuzzy duplicates)
dim(dat3) #new number of unique records
 
9. Prepare the data for exporting from R.

Modify the data frame into a format that can be imported to Rayyan (the files saved as .bib or .ris for .csv files cannot be directly uploaded to Rayyan due to some formatting changes happening during processing them in R). This is done by first selecting only the key columns, saving them into a BibTex format (.bib file) and them changing the record labels into the desired format.
 
dat3 %>% select(key, title, authors, journal, issn, volume, issue, pages, day, month, year, publisher, pmc_id, pubmed_id, url, abstract, language) -> dat4 #select the key columns
 
write_refs(dat4, format = "bib", file = "FILENAME_deduplicated.bib") #save into a bib file
 
readLines("FILENAME_deduplicated.bib") %>%
  stringr::str_replace(
    pattern = "@ARTICLE",
    replace = "@article") %>%
  writeLines(con = " FILENAME_deduplicated.bib") #fix the record labels and save again as a .bib file
 
10. Import deduplicated records into Rayyan.

Create a new project in Rayyan and import the modified .bib file. Run the algorithm for detecting duplicates in Rayyan (see Point 3 above). This will reveal potential duplicates that were below the similarity threshold used in R (or have lots of formatting differences). These will need to be resolved manually in Rayyan (usually it is not a big number and some will require human intelligence to tell what counts as a real “duplicate”). After resolving these duplicates you are ready to start screening your deduplicated records in Rayyan.
 
Note: Unfortunately, record fields with authors and keyword information (and many other fields) are stripped from the original records in the above workflow, mostly by Rayyan. For this reason, records exported from Rayyan are usually not suitable for direct use in bibliometric analyses. But, at least, you can claim that your screening of bibliographic records in Rayyan was blinded to the authors’ identity.

by Hamza Anwer

One would have heard the following quote at some stage in their life: “The journey of a thousand miles begins with the first step”. However, you don’t hear too much relating to how that journey went or how it ended.
​

When I first started my PhD, I was armed with an optimism that one feels when they hear that quote, a sense of dipping into the unknown willingly. I wasn’t quite sure what to expect. My first year could only be described as a rollercoaster. It felt like it flew and there were plenty of moments where I thought I would not make it out alive. The learning curve was a lot steeper than I thought and I had to master it, fast, otherwise I would be left behind. I look back now, and I can’t understate how valuable that year was. I learnt a lot about myself and was able to sharpen my skillset as well as my mentality and approach. I learnt to drop bad habits and develop new ones. I took criticism on board and told myself to see every opportunity, good and bad, as a learning opportunity. It set the stage for a very exciting Chapter 2.
​

This was the year everything really started to take shape. I had a good sense of direction and the work I achieved in this year really set the ultimate foundation. While I had several other tasks in the background, my major milestone was completing my zebrafish work. It was long. It was gruelling. Nailing down the tiniest details was crucial to ensure everything didn’t fall apart. There was no room for significant error although I came horrendously close several times. Whilst the process was by no means smooth, the times in the lab during this year were some of my favourites. I had a great support group and grew in confidence each day. Thankfully, I was able to complete my experiments before we entered the era of Covid-19. Out of the frying pan and into the fire I went.
​

My time at Garvan Institute of Medical Research was over. Covid-19 was sweeping across the world and soon enough, we had entered the lockdown phase. Working from home and online meetings became the norm. I embraced every moment. I looked at it as an opportunity for growth. I had to adapt and focus on moving forward. I embraced a good rhythm while working from home but there was still plenty of work that needed to be done, even when I got back to campus and was grinding away at my desk. I had completed the foundations, but it was all about putting it together in coherent pieces of writing to be published. Slowly but surely, it was all coming together but I was 3/4 into my PhD and still had not published a single paper or completed a single chapter. It was worrying but I pressed on. I still had time. I just needed to use my time wisely. I had everything I needed. I just needed to finish strong.  

