SOFTWARE - The BIOMOD package

 
 

BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. BIOMOD includes the ability to model species distributions with several techniques, test models with a wide range of approaches, project species distributions into different environmental conditions (e.g. climate or land use change scenarios) and dispersal functions. It allows assessing species temporal turnover, plot species response curves, and test the strength of species interactions with predictor variables. BIOMOD is implemented in R and is a freeware, open source, package.


R is available here: http://cran.univ-lyon1.fr/index.html




There are now two versions of BIOMOD. The former platform (BIOMOD) as explained by Thuiller et al. 2009 in Ecography, and the newer version (biomod2). Biomod2 is totally object-oriented and includes a large set of evaluation metrics, MAXENT, and the possibility to use background data directly from raster data.


BIOMOD


install.packages("BIOMOD", repos="http://R-Forge.R-project.org")


The stable version of biomod2 is on CRAN and the developing version can be found on R-Forge


http://cran.r-project.org/web/packages/biomod2/index.html


The stable version on CRAN

install.packages("biomod2")


The beta version on R-Forge

install.packages("biomod2", repos="http://R-Forge.R-project.org")


biomod2 does not include any manual but rather a list of vignettes explaining the different steps to follow:

help(biomod2, help_type="html")

And then click on index at the bottom

Then click on Overview of user guides and package vignettes at the top




Some selected publications using BIOMOD


Araújo M.B., Cabeza M., Thuiller W., Hannah L. & Williams P.H. (2004). Would climate change drive species out of reserves? An assessment of existing reserve-selection methods. Global Change Biology, 10, 1618-1626.

Araújo M.B., Pearson R.G., Thuiller W. & Erhard M. (2005). Validation of species-climate impact models under climate change. Global Change Biology, 11, 1504-1513.

Araújo M.B., Thuiller W. & Pearson R.G. (2006). Climate warming and the decline of amphibians and reptiles in Europe. Journal of Biogeography, 33, 1712-1728.

Araújo M.B., Thuiller W. & Yoccoz N.G. (2009). Reopening the climate envelope reveals macroscale associations with climate in European birds. Proceedings of the National Academy of Sciences, USA, 106, E45–E46.

Araújo M.B., Whittaker R.J., Ladle R. & Erhard M. (2005). Reducing uncertainty in projections of extinction risk from climate change. Global Ecology and Biogeography, 14, 529-538.

Ballesteros-Mejia L., Kitching I.J. & Beck J. (2011). Projecting the potential invasion of the Pink Spotted Hawkmoth (Agrius cingulata) across Africa. International Journal of Pest Management, 57, 153-159.

Barbet-Massin M., Jiguet F., Albert C.H. & Thuiller W. (2012). Selecting pseudo-absence for species distribution models: how, where and how many? Methods in Ecology and Evolution.

Barbet-Massin M., Thuiller W. & Jiguet F. (2010). How much do we overestimate local extinction rates  when restricting the range of occurrence data in climate suitability models? . Ecography, 33, 878-886.

Barbet-Massin M., Thuiller W. & Jiguet F. (2012). The fate of European breeding birds under climate, land-use and dispersal scenarios. Global Change Biology, doi: 10.1111/j.1365-2486.2011.02552.x.

Barbet-Massin M., Walther B.A., Thuiller W., Rahbek C. & Jiguet F. (2009). Potential impacts of climate change on the winter distribution of Afro-Palaearctic migrant passerines. Biology Letters, 5, 248-251.

Beaumont L.J., Gallagher R.V., Downey P.O., Thuiller W., Leishman M.R. & Hughes L. (2009). Modelling the impact of Hieracium spp. on protected areas in Australia under future climates. Ecography, 32, 757-764.

Beaumont L.J., Gallagher R.V., Thuiller W., Downey P.O., Leishman M.R. & Hughes L. (2009). Different climatic envelopes among invasive populations may lead to underestimations of current and future biological invasions. Diversity and Distributions, 15, 409-420.

Ben Rais Lasram F., Guilhaumon F., Albouy C., Somot S., Thuiller W. & Mouillot D. (2010). The Mediterranean Sea as a “cul-de-sac” for endemic fishes facing climate change. Global Change Biology, 16, 3233–3245.

