RAMAS | ConservationBytes.com

Software tools for conservation biologists

8 04 2013

Given 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 »

Comments : 23 Comments »
Tags: ARC/GIS, C#, Geographic information system, GIS, MAGICC/SCENGEN, MARK, Marxan, meta-model manager, Outbreak, population viability analysis, Python, R, RAMAS, Vortex, WINBUGS
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 »

Comments : 3 Comments »
Tags: biodiversity, climate change, extinction, management, meta-model manager, modelling, Outbreak, RAMAS, Vortex
Categories : Allee effect, buffalo, cattle, connectivity, conservation, demography, extinction, harvest, management, metapopulation, modelling, population viability analysis, PVA, software

Mega-meta-model manager

24 07 2010

As Barry Brook just mentioned over at BraveNewClimate.com, I’ll be travelling with him and several of our lab to Chicago tomorrow to work on some new aspects of linked climate, disease, meta-population, demographic and vegetation modelling. Barry has this to say, so I won’t bother re-inventing the wheel:

… working for a week with Dr Robert Lacy, Prof Resit Akcakaya and collaborators, on integrating spatial-demographic ecological models with climate change forecasts, and implementing multi-species projections (with the aim of improving estimates of extinction risk and provide better ranking of management and adaptation options). This work builds on a major research theme at the global ecology lab, and consequently, a whole bunch of my team are going with me — Prof Corey Bradshaw (lab co-director), my postdocs Dr Damien Fordham, Dr Mike Watts and Dr Thomas Prowse and Corey’s and my ex-postdoc, Dr Clive McMahon. This builds on earlier work that Corey and I had been pursuing, which he described on ConservationBytes last year.

The ‘mega-meta-model manager’ part is a clever piece of control-centre software that integrates these disparate ecological, climate and disease dynamic inputs. Should be some good papers coming out of the work soon.

Of course, I’ll continue to blog over the coming week. I’m not looking forward to the 30-hour travel tomorrow to Chicago, but it should be fun and productive once I get there.

CJA Bradshaw