“There are better starters than me, but I'm a strong finisher.” -Usain Bolt

I think this quote by Usain Bolt really sums up my PhD. If I was running a marathon, my start would be akin to one stumbling and landing face first on the ground. However, knowing I can make up for lost ground if I push that extra bit harder. Which is what I did. I started the year strong with my first publication (can read about that here). The first publication formed the first chapter of my thesis. Slowly but steadily, I worked on putting more components together. The next achievement was publishing my meta-analysis which would form the final chapter of my thesis as well as my general introduction. Two chapters down, two to go. The final two chapters were the most difficult because they comprised the bulk of my zebrafish data. In addition, they complimented one another so I had to ensure a lot of things were consistent. The final few months were intense, but after plenty of deliberation, I managed to piece all the components together. I could finally see the finish line. It looked glorious.

Fast forward to 2022, my thesis has been successfully submitted. The final two chapters have been sent in for publication. I am working full-time at Cure Brain Cancer Foundation and am better placed than ever.

To finish, I can’t emphasize enough how important my lab was in this journey. From my supervisors to lab members, everyone played a crucial part in where I am now. I thank you all.

“The way a team plays as a whole determines its success. You may have the greatest bunch of individual stars in the world, but if they don't play together, the club won't be worth a dime” – Babe Ruth
​

by Shinichi (he/his)

I used to do the end-of-the-year blog but last few years I have not done it, which is a shame. It is always good to have time to reflect on the past year. So here I am.
 
I-DEEL did remarkably well despite the pandemic limiting our interactions and slowing down empirical work we planned to do. Twelve of our members (including former members) published their first-author papers in 2021. I congratulate them as it takes a lot of work and patience to publish. This is especially so as I demand high quality and open practice, and transparency, all of which take time to do. Also, for 3 of these members (Dom, Hamza & Patrice), this was their very first lead-authored paper, so I am very happy for them. The first paper is something very special which I can give to my students as a supervisor.

by Jess (they / them)

This year marks one of the worst years so far for transgender1 (trans) folks. So far in 2021, violent hate crimes have taken the lives of at least 48 trans people in the US alone, while more deaths either go unreported or that individuals took their own lives. While our society has become more accepting, there is still strong stigma against those who challenge the existing gender norms. In addition to the lack of proper education, this stigma has led to a lack of support from family and friends of some trans individuals.

The idea that there are more than 2 genders might sound contemporary for some. On the other hand, many First Nations and Polynesian cultures have long embraced gender fluidity. For example, ‘māhū’ in Hawaiian culture represents someone ‘in between’, or someone of the third gender. The western concept of the gender binary was not introduced until colonialism, as foreign missionaries considered indigenous believes immoral. Since they were developed separately, indigenous believes of gender and the modern LGBTQIA+ framework are not identical to each other. However, both can help us describe and understand gender and its fluid-nature.

As a research student who is trans and non-binary2, I often find my identity being a source of contention among academics and graduate students. I have been a spectator of many debates surrounding trans issues, from whether or not J. K. Rowling is transphobic (she is, because she is a keen supporter of transphobic policies in the UK), to whether or not the ban on trans women, who have not undergone gender reassignment surgery, of McIver’s Ladies Bath is discriminatory (it is, because not all trans people opt for surgery). Although it is obvious to me where the problems lie within these debates, I often forget that some trans issues can be complex for those who are cisgender3 to fully understand them. Unfortunately, I find it quite jarring when these conversations are happening. To prevent myself from being emotionally triggered, I shy away from actively participating and thus failing to point out the transphobia right away.

In light of Trans Awareness Week (November 13-19) and Transgender Day of Remembrance (November 20), I would like to offer some advice as a trans and non-binary person and hopefully spark meaningful conversations around LGBTQIA+ issues. However, my perspectives are likely to differ from others of the trans community since we all live different lives and have different struggles. This is therefore based solely on my personal lived experience4 in academia. Other forms of phobias, such as homophobia, and biphobia, will not be directly covered here today. Perhaps another time! The following are some tips on how to create safer spaces for your trans colleagues:

