What's up, Doc?

  Would you like Biomapper news to be sent directly to your mailbox? As you can see, this will not overload it with tons of spam. One message per month in average. To do so, please subscribe to the Biomapper announcement list on the Yahoo-Groups page or just by sending an e-mail.

16th of June 2009 Uploaded a new paper by Veronika Braunisch and colleagues, presenting new Biomapper algorithms to deal with cases where the studied species is living at the edge of its ecological niche.
11th of February 2009 Uploaded a new version of Biomapper 4, which fixes a bug.
22nd of June 2008 Three papers have been published lately. I have uploaded the PDF of the one by Alberto Jiménez-Valverde (as I did not have access to the two others...)
  1. Jiménez-Valverde, A., Gómez, J.F., Lobo, J.M., Baselga, A. & Hortal, J. (2008) Challenging species distribution models: the case of Maculinea nausithous in the Iberian Peninsula. Annales Zoologici Fennici, 45, 200-10.
  2. Rivera, J.H.V., Huerta, M.A.O. & Guerrer, R. (2008) Analysis of the distribution of Orange-breasted Bunting (Passerina leclanchetii): An endemic species of Mexico's Pacific slope. Ornitologia Neotropical, 19(2), 265-74.
  3. Mertzanis G, Kallimanis AS, Kanellopoulos N, et al. (2008) Brown bear (Ursus arctos L.) habitat use patterns in two regions of northern Pindos, Greece - management implications. Journal of Natural History 42, 301-315.

17th of June 2008

2nd of June 2008

Major update:

.  So far, only a few selected Biomapperians had seen it (those in the discussion group). Now I am making it available to all and everybody:

  I have hereby the pleasure to introduce

Biomapper 4.0

   This new version introduces several brand new functionalities:

  • An improved Median HS algorithm allowing it to work with species living in rare or disappearing habitat. This overcomes the problem of the optimal habitat assumed to lie at the median, even on the marginality factor (See Braunisch et al. 2008, in Ecological Modelling)
  • The possibility to extrapolate any HS model to another study area, to future times, to test management scenarios. A lot of thought has been put into this module because of its potential misuse. Beyond the HS predictions, Biomapper also warns you where you are applying, interpolating or extrapolating from the available data. This module is particularly powerful when used in conjunction with the new extreme optimum median algorithm. The development of this module was financed by the US Department of Agriculture, Forest Service.
  • Several Biomapperians have recently used the ENFA to compare the niche of close species (Sattler et al. 2007, e.g. Chefaoui et al. 2005, Reutter et al. 2003). To those interested by such comparisons, Biomapper 4.0 offers two new tools: first, the Discriminant Analysis, finds the axis along which the niches of two or more species are the most separated. Second, various classical Niche Overlap indices can now be computed on the base of regular EGVs, PCA factors or Discriminant Analysis factors.
  • A very useful novelty is the possibility to model many species automatically. I have been long reluctant to provide such a functionality because I am rather suspicious about these studies where you model 1000 species with the same set of EGVs. However, in some cases, it can be correct and useful. So, now the Spirit has been released from its bottle, use it wisely. With great powers come great responsabilities.

  Other changes include:

  • The interface has slightly changed: on the left you have now a third list box where you can put the species maps. The standard way of setting a species map (by putting a red dot next to its name in the work-map list) still works and merges smoothly with the new way. Biomapper 4.0 reads without problems your old project files, and Biomapper 3.x should be able to read the new project files as well.
  • It is now much easier to save and load cross-validation results. Whenever you save such a file, this is recorded on the project log on the "Results" window. To look at it again, just double-click on this name, and voilà! This works very similarly to the way you look at the input and output maps.
  • You can do cross-validation with presence/absence data to get AUC values.
  • The help file has been updated to reflect these changes.
  • The help file mentions for the first time the existence of the wiki-Biomapper (http://biomapper.wikispaces.com/)
  For this version, I am indebted to Thomas Sattler, who was instrumental in developing and testing the Discriminant Analysis and the niche-overlap indices. Some of the new developments are used in his paper Sattler et al. (2007) in J. of Applied Ecology.

  I am very thankful to Veronika Braunisch, who originated and participated to the development of the improved median algorithm (known in the beta-version as "Veronika's"). She also tested it thoroughly. This algorithm is described in Braunisch et al.(2008), which is now on-line on the Ecological Modelling site.

  The development of the Extrapolation module was commanded and financed by the USDA Forest Service - Pacific Northwest Research Station (USA). I want to thank here Dr Gwenaëlle Le Lay who participated in its development and testing, and to all the beta-testers, in particular Beth Galleger and Becky Kerns.

