Meetings, Methods 5th, Statistical methods

Ten Top Tips for Reviewing Statistics: A Guide for Ecologists

post provided by Dr Mark Brewer.

Mark is a statistician with Biomathematics & Statistics Scotland, based in Aberdeen. His main statistical research interests are Species Distribution Modelling, Compositional Data Analysis, Bayesian Mixture Modelling and Bayesian Ordinal Regression. Mark was one of the presenters at the UK half of the Methods in Ecology and Evolution 5th Anniversary Symposium in April. You can watch his talk, ‘Model Selection and the Cult of AIC’ here.

The level of statistical analysis in ecology journals is far higher than in most other disciplines. Ecological journals lead the way in the development of statistical methodology, necessitated by challenging practical problems involving complex data sets. As a statistician, publishing also in hydrology, soil science, social science and forensic science journals, I’ve found papers in those areas are much more likely to only use well-established methods than papers in ecology.

Here’s the big question though: why then do I have the most difficulty with ecological journals when it comes to statistical analyses? Let’s be clear here: when I say “difficulty”, I mean I receive reviews which are just plain wrong. Most statisticians I’ve spoken to who work in ecology have anecdotes from reviews which demonstrate a lack of understanding by the non-statistician reviewer (including the all-too-frequent “perhaps you should consult a statistician”). So, why the apparent disconnect?

The difference seems to be in how non-statisticians in different disciplines treat the statistics in a paper. In many subject areas, reviewers are almost deferential to the statistical analysis; in ecology, reviewers can be forthright in their condemnation, often without justification. Reviewers have every right to question the statistical analysis in a paper, but the authors have the exact same right to expect a high quality review from a genuine expert in the field. Has ecology become blasé about statistics? Continue reading “Ten Top Tips for Reviewing Statistics: A Guide for Ecologists”

India StephensonJune 3, 2015June 3, 201521 Comments

General, Methods papers

What is Beta Diversity?

Post provided by Dr Andrés Baselga

A key property of biodiversity is that it is not evenly distributed around the world. In other words, different sites are usually home to different biological communities. Quantifying the differences among biological communities is a major step towards understanding how and why biodiversity is distributed in the way it is.

The term beta diversity was introduced by R.H. Whittaker in 1960. He defined it as “the extent of change in community composition, or degree of community differentiation, in relation to a complex-gradient of environment, or a pattern of environments”. In his original paper, Whittaker proposed several ways to quantify beta diversity. In its simplest form (which we will call strict sense or multiplicative beta diversity), beta diversity is defined as the ratio between gamma (regional) and alpha (local) diversities (Whittaker, 1960; Jost, 2007). Therefore, it is the effective number of distinct compositional units in the region (Tuomisto, 2010). Essentially, beta diversity quantifies the number of different communities in the region. So it’s clear that beta diversity does not only account for the relationship between local and regional diversity, but also informs about the degree of differentiation among biological communities. This is because alpha and gamma diversities are different if (and only if) the biological communities within the region are different.

It’s easy to demonstrate how beta diversity varies from the minimum to the maximum differentiation of local assemblages in a region. For simplicity, we will quantify biological diversity as species richness (number of species), but it’s important to remember that alpha, beta and gamma diversities can also be defined to account for richness and relative abundances (see Jost, 2007 for a detailed explanation). When local assemblages are all identical (minimum differentiation), alpha diversity equals gamma diversity, and beta diversity equals 1 (figure below).

Continue reading “What is Beta Diversity?”

India StephensonMay 27, 201517 Comments

Methods papers, Online extras

International Day for Biological Diversity 2015

Happy International Day for Biological Diversity everyone!

As you may know, today (Friday 22 May) is the United Nations Day for Biodiversity and we are celebrating by highlighting some of the best papers that have been published on biodiversity in Methods in Ecology and Evolution. This is by no means an exhaustive list and you can find many more articles on similar topics on the Wiley Online Library (remember, if you are a member of the BES, you can access all Methods articles free of charge).

If you would like to learn more about the International Day for Biological Diversity, you may wish to visit the Convention on Biological Diversity website, follow them on Twitter or check out today’s hashtag: #IBD2015.

Without further ado though, here are a few of the best Methods papers on Biological Diversity:

Biodiversity Soup

We begin with an Open Access article from one of our Associate Editors, Douglas Yu (et al.). This article was published in the August issue of 2012 and focuses on the metabarcoding of arthropods. The authors present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. They also demonstrate that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information.