1. Share your pronouns. 
Even if you are someone in the gender binary, i.e. a man or a woman, it signals to us that it is safe to approach you without having to hide our identities. For example, adding your pronouns to your twitter profile and presentation slides is a good start.
2. Use our pronouns. 
Adjusting to someone’s new pronouns can take time, especially if you’ve known them for a while. If you have unintentionally misgendered someone, be kind to yourself and make efforts to correctly gender them in the rest of the conversation. There is no need to feel overly guilty about it. In fact, I misgendered myself a lot when I first came out as non-binary and am still learning.
3. Use gender-neutral language. 
For example, instead of saying ‘ladies and gentlemen’, try using ‘folks’, ‘friends’, ‘everyone’, ‘distinguished guests’, etc., to accommodate all crowds.
4. Do not ask us about our genitals, surgeries, or hormonal treatments without consent. 
Although not all trans people experience gender dysphoria5, mentions of genitals, surgeries, or hormonal therapies could trigger negative emotions towards one’s body. Discussions of surgeries and treatments can also be difficult for those who require them but are unable to access them. Having trouble accessing healthcare can be caused by financial hardship, living with transphobic family members, etc. If you are curious, the internet can be a very helpful resource. Only ask these questions if you have established a trusting relationship with said trans person and/or have their consent. Personally, I am quite open to share my experience, but would also really appreciate a heads up as I struggle with gender dysphoria.
5. Know the difference between ‘sex’ and ‘gender’.
I have in the past come across numerous journal articles, books, and surveys incorrectly using the terms ‘sex’ and ‘gender’. ‘Sex’ refers to someone’s anatomical makeup, or assigned gender at birth, i.e. male, female, or intersex. While ‘gender’ refers to someone’s gender identity – one’s internal sense of their gender. Some examples of gender identities include man, woman, non-binary, agender6, and bigender7. ‘Sex’ and ‘gender’ refer to different aspects of our identities and are not interchangeable.
6. Include gender-diverse peoples in addition to women when ‘addressing gender equity’.
I have, in 2021 alone, stumbled upon job listings of 2 respective ecology labs from reputable Australian universities that had set aside certain positions for candidates who identify as women, to ‘address goals for gender equity’. While we need more women in academia, including gender-diverse peoples is a nod to our existence. Being inclusive will also show your potential candidates that your research group is a safe space for members of the queer community.
7. Invite queer and trans colleagues into conversations on LGBTQIA+ issues.
As with all discussions surrounding social issues, it is vital that we listen to the concerns and needs of the targeted communities, e.g. actively listening to people of colour on their views towards racial issues and injustices. If you are cisgender, you are unlikely to experience active forms of transphobia. Include us in your conversations to gain new perspectives on issues that directly affect us.
8. Being an academic doesn’t mean that you must flex your academic muscles in all situations.
It might seem ‘fun’ or ‘challenging’ for you looking for evidence to validate our existence, but being constantly questioned and doubted can cause us unnecessary emotional stress. While discussions about queer issues are important, we must also learn to listen and understand. After all, knowledge and experience can be mutually exclusive.
9. Call out transphobia.
Although scientists are generally quite open-minded and accepting, academia isn’t immune to transphobia. While I have not personally experienced any active forms of transphobia, I have heard comments such as ‘that’s really weird’, or others discuss certain issues with a negative tone. It is therefore a good idea for us all to regularly challenge and unlearn our assumptions about gender and educate ourselves. Actively help one another and raise questions gently. If you have been called out for making transphobic comments, instead of taking it as an offence, actively listen and learn from the point of view of trans people.
10. Show empathy when a trans colleague has experienced transphobia.
Instead of listing all your Equity, Diversity, and Inclusion (EDI) awards and policies, be human and express compassion. Receiving harassment for simply being our true selves is a very distressing situation. It makes us feel unsafe and rejected. Let them know that you will work on providing a safer environment, actively listen to their concerns, and take actual steps to improve existing policies to create a safer workplace.
​

This might seem like a long list of etiquettes, but with time and practice, things will come naturally. I’m sure if I think hard enough, I can come up with even more tips, but this will suffice for the time-being. Although Trans Awareness Week only lasts for a single week, it doesn’t mean that our education ends here. Even as a trans person, I find myself gaining new insights all the time. Transgender people experience transphobia everyday around the world. If we can comprehend complicated models and equations, surely, we can accept those who are different from us. Actively listen, learn, and lift each other up.
​
To end this article, please enjoy this lovely comic that my good friend Mira had shared with me, created by the artist Aaron Billings on Instagram (@dillings).