  I am also very grateful to Dr Nicolas Titeux, who motivated the implementation of the multi-species automatic analysis and tested it thoroughly.

  I hope you will enjoy this new version of Biomapper. You can download it from the "Download" page of the Biomapper website, at www.unil.ch/biomapper

  Ecologically yours,

        Alexandre Hirzel


  • Braunisch, V., Bollmann, K., Graf, R.F. & Hirzel, A.H. (2008) Living on the edge Modelling habitat suitability for species at the edge of their fundamental niche. Ecological Modelling, on line.
  • Chefaoui, R., Hortal, J. & Lobo, J.M. (2005) Potential distribution modelling, niche characterization and conservation status assessment using GIS tools: a case study of Iberian Copris species. Biological Conservation, 122, 327-38.
  • Reutter, B.A., Helfer, V., Hirzel, A.H. & Vogel, P. (2003) Modelling habitat-suitability using museum collections: an example with three sympatric Apodemus species from the Alps. Journal of Biogeography, 30, 581-90.
  • Sattler, T., Bontadina, F., Hirzel, A.H. & Arlettaz, R. (2007) Ecological niche modelling of two cryptic bat species calls for a reassessment of their conservation status. Journal of Applied Ecology, 44(6), 1188-99. 

13th of May 2008

5th of May 2008

25th of February 2008

  • Added a new PDF of a report: Clark MR, Tittensor D, Rogers AD, Brewin P, Schlacher T, Rowden A, Stocks K, Consalvey M (2006). Seamounts, deep-sea corals and fisheries: vulnerability of deep-sea corals to fishing on seamounts beyond areas of national jurisdiction. UNEPWCMC,Cambridge, UK. (Downloadable from the bibliography page, section "Reports")
  • Added a couple of new entries in the FAQ page.

31st of January 2008

  • Added two new publications by Rosa Chefaoui:
    • Chefaoui, R.M., Lobo, J.M. 2008. Assessing the effects of pseudo-absences on predictive distribution model performance. Ecological Modelling 210:478-486. (Downloadable from the bibliography page (section "Theory"))
    • Chefaoui, R.M., Lobo, J.M. 2007. Assessing the conservation status of an iberian moth using pseudo-absences. Journal of Wildlife Management 71:2507-2516. (Downloadable from the bibliography page (section "Applications, International journals"))

30th of January 2008

  • Added two new publications. I particularly recommand the first one, a new report by Ray Davis.
    • Olson D.E and Davis R.J. Conservation Assessment for the Foothill Yellow-legged Frog (Rana boylii) in Oregon, Appendix 1. 2007. USDA Forest Service Region 6 and USDI Bureau of Land Management. Downloadable from the bibliography page (section "Reports").
    • Estrada-Peña, A., Venzal, J.M. 2007. Climate niches of tick species in the mediterranean region: Modeling of occurrence data, distributional constraints, and impact of climate change. Journal of Medical Entomology 44:1130-1138. Downloadable from the bibliography page (section "Applications, international journals").
  • I have also uploaded a poster about presence-only evaluation, which I presented to the ECEM 2007 conference:
    • Hirzel A.H., Le Lay G., Helfer V., Randin C. and Guisan A. 2007. Evaluating presence-only habitat-suitability models. European Conference of Ecological Modelling. Downloadable from the bibliography page (section "Posters")

12th of December 2007

  • Added a bunch of new postcards to the postcard page. Also, I reordered them from the latest to the oldest so that the newest get a chance to be seen too.

22nd of November 2007

  • I had missed a publication in 2006. It is now on the bibliography page (Section "Applications, international journals"), among the 2006 papers:
    • Santos, X., Brito, J.C., Sillero, N., Pleguezuelos, J.M., Llorente, G.A., Fahd, S. & Parellada, X. (2006) Inferring habitat-suitability areas with ecological modelling techniques and GIS: A contribution to assess the conservation status of Vipera latastei. Biological Conservation, 130(3), 416-25.

1st of November 2007

  • New publication on the bibliography page (Section "My other publications"):
    • Hirzel, A.H., Nisbet, R.M. & Murdoch, W.W. (2007) Host-parasitoid spatial dynamics in heterogeneous landscapes. Oikos, on-line.

1st of October 2007

  • New publication on the bibliography page (Section "Applications, international journals"):
    • Sattler, T., Bontadina, F., Hirzel, A.H. & Arlettaz, R. (2007) Ecological niche modelling of two cryptic bat species calls for a reassessment of their conservation status. Journal of Applied Ecology, on-line.