Continue reading “International Day for Biological Diversity 2015”

India StephensonMay 22, 2015May 22, 20151 Comment

Journal updates, Methods papers

Issue 6.5

Issue 6.5 is now online!

The May issue of Methods is now online!

We have two freely available articles this month: one Application and one Open Access Article.

– rSPACE: An open-source R package for implementing a spatially based power analysis for designing monitoring programs. This method incorporates information on species biology and habitat to parameterize a spatially explicit population simulation.

Tim Lucas et al. provide this month’s Open Access article: A generalised random encounter model for estimating animal density with remote sensor data. The authors have developed a Generalised Random Encounter Model (gREM) to estimate absolute animal density from count data from both camera traps and acoustic detectors. They show that gREM produces accurate estimates of absolute animal density for all combinations of sensor detection widths and animal signal widths. This model is applicable for count data obtained in both marine and terrestrial environments, visually or acoustically. It could be used for big cats, sharks, birds, echolocating bats, cetaceans and much more. Continue reading “Issue 6.5”

India StephensonMay 15, 2015May 15, 2015Leave a comment

Journal updates, Methods papers

The Delphi Technique: Unleashing the Power of Structured Collaboration in Anonymity

Post provided by Nibedita Mukherjee (author of The Delphi technique in ecology and biological conservation)

The quirky nature of decision making

Two heads are often better than one in decision making. Several heads might have an even higher probability of being better than one. However, people in a group often have different modes of thinking or problem solving, alternate reference frames, subjective biases and varying levels or domains of expertise. How do we harness these messy thought processes and channel them for effective decision-making for biodiversity management?

© Henry Martin (The New Yorker Collection/The Cartoon Bank)

Continue reading “The Delphi Technique: Unleashing the Power of Structured Collaboration in Anonymity”

India StephensonMay 12, 2015May 12, 20152 Comments

Methods papers, Statistical methods

Traits, community ecology and demented accountants

McGill et al. (2006) argued that community ecology had lost its way. Shipley (2010) accused community ecologists of acting like a bunch of demented accountants. Strong words – so what’s the issue exactly? And what can we do about it?

Dannymanic Image — Doing some end-of-financial-year field work? © Dannymanic

Their beef was that when studying groups of species and their environmental association, ecologists often were not thinking enough about the reasons for variation across species. (In this post we’ll focus on variation in abundance or in environmental response of abundance across species. We’re interpreting “abundance” loosely – counts, biomass, 1-0, whatever.) While alternative methods are more readily available nowadays, “accountancy” is still common.

Continue reading “Traits, community ecology and demented accountants”

davidwartonApril 29, 2015May 5, 20154 Comments

General, Meetings

Methods 5th Anniversary Symposium: A Gender Balanced Event?

Post provided by Alison Johnston

The Methods in Ecology and Evolution Symposium was an excellent conference with dynamic and interesting speakers representing a wide range of topics which have been published in the journal over the last five years. It was an unusual conference for a couple of reasons:

It wasn’t all in one place. Talks were relayed between London and Calgary (during convenient times!), a couple of speakers presented via Skype from neither location and it was watched via livestream.com by hundreds of other participants
There were equal numbers of male and female presenters. In my experience this gender balance of invited speakers is unusual and notable

Equal attendance
The gender balance of the speakers encouraged me to look around the room and write down a few figures for other gender dimensions of the London section of the symposium. As well as equal gender representation of speakers, there was also a good gender balance in the attendees – 42% of the attendees were female at the time I wrote down the numbers. These two figures suggest that it was a good conference for gender equality. However, I think these headline figures hide a number of more tricky aspects of gender equality.

Questionable numbers
There were a total of 23 questions asked of the 12 speakers presenting or livestreamed in London and only 3 of these were from women (2 out of 22 if I exclude my own question to reduce any investigator effects). These data points are not independent, as some people asked several questions, but I didn’t keep a record of individuals. Twitter revealed a similar reduced female presence compared to attendance: of those people tweeting to #Methods5th only 37% were women.

Proportion of different symposium participants that were female. Half the speakers and nearly half the attendees were female. But only just over 10% of questions were asked by women. — Proportion of different symposium participants that were female. Half the speakers and nearly half the attendees were female. But only around 10% of questions were asked by women.

Continue reading “Methods 5th Anniversary Symposium: A Gender Balanced Event?”