Broennimann O. & Guisan A. (2008). Predicting current and future biological invasions: both native and invaded ranges matter. Biology Letters, 4, 585-589.

Broennimann O., Thuiller W., Hughes G.O., Midgley G.F., Alkemade J.R.M. & Guisan A. (2006). Do geographic distribution, niche property and life form explain plants’ vulnerability to global change? Global Change Biology, 12, 1079-1093.

Broennimann O., Treier U.A., Muller-Scharer H., Thuiller W., Peterson A.T. & Guisan A. (2007). Evidence of climatic niche shift during biological invasion. Ecology Letters, 10, 701-709.

Buisson L., Thuiller W., Casajus N., Lek S. & Grenouillet G. (2010). Uncertainty in ensemble forecasting of species distribution. Global Change Biology, 16, 1145-1157.

Buisson L., Thuiller W., Lek S., Lim P. & Grenouillet G. (2008). Climate change hastens the turnover of stream fish assemblages. Global Change Biology, 14, 2232–2248.

Coetzee B.W.T., Robertson M.P., Erasmus B.F.N., van Rensburg B.J. & Thuiller W. (2009). Ensemble models predict Important Bird Areas in southern Africa to become less effective for conserving endemic birds under climate change. Global Ecology and Biogeography, 18, 701-710.

Domisch S., Jaehnig S.C. & Haase P. (2011). Climate-change winners and losers: stream macroinvertebrates of a submontane region in Central Europe. Freshwater Biology, 56, 2009-2020.

Engler R., Randin C.F., Thuiller W., Dullinger S., Zimmermann N.E., Araújo M.B., Pearman P.B., Le Lay G., Piedallu C., Albert C.H., Choler P., Coldea G., De Lamo X., Dirnböck T., Gégout J.-C., Gomez-Garcia D., Grytnes J.-A., Heegaard E., HoIstad F., Nogués-Bravo D., Normand S., Puscas M., SebastiÀ M.-T., Stanisci A., Theurillat J.-P., Trivedi M.R., Vittoz P. & Guisan A. (2011). 21st century climate change threatens mountain flora unequally across Europe. Global Change Biology, 17, 2330-2341.

Fronzek S., Carter T.R. & Luoto M. (2011). Evaluating sources of uncertainty in modelling the impact of probabilistic climate change on sub-arctic palsa mires. Natural Hazards and Earth System Sciences, 11, 2981-2995.

Gallagher R.V., Beaumont L.J., Hughes L. & Leishman M.R. (2010). Evidence for climatic niche and biome shifts between native and novel ranges in plant species introduced to Australia. Journal of Ecology, 98, 790-799.

Gallien L., Douzet R., Pratte S., Zimmermann N.E. & Thuiller W. (2012). Invasive species distribution models - how violating the equilibrium assumption can create new insights? Global Ecology and Biogeography.

Heikkinen R.K., Luoto M., Leikola N., Pöyry J., Settele J., Kudrna O., Marmion M., Fronzek S. & Thuiller W. (2010). Assessing the vulnerability of European butterflies to climate change using multiple criteria. Biodiversity and Conservation, 19, 695–723.

Hughes G.O., Thuiller W., Midgley G.F. & Collins K. (2008). Environmental change hastens the demise of the critically endangered riverine rabbit (Bunolagus monticularis). Biological Conservation, 141, 23-34.

Jiguet F., Barbet-Massin M. & Henry P.-Y. (2010). Predicting potential distributions of two rare allopatric sister species, the globally threatened Doliornis cotingas in the Andes. Journal of Field Ornithology, 81, 325-339.

Keenan T., Maria Serra J., Lloret F., Ninyerola M. & Sabate S. (2011). Predicting the future of forests in the Mediterranean under climate change, with niche- and process-based models: CO(2) matters! Global Change Biology, 17, 565-579.

Kramer K., Degen B., Buschbom J., Hickler T., Thuiller W., Sykes M.T. & de Winter W. (2010). Modelling exploration of the future of European beech (Fagus sylvatica L.)  under climate change - Range, abundance, genetic diversity and adaptive response. Forest Ecology and Management, 259, 2213–2222.