24th of September 2007

  • New publication on the bibliography page (Section "Applications, international journals"):
    • Jimenez-Valverde A, Ortuno VM, Lobo JM (2007) Exploring the distribution of Sterocorax Ortuno, 1990 (Coleoptera, Carabidae) species in the Iberian peninsula. Journal of Biogeography 34, 1426-1438.

30th of July 2007

  • New publication on the bibliography page (Section "Applications, international journals"):
    • Braunisch, V. and Suchant, R. 2007. A model for evaluating the 'habitat potential' of a landscape for capercaillie Tetrao urogallus: a tool for conservation planning. - Wildlife Biology 13: 21-33.

2nd of July 2007

  • New publication on the bibliography page (Section "Applications"):
    • Soares, C. and Brito, J. C. 2007. Environmental correlates for species richness among amphibians and reptiles in a climate transition area. - Biodiversity and Conservation 16: 1087-1102.
  • New classification for the bibliography page, with publications listed as journal articles, PhD theses, reports, books or MSc theses.

19th of June 2007

Pre-release of Biomapper 4.0 beta to the members of the discussion list.

18th of June 2007

A new publication on the bibliography page (Section "Applications"):
  • Titeux, N., Dufrêne, M., Radoux, J., Hirzel, A.H. & Defourny, P. (2007) Fitness-related parameters improve niche-based distribution modelling: the case of the Red-backed Shrike. Biological Conservation, 138, 207-23.
Added a new section in the bibliography page, listing papers related to Biomapper in some way.

14th of June 2007

  One new publication on the bibliography page:
  • Mestre, F.M., Ferreira, J.P. & Mira, A. (2007) Modelling the distribution of the European Polecat Mustela putorius in a Mediterranean agricultural landscape. Revue d'Ecologie (Terre Vie), 62, 35-47.

6th of June 2007

  Two new publications on the bibliography page:
  • Traill, L.W. & Bigalke, R.C. (2007) A presence-only habitat suitability model for large grazing African ungulates and its utility for wildlife management. African Journal of Ecology, in press.

  • Wilson, M.F.J., O’Connell, B., Brown, C., Guinan, J.C. & Grehan, A.J. (2007) Multiscale Terrain Analysis of Multibeam Bathymetry Data for Habitat Mapping on the Continental Slope. Marine Geodesy, 30:3-35.

17th of May 2007

  Two new PDF on the bibliography page:
  • A poster comparing ENFA to Idrisi's Mahalanobis typicality by Ortega & Vaclavik
  • The manuscript of an old paper of mine, published in the proceedings of a conference on Mountain Ungulates (not related to Biomapper)

18th of April 2007

  I am considering organising a Biomapper workshop. Would you be interested? Please answer the poll so that I can see what the needs and wishes of the Biomapper community are.

22nd of February 2007

Two new publications (Available from the bibliography page, in the Applications section):
  • Bryan, T.L. and Metaxas, A. 2007. Predicting suitable habitat for deep-water gorgonian corals on the Atlantic and Pacific Continental Margins of North America. Marine Ecology Progress Series 330:113-126.
  • Wilson, Margaret F.J. (2006) Deep sea habitat mapping using a remotely operated vehicle: Mapping and modelling seabed terrain and benthic habitats at multiple scales in the Porcupine Seabight, SW Ireland.  PhD Thesis, National University of Ireland, Galway. 266pp.

12th of February 2007

  • New publication: Raphael, M. G., B. Galleher, M. H. Huff, S. L. Miller, S. K. Nelson, and R. D. Young. 2006. Spatially-explicit estimates of potential nesting habitat for the Marbled Murrelet. Pages 97-146 in M. H. Huff, R. M.G., M. S.L., N. S.K., and Baldwin, editors. Northwest Forest Plan—the first 10 years (1994-2003): statuss and trends of populations and nesting habitat for the marbled murrelet. PNW-GTR-650, U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Portland, USA. Available from the bibliography page, in the Applications section.

8th of February 2007

  • Uploaded a new publication: Cassinello, J., P. Acevedo, and J. Hortal. 2006. Prospects for population expansion of the exotic aoudad (Ammotragus lervia; Bovidae) in the Iberian Peninsula: clues from habitat suitability modelling. Diversity and Distributions 12:666-678. Available from the bibliography page, in the Applications section.
  • Updated the FAQ, Links and Home page to mention the new Wiki-Biomapper. This site is destined to be the ultimate help resource for Biomapper, where Biomapperians can share and organise their knowledge and experience.

22nd of November 2006

  • A new powerpoint presentation is available for download on the Presentation page. It is about the process of evaluating presence-only models with the continuous Boyce index.