India StephensonApril 28, 20152 Comments

Journal updates, Meetings

Methods in Ecology and Evolution 5th Anniversary Symposium: The Livestream

On Wednesday 22 April 2015, Methods in Ecology and Evolution will be celebrating its 5th Anniversary. Methods is the British Ecological Society’s youngest journal and over the past five years it has established itself as the leading publication for methodological advances for both the ecological and evolutionary academic communities.

For those of you who can’t make it to either the first half or the Symposium in London (Looking Forward to the Next Five Years) or the second half in Calgary (Next Generation Ecology and Evolution: Genomics Tools for the Study of Ecology, Evolution, and Biomonitoring) we will be livestreaming every presentation.

What You Need to Watch the Livestream

Our 5th Anniversary Symposium will be streamed though Livestream.com. This platform is optomised for all browsers as well as Android and iOS devices. So all that you need is a computer, tablet or smart phone and the ability to connect to the internet.

Continue reading “Methods in Ecology and Evolution 5th Anniversary Symposium: The Livestream”

India StephensonApril 21, 2015April 21, 2015Leave a comment

General, Methods digest

Bat Appreciation Day: The Latest Methodological Advances

Post provided by Kate Jones and the Biodiversity Modelling Research Group

The Funnel-eared bat (Natalus stramineus) – © Veronica Zamora-Gutierrez

Today (17 April) is Bat Appreciation Day! Yes I know, a whole day to appreciate bats. Although my biodiversity modelling research group at University College London would argue that 24 hours is just not enough time to appreciate these cool, yet misunderstood animals, we wanted to mark the day by giving MEE a round-up of the latest methodological advances in bat monitoring and what we hope to see in the next few years.

Bat Detectives and Machine Learning

Oisin Mac Aodha PostDoc – If you have ever tried to spot bats flying around at night you will know that it can be very difficult. However, bats leak information about themselves into the environment in the form of the sounds they make while navigating and feeding. These calls are often too high for us to hear, but we can use devices known as bat detectors to transform them into a form that we can record and listen to. Monitoring bat populations over wide areas or long periods can result in huge amounts of data which is difficult to analyse though. To address this problem, our group, along with Zooniverse, have setup a citizen science project called Bat Detective which asks members of the public help us find bat calls in audio recordings that have been collected from all over Europe (the infographic below gives a bit more information on this). We have had an amazing response to date and our detectives have already located several thousand bat calls. However, to scale up monitoring, we need more automated methods of detecting calls. Using the analysis provided by our Bat Detectives, we are currently working on building algorithms that can automatically tell us if a recording contains a bat call.

In this video we see a visual representation of an audio signal called a spectrogram that features several bat calls. On top you see the result of an automated method we have developed for detecting bat calls. The larger the value, the more certain the algorithm is that there is a bat call at that point in time. Continue reading “Bat Appreciation Day: The Latest Methodological Advances”

India StephensonApril 17, 2015April 28, 20153 Comments

Journal updates, Methods papers

A Dog’s Nose Knows: The Science is in on Wildlife Sniffer Dogs

Below is a press release about the Methods paper, ‘An assessment of the effects of habitat structure on the scat finding performance of a wildlife detection dog‘, taken from Science for Wildlife:

Scientists have for the first time tested wildlife detection dogs to see how they perform in different habitats, and the results are very impressive.

Wildlife sniffer dogs are trained to find the scats (poo) or scent of hard to find wildlife species. As threatened species continue to drop in numbers, they become much harder to find and conserve. Detection dogs are a potential solution to that problem.

Despite their amazing skills the use of sniffer dogs by wildlife management agencies is still limited, partly because there are many factors that might impact the dogs’ performance. One well-toted theory states that dogs might not perform well in thicker vegetation, compared to open areas. The lead author of the new study, Dr Kellie Leigh from Science for Wildlife, explains “Scent is heavier than air so it pools and gets caught up in vegetation and depressions, rather than dispersing from its source. That means the dogs might have more trouble finding the scent in some areas.”

Working together with professional dog trainer Martin Dominick from K9-Centre Australia, Dr Leigh ran an experiment with Badger, an Australian Shepherd trained to find the scat of spotted-tailed quolls. The quolls are the largest marsupial predator on mainland Australia and are becoming very hard to find in some areas. Over 120 searches, Badger scoured for quoll scats in three different Australian habitats, from open grassland to thick vegetation, under both winter and summer conditions. Continue reading “A Dog’s Nose Knows: The Science is in on Wildlife Sniffer Dogs”

India StephensonApril 16, 2015April 16, 20151 Comment