Footnotes
1  transgender – describes a person whose assigned gender at birth does not align with their inner sense of gender
2  non-binary – describes a person who identify as neither man nor woman
3  cisgender – describes a person whose assigned gender at birth is aligned with their inner sense of gender
4  lived experience – a representation of the experiences and choices of a given person, and the knowledge that they gain from these experiences and choices (Wikipedia)
5  gender dysphoria – emotional distress caused by a mismatch between one’s body and gender
6  agender – describes a person who does not have a gender
7  bigender – describes a person who identify as a man and woman simultaneously

by Szymek Drobniak

​The 2021 Mental Health Month has just ended – in October we gave special attention to people suffering from all sorts of mental health issues. This was also a perfect opportunity to emphasize the importance of support and respect towards any mental health problems, no matter how big or small they might seem. The general attitude towards psychological disorders has changed tremendously over the past decades. The dynamics of this change varied a lot between countries and social groups but overall, there seem to be greater awareness of the importance of caring for one’s mental health, and deeper understanding of psychological challenges other people around us may be facing.

In academia, the issue of mental health is still largely neglected. Many institutions often offer specialist counselling services to their employees or organize events aimed at alleviating some of the psychological impact academic lifestyle can have on scientists (like, e.g., two Recharge Weeks organized at UNSW during the last COVID-19 lockdown). We still, however, lack universal acknowledgment of psychological difficulties so tightly linked to an academic career. The current research culture, by incentivizing productivity and overachievement as core characteristics of a successful academic, lacks mechanisms that would protect the mental wellbeing of scientists. In 2018, Evans et al. published a report in Nature Biotechnology that painted a bleak image of the mental wellbeing of graduate students: with roughly 40% of them suffering from various forms of anxiety or depression, the report concluded that this group was more than six time as likely to experience these psychological disorders than the general population. Independent researchers and faculty members may be similarly affected, although precise numbers are more difficult to extract. Towering piles of to-dos, faculty meetings, supervision of students that we would like to see excel and shine, and grant proposals only add to the constant pressure exerted by the community that seems to value unrealistically productive publishing activity, and that places more emphasis on one’s citation scores than on all aspects of the academic life. At times we are almost convinced the culture has moved away from traditionally valued h-indices and impact factors, only to realise it is like that all over again when we try to submit our next grant application.

​Throughout my academic life, I always struggled to navigate this narrow labyrinth of expectations, having to tackle my own mental health issues. Mine were of the kind that could easily stop my scientific career to a grind: severe social anxiety has always prevented me from taking full advantage of conferences and meetings, and my attention deficit disorder (ADD) constantly makes it difficult to stay on top of my tasks and to-dos. For people that have never experienced ADD it may seem bizarre not to be able to focus on one task and lead it to successful fruition: it should be so easy to just sit and work your way through it, right? The key thing to understand is that in case of all similar psychological conditions we are trying to fight our own  mind. In the same way as we would not expect anyone to be able to “will” one’s broken limb to suddenly heal and mend itself, it is impossible to wield one’s brain to repair mental illness or neurological differences. Also, as we would expect someone with a broken arm to seek specialist’s help, the same should be true for those struggling with their own mental wellbeing. Thus, in spite of still occasionally heard encouragements to “put oneself together” or “it’s only in your head” – we should never underestimate the importance of good mental health, and we should never delay seeking professional help if our mind makes our life difficult. Psychotherapy and medication are no longer a stigma – and your mind will thank you tremendously for the love and care you can provide it with.

​Having said that – it is worth having a few tricks in your toolkit, to ward off the negative impacts of mental conditions you may be experiencing. Procrastination – a milder form of what people with ADD are experiencing – can be managed in everyday life by following a few simple rules:

​You are probably wondering – what about social anxiety? For a long time, it has defined my life and the way I participated in conferences and similar meetings. With some surprise, I also learned a while ago that it is a much bigger issue than I expected and that many more people experience similar limitations. Although I have never fully overcome mine – there are some tricks you can use to help you push yourself a tiny bit out of your comfort zone:

​Above all – if you feel overwhelmed – do not stay at home. Meet or call your friends, or just go for a walk. Nothing clears head better than mixing with a crowd of strangers or exploring a quiet forest path – whatever suits you better.

​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.
​
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).

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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):
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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