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.

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.

4. MARXAN: No list of conservation software tools would be complete without MARXAN (and the Huge Possum would be more than a little perturbed if I didn’t include it here). If conservation planning and reserve design are your interests, look no further than this clever bit of software, with full GIS capability.

5. InVEST: This is a family of tools to map and value the goods and services from nature, enabling decision-makers to assess the tradeoffs associated with alternative choices and to identify areas where investment in natural capital can enhance human development and conservation.

6. ARC/GIS: Speaking of things spatial, if you need good GIS capability, you’ll probably need to splash out for the (rather heftily priced) ARC/GIS package. I’m not a big fan of the corporate aspects of this monster, but it’s arguably the most powerful GIS around. I have yet to find a decent open-source GIS package for PC or Mac.

7. BIOMOD: While we tend to do species distribution modelling from scratch in packages like R, those with less experience will probably need something like open-source BIOMOD. The software is specifically designed for ensemble forecasting of species distributions (combining outputs from many different models), and is implemented in R.

8. MAGICC/SCENGEN: This, the ‘Model for the Assessment of Greenhouse-gas Induced Climate Change/A Regional Climate SCENario GENerator’ is a powerful global circulation model (GCM) emulator developed by Tom Wigley (now part of our lab). If you’re doing any regional climate change projections, you’ll need this.

9. ECOPATH with ECOSIM: This powerful trio (it includes ECOSPACE) of applications models trophic linkages and than simulates how perturbations cascade through communities. With ECOSPACE, you can even simulate the effects of virtual reserves on the dynamics of community composition.

10. WINBUGS: If Bayesian inference is your thing, than WINBUGS is useful. A powerful (and free) Bayesian statistical software, you can also call it from R using R2WINBUGS.

11. MARK: I wouldn’t have got very far without this software – the bee’s knees of capture-mark-recapture parameter estimation. Developed by Gary White and Ken Burnham years ago, it has every possible mark-recapture model variant under the sun now included. If you need to estimate survival, capture, emigration, immigration, etc. with marked individuals, you need to master MARK.

Like I said, this list is not complete. I’m sure many of you have your favourite packages, so if you have other suggestions for this list, please add them below and include an URL for software download.

CJA Bradshaw


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17 responses

21 03 2014
Gabriela Ibarguchi

Thank you – a fantastic post!

21 03 2014
Gabriela Ibarguchi

I wanted to mention that I have found some very useful basemaps for GIS applications at Databasin.org and including many peer-reviewed datasets (map layers) for conservation. For example, see: http://databasin.org/showcase

6 06 2013
CJAB

From Atte Moilanen: Zonation has the broadest set of methods available for spatial conservation prioritisation (like three different biodiversity models instead of only target-based planning; 8 ways of dealing with connectivity; uncertainty analysis; ability to handle hierarchical analysis and different priorities in different admin units, etc; operates on grids of up to tens or hundreds of millions of elements in size).

16 04 2013
Top 10+ Software Tools for Conservation Biologists

[...] This article by Corey Bradshaw, Director, Ecological Modelling (Professor) at the Environment Institute and School of Earth & Environmental Sciences, University of Adelaide,  Australia,  first appeared on his blog ConservationBytes.com, a website dedicated to highlighting, discussing, and critiquing the science of conservation that has demonstrated measurable, positive effects for global biodiversity. [...]

9 04 2013
BSMNS

EstimateS is very useful for estimating species richness from samples – does sample-based and individual-based rarefaction curves. http://viceroy.eeb.uconn.edu/EstimateS/index.html

9 04 2013
Philip Martin

EstimateS is good for rarefaction curves, and I have yet to find an R based equivalent that will allow you to plot CIs on your curves. Anyway, find it here: http://viceroy.eeb.uconn.edu/EstimateS/

9 04 2013
Simon Pierce

SOCPROG is brilliant for modelling residency/movement patterns and inter-site connectivity from opportunistic photo-ID data (http://myweb.dal.ca/hwhitehe/social.htm). As I don’t have MATLAB, I use the compiled version: http://myweb.dal.ca/hwhitehe/SOCPROG_compile.htm

8 04 2013
8 04 2013
Steven Bachman

Great starting list, but you may have opened a pandora’s box – so many useful tools out there. Have you tried GeoCAT? (http://geocat.kew.org). It produces rapid preliminary Red list assessments based on spatial data.

8 04 2013
CJAB

That was sort of the idea ;-). Haven’t tried GeoCAT yet.

8 04 2013
Falko Buschke

Three more useful freeware packages. They are Maybe not as powerful as R or ArcGiS, but they are easy to use and not as intimidating for a beginner.

PAST (Palaeontological Statistics): is handy for basic stats (uni- and multivariate) as well as calculating common diversity indices.

http://folk.uio.no/ohammer/past/

SAM (Spatial Analysis in Macoecology): Again, a semi-powerful but easy-to-use software platform for spatial statistics.

http://www.ecoevol.ufg.br/sam/

NetLogo: This powerful package is an awesome way to learn about agent-based models and/dynamics modelling as it has the most intuitive way of setting up models.

http://ccl.northwestern.edu/netlogo/

8 04 2013
CJAB

Even more:

BIODIVERSE: a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic and matrix-based relationships.

8 04 2013
CJAB

Other suggestions:

HEXSIM: a spatially explicit, individual-based computer model designed for simulating terrestrial wildlife population dynamics and interactions
AD MODEL BUILDER: built for the development of state-of-the-art nonlinear statistical models.
POPTOOLS: an add-in for 32-bit PC versions of Microsoft Excel (version 97 and up) that helps with the analysis of matrix population models and simulation of stochastic processes (not available for Mac).

8 04 2013
Suranjith

Thank you for sharing your list with us, really usefull…

8 04 2013
Rob

How about Distance? http://www.ruwpa.st-and.ac.uk/distance/ Our team uses Cybertracker and Logger for field data collection (both of which integrate nicely with Distance, and the GIS tools you mention). For GIS software, what about a compromise between free and expensive? A lot of people at St Andrews use Manifold. I haven’t tried it yet.

8 04 2013
Fábio Vieira

Quantum GIS (QGIS) is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, Windows and Android and supports numerous vector, raster, and database formats and functionalities.
Our latest release is QGIS 1.8.0 you can read the release annoucement here

http://www.qgis.org/

8 04 2013
CJAB

Thanks. I’ve tried this – it’s certainly the best open-source GIS package I’ve found, but still limited.

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