Le Maitre D.C., Thuiller W. & Schonegevel L. (2008). Developing an approach to defining the potential distributions of invasive plant species: a case study of Hakea species in South Africa. Global Ecology and Biogeography, 17, 569-584.

Lomba A., Pellissier L., Randin C., Vicente J., Moreira F., Honrado J. & Guisan A. (2010). Overcoming the rare species modelling paradox: A novel hierarchical framework applied to an Iberian endemic plant. Biological Conservation, 143, 2647-2657.

Marini M.A., Barbet-Massin M., Lopes L.E. & Jiguet F. (2009). Predicted Climate-Driven Bird Distribution Changes and Forecasted Conservation Conflicts in a Neotropical Savanna. Conservation Biology, 23, 1558-1567.

Marini M.A., Barbet-Massin M., Lopes L.E. & Jiguet F. (2009). Major current and future gaps of Brazilian reserves to protect Neotropical savanna birds. Biological Conservation, 142, 3039-3050.

Marini M.A., Barbet-Massin M., Martinez J., Prestes N.P. & Jiguet F. (2010). Applying ecological niche modelling to plan conservation actions for the Red-spectacled Amazon (Amazona pretrei). Biological Conservation, 143, 102-112.

Marmion M., Hjort J., Thuiller W. & Luoto M. (2008). A comparison of predictive methods in modelling the distribution of periglacial landforms in Finnish Lapland. Earth Surface Processes and Landforms, 33, 2241–2254.

Marmion M., Hjort J., Thuiller W. & Luoto M. (2009). Statistical consensus methods for improving predictive geomorphology maps. Computers and Geosciences, 35, 615– 625.

Marmion M., Luoto M., Heikkinen R.K. & Thuiller W. (2009). The performance of state-of-the-art modelling techniques depends on geographical distribution of species Ecological Modelling, 220, 3512-3520.

Marmion M., Parviainen M., Luoto M., Heikkinen R.K. & Thuiller W. (2009). Evaluation of consensus methods in predictive species distribution modelling. Diversity and Distributions, 15, 59-69.

Midgley G.F. & Thuiller W. (2011). Potential responses of terrestrial biodiversity in Southern Africa to anthropogenic climate change. Regional Environmental Change, 11, S127-S135.

Midgley G.F., Thuiller W. & Higgins S.I. (2007). Plant species migration as a key uncertainty in predicting future impacts of climate change on ecosystems: Progress and challenges. In: Terrestrial Ecosystems in a Changing World (eds. Canadell JG, Pataki DE & Pitelka LF). Springer-Verlag New York, pp. 129-137.

Morin X. & Thuiller W. (2009). Comparing niche- and process-based models to reduce prediction uncertainty in species range shifts under climate change. Ecology, 90, 1301–1313.

Parker-Allié F., Musil C.F. & Thuiller W. (2009). Effects of climate warming on the distributions of invasive european annual grasses: a Southern African perspective. . Climatic Change, 94, 87-103.

Parviainen M., Marmion M., Luoto M., Thuiller W. & Heikkinen R.K. (2009). Using summed individual species models and state-of-the-art modelling techniques to identify threatened plant species hotspots. Biological Conservation, 142, 2501-2509.

Pearman P.B., D'Amen M., Beaumont L.J., Graham C.H., Thuiller W. & Zimmermann N.E. (2010). Within-taxon niche structure: niche conservatism, divergence and predicted effects of climate change. Ecography, 33, 990-1003.

Pearman P.B., Randin C.F., Broennimann O., Vittoz P., van der Knaap W.O., Engler R., Le Lay G., Zimmermann N.E. & Guisan A. (2008). Prediction of plant species distributions across six millennia. Ecology Letters, 11, 357-369.

Randin C., Engler R., Normand S., Zappa M., Zimmermann N.E., Pearman P., Vittoz P., Thuiller W. & Guisan  A. (2009). Climate change and plant distribution: local models predict high-elevation persistence. Global Change Biology, 15, 1557-1569.

Randin C.F., Dirnbock T., Dullinger S., Zimmermann N.E., Zappa M. & Guisan A. (2006). Are niche-based species distribution models transferable in space? Journal of Biogeography, 33, 1689-1703.