19th of October 2006

Major update:

.  So far, only a few selected Biomapperians had seen it (those in the discussion group). Now I am making it available to all and everybody:

Biomapper 3.2

  Here are the main points of this new version:

  • A brand new evaluation procedure, which is compatible with presence-only data, robust, threshold independent, and which points at the strengths and weaknesses of your model: the so-called Boyce continuous index.
  • The possibility to save and load evaluation data, so that you can easily compare several models before choosing the best one.
  • The MapManager module can now export Biomapper/Idrisi maps into other formats, such as Text, ArcGIS ASCII format, Bitmap and JPEG. And several at once, with that. This allows making pictures for your next presentation a very simple process indeed.
  • Do you want to have a quick look at one of your maps? Easy: just drag and drop it on the MapViewer module. You can also link the .rst or .rdc extension to the MapViewer and just double-clicking on a map will bring it to your screen.

  All these novelties are in the Biomapper package, version

  • There is also a new paper, which describes and tests the new evaluation procedure: Hirzel, A. H., G. Le Lay, V. Helfer, C. Randin, and A. Guisan. 2006. Evaluating the ability of habitat suitability models to predict species presences. Ecological Modelling 199:142-152. You can download it from the bibliography page (section "Theory").

  More is coming, so stay tuned:

  • The possibility to extrapolate a Biomapper model on another area, or in the future. A project funded by the US Department of Agriculture, Forest Service, Olympic National Forest, thanks to Prof. Martin Raphael
  • Improvements to the median algorithm (devised by Veronika Braunish)
  • The possibility to pilot R from Biomapper and conduct GLM analyses (if by miracle you happen to have put your hands on reliable absences)
  • Procedures to test and control for misleading presences found in sink habitat (devised by Nicolas Titeux)


8th of August 2006

  • A new poster is available in PDF on the bibliography page (section "Posters") by Liz White, about her work on Mandrill habitat.

13th of July 2006

  • A new publication is available in PDF on the bibliography page (section "Applications of ENFA") concerning an application of Biomapper to veterinary issues: Estrad-Peña, A., Venzal, J.M., Acedo, C.S., 2006. The tick Ixodes ricinus: distribution and climate preferences in the western Palaearctic. Medical and Veterinary Entomology 20, 189-197.

6th of July 2006

  • A new publication is available in PDF on the bibliography page (section "Applications of ENFA"): The PhD thesis of Dr. Nicolas Titeux, "Modelling species distribution when habitat occupancy departs from suitability: Application to birds in a landscape context". This thesis offers so many brilliant ideas that it is difficult to give them all here, but among others, he tests with field data how habitat suitability is related to individual fitness, he introduces a robust method for using ENFA and GLM conjointly to improve model predictions, he shows how conspecific attraction may fool management strategies, etc..

  • Pre-release version of Biomapper 3.2 is now available for test by all users subscribed to the Biomapper discussion list (http://groups.yahoo.com/group/Biomapper-List/). This version introduces the new validation procedure, known as the "Continuous Boyce index".

19th of June 2006

  • A new publication is available in PDF on the bibliography page (section "Applications of ENFA"), by Lise Tole, who was known as an active participant of the Biomapper discussion list: Tole, L., 2006. Choosing reserve sites probabilistically: A Colombian Amazon case study. Ecological Modelling 194, 344-356.

26th of April 2006

  Three great help documents (in PDF) written by Emil Peter. They are step-by-step guides, complete with screenshots and all! They cover these topics:
  • Habitat modelling with Biomapper 3
  • File conversion between ArcGIS and Idrisi/Biomapper
  • Comparing and selecting ENFA models by using an Excel spreadsheet

  You can download them from the "Presentations & courses" page.

24th of March 2006

  • A new publication is available in PDF on the bibliography page (section "Applications of ENFA"), by Benjamin Boisteau and Loïc Marion: Definition of potential habitats of Grey Heron using landscape analysis and the species ecological niche [Définition des habitats potentiels du héron cendré Ardea cinerea par l'analyse du paysage et de sa niche écologique]. Alauda 73, 431-440. Article in French with abstract in English.

10th of February 2006

  • FAQ available in PDF and OpenOffice format, thanks to Paulo van Breugel.

24th of January 2006

  • New publication: General report by Joseph Lint et al.: Northwest Forest Plan—the first 10 years (1994–2003): status and trends of Northern spotted owl populations and habitat. The PDF (a big one!) can be downloaded from the bibliography page (section "Applications of ENFA").

2nd of December 2005

  • Added a few new entries in the FAQ
  • New publication: Book chapter by Joaquín Hortal et al.: "Using ATLANTIS - TIERRA 2.0 and GIS environmental information to predict the spatial distribution and habitat suitability of endemic species.". The PDF (a big one!) can be downloaded from the bibliography page (section "Applications of ENFA"). This is a bilingual book, English and Portuguese.
  • I have built a brand new page where you will find powerpoint presentations, courses, etc.. I wish to thanks Joaquín Hortal for giving me this idea, and providing the first material to put there: a complete Biomapper course. I've put one of my own presentations and a poster as well. Please send me any material that could fit there so that other can benefit from your experience.

