Need to predict population trends, but can’t code? No problem

2 12 2020

Yes, yes. I know. Another R Shiny app.

However, this time I’ve strayed from my recent bibliometric musings and developed something that’s more compatible with the core of my main research and interests.

Welcome to LeslieMatrixShiny!

Over the years I’ve taught many students the basics of population modelling, with the cohort-based approaches dominating the curriculum. Of these, the simpler ‘Leslie’ (age-classified) matrix models are both the easiest to understand and for which data can often be obtained without too many dramas.

But unless you’re willing to sit down and learn the code, they can be daunting to the novice.

Sure, there are plenty of software alternatives out there, such as Bob Lacy‘s Vortex (a free individual-based model available for PCs only), Resit Akçakaya & co’s RAMAS Metapop ($; PC only), Stéphane Legendre‘s Unified Life Models (ULM; open-source; all platforms), and Charles Todd‘s Essential (open-source; PC only) to name a few. If you’re already an avid R user and already into population modelling, you might be familiar with the population-modelling packages popdemo, OptiPopd, or sPop. I’m sure there are still other good resources out there of which I’m not aware.

But, even to install the relevant software or invoke particular packages in R takes a bit of time and learning. It’s probably safe to assume that many people find the prospect daunting.

It’s for this reason that I turned my newly acquired R Shiny skills to matrix population models so that even complete coding novices can run their own stochastic population models.

I call the app LeslieMatrixShiny.

Read the rest of this entry »

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Categories : conservation, demography, extinction, mathematics, minimum viable population, modelling, population dynamics, population viability analysis, software

History of species distribution models

21 07 2020

This little historical overview by recently completed undergraduate student, Sofie Costin (soon to join our lab!), nicely summarises the history, strengths, and limitations of species distribution modelling in ecology, conservation and restoration. I thought it would be an excellent resource for those who are just entering the world of species distribution models.

SDM

Of course, there is a strong association between and given species and its environment1. As such, climate and geographical factors have been often used to explain the distribution of plant and animal species around the world.

Predictive ecological models, otherwise known as ‘niche models’ or ‘species distribution models’ have become a widely used tool for the planning of conservation strategies such as pest management and translocations2-5. In short, species distribution models assess the relationship between environmental conditions and species’ occurrences, and then can estimate the spatial distribution of habitats suited to the study species outside of the sampling area3,6.

While the application of species distribution models can reduce the time and cost associated with conservation research, and conservation managers are relying increasingly on them to inform their conservation strategies4, species distribution models are by no means a one-stop solution to all conservation issues. Read the rest of this entry »


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Categories : bioclimatic envelope, climate change, conservation, conservation biology, ecology, invasive species, management, modelling, niche model, software, species distribution model

Giving a monkey’s about primate conservation

12 12 2017

Urban monkey living (Macaque, Gibraltar) small

Concrete jungle. A Barbary macaque sits in a human-dominated landscape in Gibraltar. Photo: Silviu Petrovan

Saving primates is a complicated business. Primates are intelligent, social animals that have complex needs. They come into conflict with humans when they raid rubbish bins and crops, chew power cables, and in some cases become aggressive towards people.

Humans, however, have the upper hand. While 60% of non-human primate species are threatened, humans grow in numbers and power, building roads through forests, hunting and trapping primates, and replacing their habitat with farms and houses.

To help primatologists choose the most effective conservation approaches to resolve these problems, researchers in the Conservation Evidence project teamed up with primate researchers to produce a global database on the effectiveness of primate conservation solutions. This free database, which can also be downloaded as a single pdf, summarizes the evidence for 162 conservation interventions — actions that conservationists might take to conserve primates. The data come from searches of over 170 conservation journals and newsletters, and each study is summarized in a single paragraph in plain English, making it possible for conservationists without access to scientific journals to read the key findings.

Front cover primate synopsisSo what works in primate conservation? Well, the picture is rarely straightforward — partly due to the lack of data — but there are some interesting trends. Reducing hunting is one area where there seem to be a range of potentially effective approaches. Community control of patrolling, banning hunting and removing snares was effective in the three studies in which it was tested, all in African countries.