Rickebusch S., Thuiller W., Hickler T., Araujo M.B., Sykes M.T., Schweiger O. & Lafourcade B. (2008). Incorporating the effects of changes in vegetation functioning and CO2 on water availability in plant habitat models. Biology Letters, 4, 556-559.

Roedder D. & Schulte U. (2010). Potential loss of genetic variability despite well established network of reserves: the case of the Iberian endemic lizard Lacerta schreiberi. Biodiversity and Conservation, 19, 2651-2666.

Sauer J., Domisch S., Nowak C. & Haase P. (2011). Low mountain ranges: summit traps for montane freshwater species under climate change. Biodiversity and Conservation, 20, 3133-3146.

Schroter D., Cramer W., Leemans R., Prentice I.C., Araujo M.B., Arnell N.W., Bondeau A., Bugmann H., Carter T.R., Gracia C.A., de la Vega-Leinert A.C., Erhard M., Ewert F., Glendining M., House J.I., Kankaanpaa S., Klein R.J.T., Lavorel S., Lindner M., Metzger M.J., Meyer J., Mitchell T.D., Reginster I., Rounsevell M., Sabate S., Sitch S., Smith B., Smith J., Smith P., Sykes M.T., Thonicke K., Thuiller W., Tuck G., Zaehle S. & Zierl B. (2005). Ecosystem service supply and vulnerability to global change in Europe. Science, 310, 1333-1337.

Singh N.J. & Milner-Gulland E.J. (2011). Conserving a moving target: planning protection for a migratory species as its distribution changes. Journal of Applied Ecology, 48, 35-46.

Thuiller W. (2003). BIOMOD: Optimising predictions of species distributions and projecting potential future shifts under global change. Global Change Biology, 9, 1353-1362.

Thuiller W. (2004). Patterns and uncertainties of species' range shifts under climate change. Global Change Biology, 10, 2020-2027.

Thuiller W., Araujo M.B., Pearson R.G., Whittaker R.J., Brotons L. & Lavorel S. (2004). Biodiversity conservation - Uncertainty in predictions of extinction risk. Nature, 430.

Thuiller W., Broennimann O., Hughes G.O., Alkemade J.R.M., Midgley G.F. & Corsi F. (2006). Vulnerability of African mammals to anthropogenic climate change under conservative land transformation assumptions. Global Change Biology, 12, 424-440.

Thuiller W., Brotons L., Araujo M.B. & Lavorel S. (2004). Effects of restricting environmental range of data to project current and future species distributions. Ecography, 27, 165-172.

Thuiller W., Lafourcade B., Engler R. & Araujo M.B. (2009). BIOMOD – A platform for ensemble forecasting of species distributions. Ecography, 32, 369-373.

Thuiller W., Lavergne S., Roquet C., Boulangeat I. & Araujo M.B. (2011). Consequences of climate change on the Tree of Life in Europe. Nature, 470, 531-534.

Thuiller W., Lavorel S., Araújo M.B., Sykes M.T. & Prentice I.C. (2005). Climate change threats to plant diversity in Europe. Proceedings of the National Academy of Sciences, USA, 102, 8245-8250.

Thuiller W., Lavorel S., Sykes M.T. & Araújo M.B. (2006). Using niche-based modelling to assess the impact of climate change on tree functional diversity in Europe. Diversity and Distributions, 12, 49-60.

Thuiller W., Midgley G.F., Hughes G.O., Bomhard B., Drew G., Rutherford M.C. & Woodward F.I. (2006). Endemic species and ecosystem vulnerability to climate change in Namibia. Global Change Biology, 12, 759–776.

Thuiller W., Richardson D.M., Pyšek P., Midgley G.F., Hughes G.O. & Rouget M. (2005). Niche-based modelling as a tool for predicting the risk of alien plant invasions at a global scale. Global Change Biology, 11, 2234–2250.

Vallecillo S., Brotons L. & Thuiller W. (2009). Dangers of predicting bird species distributions in response to land-cover changes. Ecological Applications, 19, 538-549.

Zimmermann N.E., Yoccoz N.G., Edwards J., T.C., Meier E.C., Thuiller W., Guisan A., Schmatz D.R. & Pearman P.B. (2009). Climatic extremes improve predictions of spatial patterns of tree species. Proceedings of the National Academy of Sciences, USA, 106, 19723–19728.




 

BIOMOD