8th of September 2005

  • Uploaded a minor upgrade of Biomapper (, which optimises the memory management in the geometric, harmonic and minimal distance algorithms. Download the new Biomapper package.

18th of July 2005

Arditi R., Michalski J., Hirzel A.H., 2005. Rheagogies: Modelling non-trophic effects in food webs. Ecological Complexity 2, 249-258

30th of May 2005

Compton, R. C. 2004. Predicting key habitat and potential distribution of Northern Bottlenose Whales (Hyperoodon ampullatus) in the northwest Atlantic ocean. MSc thesis. University of Plymouth, 40 p.

14th of February 2005

Mandleberg, L. 2004. A comparison of the predictive abilities of four approaches for modelling the distribution of cetaceans. School of Biological Sciences, University of Aberdeen, UK, 54p.

2nd of February 2005

Leverette, T. L. 2004. Predicting suitable habitat for deep water corals in the Pacific and Atlantic Continental Margins of North America. Department of Oceanography. - Dalhousie University, 81 p.

12th of January 2005

Freer R.A. 2004. The spatial ecology of the Güiña (Oncifelis guigna) in Southern Chile. Durham: University of Durham. 219 p.

10th of January 2005

  • A new paper has just been published applying ENFA to beetles of Scolytidae family, in Spain. You can download it from the bibliography page (section applications):

Gallego D, Canovas F, Esteve MA, Galian J, Schwerdtfeger F. 2004. Descriptive biogeography of Tomicus (Coleoptera : Scolytidae) species in Spain. Journal of Biogeography 31(12):2011-2024.

22nd of December 2004

Zimmermann F. 2004. Conservation of the Eurasian Lynx (Lynx lynx) in a fragmented landscape - habitat models, dispersal and potential distribution [PhD thesis]. Lausanne: University of Lausanne. 180 p.

7th of December 2004

  • A new paper has just been published, applying Biomapper and the new geometric distance algorithm to model the ecological niche of the bearded Vulture (Gypaetus barbatus):

    Hirzel AH, Posse B, Oggier P-A, Crettenand Y, Glenz C, Arlettaz R. 2004. Ecological requirements of a reintroduced species, with implications for release policy: the Bearded vulture recolonizing the Alps. Journal of Applied Ecology 41:1103-1116.

     The PDF can be downloaded from the bibliography page.

26th of October 2004

  • A new paper has just been published by Rosa Chefaoui, applying Biomapper to model beetle habitat in Spain:

Chefaoui, R., Hortal, J. and Lobo, J.M. (2005) Potential distribution modelling, niche characterization and conservation status assessment using GIS tools: a case study of Iberian Copris species. Biological Conservation, 122, 327-338

 The PDF can be downloaded from the bibliography page.

25th of October 2004

  • New entry and PDF in the bibliography: Poster by J.Witt and S. Menon.
  • New entry and PDF in the bibliography: Famous, unfindable paper by Hutchinson (1957) where he introduced the concept of the multidimensional niche.
  • Hirzel & Arlettaz 2003 (in Environmental Management): Replaced the html "full paper" by the true pdf.

25th of August 2004

  • Added a new entry in the FAQ about conversion errors from Biomapper to ArcView 3.x. Thanks to G. Le Lay and J. Fahr.

21st of July 2004

  • Uploaded a brand new publication on the bibliography page: Brotons, L., Thuiller, W., Araujo, M.B., & Hirzel, A.H. (2004) Presence-absence versus presence-only modelling methods for predicting bird habitat suitability. Ecography, 27, 437-448. Availabe in PDF.
  • Also uploaded a PDF of an older proceedings chapter: Hirzel, A.H. & Arlettaz, R. (2003) Environmental-envelope based habitat-suitability models. In 1st Conference on Resource Selection by Animals (ed B.F.J. Manly). Omnipress, Laramie, USA.

14th of July 2004

  • Uploaded a new PhD thesis in PDF on the bibliography page: Williams, A.K. (2003) The Influence of Probability of Detection When Modeling Species Occurrence Using GIS and Survey Data. PhD thesis, Blacksburg University, Blacksburg (USA).
  • Added a new postcard as well.