Further emphasizing the importance of involving local communities, implementing no-hunting community policies or traditional hunting bans also appeared helpful in boosting primate numbers. In other places, a more traditional approach of using rangers to protect primates has proved a winning strategy. Training rangers, providing them with arms, and increasing ranger patrols all worked to protect primates from poachers. Identifying the circumstances in which community led approaches or ranger patrols work will be key to implementing the most appropriate response to each conservation challenge. Read the rest of this entry »


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Categories : biodiversity, conservation, conservation biology, decline, deforestation, development, education, environmental policy, exploitation, extinction, habitat loss, harvest, implementation, logging, management, monitoring, planning, research, restoration, software, threatened species, tropical

Software tools for conservation biologists

8 04 2013

computer-programmingGiven the popularity of certain prescriptive posts on ConservationBytes.com, I thought it prudent to compile a list of software that my lab and I have found particularly useful over the years. This list is not meant to be comprehensive, but it will give you a taste for what’s out there. I don’t list the plethora of conservation genetics software that is available (generally given my lack of experience with it), but if this is your chosen area, I’d suggest starting with Dick Frankham‘s excellent book, An Introduction to Conservation Genetics.

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1. R: If you haven’t yet loaded the open-source R programming language on your machine, do it now. It is the single-most-useful bit of statistical and programming software available to anyone anywhere in the sciences. Don’t worry if you’re not a fully fledged programmer – there are now enough people using and developing sophisticated ‘libraries’ (packages of functions) that there’s pretty much an application for everything these days. We tend to use R to the exclusion of almost any other statistical software because it makes you learn the technique rather than just blindly pressing the ‘go’ button. You could also stop right here – with R, you can do pretty much everything else that the software listed below does; however, you have to be an exceedingly clever programmer and have a lot of spare time. R can also sometimes get bogged down with too much filled RAM, in which case other, compiled languages such as PYTHON and C# are useful.

2. VORTEX/OUTBREAK/META-MODEL MANAGER, etc.: This suite of individual-based projection software was designed by Bob Lacy & Phil Miller initially to determine the viability of small (usually captive) populations. The original VORTEX has grown into a multi-purpose, powerful and sophisticated population viability analysis package that now links to its cousin applications like OUTBREAK (the only off-the-shelf epidemiological software in existence) via the ‘command centre’ META-MODEL MANAGER (see an examples here and here from our lab). There are other add-ons that make almost any population projection and hindcasting application possible. And it’s all free! (warning: currently unavailable for Mac, although I’ve been pestering Bob to do a Mac version).

3. RAMAS: RAMAS is the go-to application for spatial population modelling. Developed by the extremely clever Resit Akçakaya, this is one of the only tools that incorporates spatial meta-population aspects with formal, cohort-based demographic models. It’s also very useful in a climate-change context when you have projections of changing habitat suitability as the base layer onto which meta-population dynamics can be modelled. It’s not free, but it’s worth purchasing. Read the rest of this entry »


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Categories : climate change, conservation, conservation biology, disease, extinction, genetics, management, mathematics, metapopulation, minimum viable population, population dynamics, population viability analysis, protected area, PVA, research, reserve, software

Linking disease, demography and climate

1 08 2010

Last week I mentioned that a group of us from Australia were travelling to Chicago to work with Bob Lacy, Phil Miller, JP Pollak and Resit Akcakaya to make some pretty exciting developments in next-generation conservation ecology and management software. Also attending were Barry Brook, our postdocs: Damien Fordham, Thomas Prowse and Mike Watts, our colleague (and former postdoc) Clive McMahon, and a student of Phil’s, Michelle Verant. At the closing of the week-long workshop, I thought I’d share my thoughts on how it all went.

In a word, it was ‘productive’. It’s not often that you can spend 1 week locked in a tiny room with 10 other geeks and produce so many good and state-of-the-art models, but we certainly achieved more than we had anticipated.

Let me explain in brief why it’s so exciting. First, I must say that even the semi-quantitative among you should be ready for the appearance of ‘Meta-Model Manager (MMM)’ in the coming months. This clever piece of software was devised by JP, Bob and Phil to make disparate models ‘talk’ to each other during a population projection run. We had dabbled with MMM a little last year, but its value really came to light this week.

We used MMM to combine several different models that individually fail to capture the full behaviour of a population. Most of you will be familiar with the individual-based population viability (PVA) software Vortex that allows relatively easy PVA model building and is particular useful for predicting extinction risk of small populations. What you most likely don’t know exists is what Phil, Bob and JP call Outbreak – an epidemiological modelling software based on the classic susceptible-exposed-infectious-recovered framework. Outbreak is also an individual-based model that can talk directly to Vortex, but only through MMM. Read the rest of this entry »


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Categories : Allee effect, buffalo, cattle, connectivity, conservation, demography, extinction, harvest, management, metapopulation, modelling, population viability analysis, PVA, software


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