30th of June 2004

  • Minor update: Cross-validation box improved. Automatic analysis reprogrammed. Several minor bug fixed. Download Biomapper package, version

1st of April 2004

  • A new entry in the FAQ explaining how to interpret the cross-validation curves.
  • Fixed a bug related to the Spearman rank in the cross-validation module, appearing for small number of species points. Download Biomapper package, version

27th of March 2004

   Medium update: Biomapper 3.1
  • Sometimes you have maps at the same resolution, but as they are derived from different data bases, they do not cover exactly the same area and are therefore doomed to be not overlayable by Biomapper. So far, it was needed to do several operations in Idrisi or some other GIS software to clip them all to the same area. Now, it will be easier: I have implemented a Clip module in Biomapper, which will look at a list of maps, find the largest common area and clip them all accordingly. You will find this module in the menu Ecogeographical Maps/Formatting/Clip...
  • There are also several novelties in the module DistAn, the main one being the topographic dsitance. This distance, suggested by G. Le Lay, needs a digital elevation model map to be provided and is measured following the terrain; as lemmings run instead of as crows fly. As computing this distance with an exact algorithm was rather time consuming, I implemented a faster but approximate algorithm. Both algorithms are available, and implemented the fast one for the minimum distance too, as it is so quick. Check DistAn's help file for more details.
  • There are also a few new entries in the FAQ, related to the area-adjusted cross-validation. Thanks to Tanya for asking them on the Biomapper-List discussion group.
  • Added a new PDF in the bibliography: masters thesis by M. Bassi (in German).

  All these novelties are in the Biomapper package, version

24th of March 2004

  Uploaded a new PDF on the bibliography page: this is not yet the official PDF, but a copy of the full-text version of Hirzel, A.H. & Arlettaz, R. (2003) Modelling habitat suitability for complex species distributions by the environmental-distance geometric mean. Environmental Management, 32, 614-623.

18th of March 2004

  Several bug fixes. Download the Biomapper package, version

4th of March 2004

  New entries in the FAQ.

  EGV's standardisation added in the transformation menu.

4th of February 2004

  New module: MapCalculator.

   MapCalculator computes a new map by applying to each cell a user-defined function of several other maps.

  It is similar to Idrisi's "IMAGE CALCULATOR". However, here the expression is first parsed internally and all computations made simultaneously. With complex expressions this will make the process faster and will not generate all these temporary files, which can take a lot of hard-disk space.

   It has been included into the Biomapper package.

19th of January 2004

  Added "Huberty's rule" button in the cross-validation dialog box. Fixed a few bugs in the cross-validation module (problems with low sample sizes).

14th of January 2004

  Fixed a bug in normalisation that prevented maps from being normalised.
10th of January 2004
  Great news:
Biomapper 3.0 is arrived!

  It contains the followings novelties:

  • Three new Habitat Suitability algorithms have been added: Distance Geometric Mean, Distance Harmonic Mean, and Minimum Distance. They allow to cope with some short-comings of the previous Median-based algorithm. Namely, the assumption of unimodality and symmetry of the species distribution on the factors has been relaxed.
  • The cross-validation has been entirely rebuilt and is now based on the area-adjusted frequency method described by Boyce et al. (2002, Ecological Modelling 157: 281-300.). Evaluating a model based only on presence data is now much easier and stronger.
  • HS map reclassification made easy. Visualize the species and global histograms and just drag the bars boundaries to choose the best class boundaries.
  • You can now visualize the species ecological niche in 2D in the environmental space (you select which factors you want to display).
  • The results window is more active than ever: a right-click on the map names will open a pop-up menu proposing the most frequent tools, including a brand new "metadata" quick visualisation. A small addition, but it really makes life easier.
  • Biomapper 3 has been compiled with Borland Delphi 6 (was Delphi 4 for Biomapper 2).
  • The module DistAn has a new feature suggested by Richard Zink: "In-and-out distance", a distance that is positive outside the focal land-cover class and negative inside.
  • An updated help file.
  • For the first time, a user's manual in PDF format (well, that's just a print-out of the help file, but someone asked for it).
  • And many more minor improvements I've forgotten.
  Run and download it! Biomapper 2.1 is now obsolete and will not be supported anymore.
11th of November 2003
  Patrick Patthey's PhD thesis uploaded on the bibliography page.
  "Products" page updated.
31st of October 2003
  Minor update (FAQ, bibliography, ...)
27th of April 2003
  Added the new paper by Reutter et al. (with PDF) in the bibliography page.
5th of April 2003
  A few PDF papers added to the bibliography page.
26th of March 2003
  The FAQ was beginning to be so cluttered it was difficult to find an answer in the middle of all this bunch of information. I have completely reorganised it by following a chronological structure: questions and answers are now ordered in the sequence they are going to appear as you walk through an analysis procedure. Titles and sub-titles also achieve a better classification than before.

  I also added several new entries, mainly about masking and discrepancy issues (Many thanks to Thomas Sattler).

  The previous version of the FAQ will still be available for some time here.

9th of February 2003
  Added a few words about me...
2nd of December 2002
  New entries in the FAQ, in particular about the difference between "explained variance" and "explained information".
17th of October 2002
  A new paper dealing with ENFA and GAMs on habitat suitability modelling of New Zealand ferns has been published in Ecological Modelling by E. Zaniewski et al.. Full reference has been added in the bibliography page.
11th of September 2002
Medium update:
  • In Biomapper2, you will find a new way to present the score matrix without ugly numbers. Look into the menu Multivariate Analysis/Factor computation/Score table.
  • There is also a new module named Map Manager. It is mainly designed for Biomapperians who do not have Idrisi. As Idrisi and Biomapper have three data types (Real, integer and byte) whilst ArcView has only two (Real and integer), this could cause some difficulties. Map Manager implements the conversion between all three types with various options (including stretching between 0 and 100 or 0 and 1), but also deleting and renaming the maps, fixing the -9999 background bug appearing when converting boolean maps from ArcView, looking at metadata, adding comments and launching multiple Map Viewer sessions.
  Download it now! Everything is in the Biomapper 2.1 package.
22nd of August 2002
  A new PDF (in French) has been added in the bibliography page and three new topics have been added in the FAQ
14th of August 2002
   Finally, after 2 years and a half of waiting, the fundamental paper that presents all the details of the ENFA is available (PDF downloadable from the bibliography page):
Hirzel A.H., Hausser J., Chessel D. & Perrin N. (2002) Ecological-niche factor analysis: How to compute habitat- suitability maps without absence data? Ecology, 83, 2027-2036
  We propose a multivariate approach to the study of geographic species distribution which does not require absence data. Building on Hutchinson's concept of the ecological niche, this factor analysis compares, in the multidimensional space of ecological variables, the distribution of the 
localities where the focal species was observed to a reference set describing the whole study area. The first factor extracted maximizes the marginality of the focal species, defined as the ecological distance between the species optimum and the mean habitat within the reference area. The other factors maximize the specialization of this focal species, defined as the ratio of the ecological variance in mean habitat to that observed for the focal species. Eigenvectors and eigenvalues are readily interpreted and can be used to build habitat-suitability maps. This approach is recommended in Situations where absence data are not available (many data banks), unreliable (most cryptic or rare species), or meaningless (invaders). We provide an illustration and validation of the method for the alpine ibex, a species reintroduced in Switzerland which presumably has not yet recolonized its entire range.

Author Keywords:
Capra ibex, ecological niche, GIS, habitat suitability, marginality, multivariate analysis, presence-absence elata, specialization, species distribution, Switzerland

6th of August 2002
  The color scheme used in Biomapper map has been converted into an Idrisi palette. You will find it in the new Biomapper 2.1 package under the name Biomapper.smp. You can now use Biomapper colors also in Idrisi.
7th of May 2002
  Habitat Suitability map accuracy can now be better evaluated through a jack-knife (Leave-One-Out) cross-validation process. You have no longer to separate your data into calibration and validation sets, which simplifies the whole procedure. Moreover, the jack-knife computes confidence limits for HS model accuracy, as well as confidence limits HS maps.Check the Modus Operandi in the help file to see how to proceed now.

  The jack-knife and the new help file are included into the Biomapper 2.1 package.

21st of March 2002
  First day of the Spring... The nature is putting on its new clothes. Biomapper, as ever, is following it close behind; a new version of Biomapper is waking up:

Biomapper 2.0 is here!

  The analysis process has been profoundly modified although the user-interface has not changed so much. These changes were made in order to add more easily the new algorithms I am currently developping.

  But there are anyway several new functionalities, which will help you all along the Biomapper's process. By order of apparition, we have:

  • The whole "map preparation" procedures have been improved and debugged (I cannot list here all the minor changes I did, but you will find them in the help files of each module).
  • When you mask or normalise your EGV, you can choose to replace the original maps into the EGV map list box. You don't have anymore to create a new project and add the modified maps.
  • The "EGV map verification" procedure has been greatly improved: it produces now a map of discrepancies allowing the user to better understand where and why his/her maps may be discrepant. Moreover, the verification process is now able to detect not only nearly-constant maps, but also nearly-boolean maps, which were causing problems during the ENFA computation (eigenvalues either negative or huge).
  • You can now easily get the "original" medians and quartile of your EGVs when you have normalised them before the ENFA (e.g. by the Box-Cox transformation). It helps to interprete the score matrix resulting from the ENFA.
  • But probably the most useful functionnality will be the so-called "automatic analysis": Now, once your EGV maps have passed the verification test, you can do all subsequent steps - or only some of them -  in one single process: covariance matrix, ENFA computation, score matrix sorting, habitat suitability computation, HS map validation and species distribution on the original (untransformed) EGV will be done in one step, allowing the user to take nap during the process.

  •   Nevertheless, I was a little bit reluctant to put such a facility into Biomapper as it could make the user to loose the "feeling" of what is really happening. My advice is that you should still make the analysis step by step, manually, the first time you are looking at your data. Once you are sure that everything is right and you want to tune the results, the automatic analysis will then prove most useful.
  • Finally, MapViewer and Map3D have been improved.
  • Of course, the help file has been modified to reflect the changes in the modus operandi.
  • The file formats have not been changed and therefor you can pass without any problem from Biomapper 1 to Biomapper 2 and back again.
  Now, to benefit from all these novelties, hurry up and download Biomapper 2.0 package!

  For the nostalgic ones, the last version of Biomapper 1.0 is still available for download at the same place.

9th of January 2002
  I just found an ArcView extension designed to convert ESRI grids to Idrisi rasters and conversely. I put the link in the FAQ.
19th of December 2001
  •  Added several entries in the FAQ about statistical questions. Thanks to Dr Brotons.
  • Two unpublished student reports involving ENFA have been uploaded in PDF format on the bibliography page. They are in French though.
  • Official launch of the Biomapper discussion list. You can subscribe to it by sending an blank e-mail to Biomapper-List-subscribe@yahoogroups.com. It will be dedicated to Biomapper- and ENFA-related topics, as well as to general questions in spatial ecology modelling. Everyone is welcome.
13th of December 2001
  A new version of Biomapper has been uploaded. It contains a new module MapViewer which is an independent implementation of the display facility included into the main Biomapper program. Map displaying has been greatly improved:
  - It is now far more faster
  - Zooming and panning has been improved
  - When overlaying two maps, you can now control the transparency rate of the overlaid one.
   You just have to download the Biomapper package.
3rd of December 2001
  First paper dealing with ENFA (not the big one though), published in Ecological Modelling 145 (November 2001). Check the bibliography page.
5th of November 2001
  It is now possible to see Biomapper working... (a little souvenir of my PhD defence)
1st of November 2001
  Added an entry in the FAQ about ESRI grid conversion.
27th of September 2001
  A bibliography page has been added to the site. You will find there all publications related to ENFA and Biomapper. In particular, you can download there a PDF version of my PhD.
17th of September 2001
  New entry in the FAQ.
18th of August 2001
  A new module has been added to the package: DistAn, or Distance Analysis. It should prove helpful for home-range analyses and simple distance computations.

  It has been included into the free Biomapper package.

  Two ENFA-related papers have just been accepted for publication, one in Ecology and another in Ecological Modelling. Biomapperians will be informed by mail when they will be available.

3rd of July 2001
  The new module GridConvertor opens the Biomapper world to ArcView users. This module allows Idrisi raster - Esri grid format conversion. As several files may be converted in one easy operation, it makes mixing Idrisi, ArcView and Biomapper functions in one project easier than ever. Anyway, due to ESRI proprietary politics, GridConvertor does only work if you have ArcView with Spatial Analyst installed on your computer.

  The module Sampler can now generate regular (grid) sampling design.

  Both modules are included into the free Biomapper package.

20th of May 2001
A few cosmetic changes on the site.
14th of May 2001
Several new entries have been added in the FAQ (thanks to Dr. Larrinaga).
27nd of april 2001
- New entries in the FAQ about extrapolation process and Biomapper extensions
- Links page modified. Check the new TetrasPool website!
21st of april 2001
Minor update (fixed a few bugs):
  - Biomapper (v
  - GroupStat
  - BigGroup
Several new entries have been added in the FAQ (thanks to Dr. Larrinaga).
29nd of march 2001
New entry in the FAQ about "documention file not found" error message.
19nd of march 2001
New entries in the FAQ about user manual and file conversion.
2nd of march 2001
New page describing the Biomapper modules
New module: Booleanisator
The following modules were updated (check their help-file to see what has been updated):
- BioMapper (v
- BigGroup (v 2.1)
- Convertor
- GroupStat
- Map-3D (v 1.1) (with Idrisi palette summer and spring landscape)

Download them!

31st of january 2001
Validation statistics described in the FAQ
26th of january 2001
Decimal separator problem addressed in the FAQ
8th of december 2000
Biomapper minor update. Check the history of
- Biomapper
- Convertor
20th of october 2000
New page added: List of "biomapperised" species
10th of october 2000
Creation of the site.

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