Institute for Biodiversity and Ecosystem Dynamics

Photographer: onbekend

dr. ir. E.E. (Emiel) van Loon

Assistant Professor
  • Faculty of Science
    Institute for Biodiversity and Ecosystem Dynamics
  • Visiting address
    Science Park A
    Science Park 904  Room number: C4.168
  • Postal address:
    Postbus  94248
    1090 GE  Amsterdam
    T: 0205257448

I work as Assistant Professor on statistical ecology, dividing my time between teaching applied statistics to ecology and earth science students and research into the analyis of the movement and distribution of organisms in their natural environment.

In my research I currently focus on developing and applying statistical and measurement theory for the analysis of animal movement and distribution through three three projects:

  • developing techniques to learn about animal memory and navigation on the basis of gps-tracking data,
  • space-time modeling of the Dutch muskrat population, and
  • the standardisation of species-distribution modeling workflows. 

Furthermore, I have a continuing interest in enhance reproducibility in the natural sciences though standardization and calibration of observation techniques as well as better storage, documentation and curation of observations and computer code.

Soaring bird migration

A while ago we created an agent-based model in Matlab, which can be used to investigate soaring bird migration. The model design and an example of it's application is described in: E.E. van Loon, J. Shamoun-Baranes, W. Bouten & S.L. Davis (2011). Understanding soaring bird migration through interactions and decisions at the individual level. Journal of Theoretical Biology, 270 (1), 112-126.

vegetation reconstruction

Boris Jansen and I developed a model to reconstruct past vegetation on the basis of biomarker data. The model is conceptually fairly simple, but performed well in the studies where it was applied so far. The model is coded in Matlab, and described in:
B. Jansen, E.E. van Loon, H. Hooghiemstra & J.M. Verstraten (2010). Improved reconstruction of palaeo-environments through unravelling of preserved vegetation biomarker patterns. Palaeogeography, Palaeoclimatology, Palaeoecology, 285 (1-2), 119-130.

Mapcurves implementation

Mapcurves is a goodness-of-fit measure to compare two categorical maps by Hargrove et al. 2006. Niels Raes and I have applied it in a study to floristic regions in Borneo. For this study we coded the Mapcurves algorithm in Matlab and R.
Our Mapcurves implementation contains a Matlab function (which includes a demo option), an R function and a separate (R) demo script. The Matlab and R functions do exactly the same, but differ slightly with respect to the way in which the output is formatted. For background info about Mapcurves, see William W. Hargrove, Forrest M. Hoffman and Paul F. Hessburg (2006) Mapcurves: a quantitativemethod for comparing categorical maps. J Geograph Syst, 8, 187-208. DOI 10.1007/s10109-006-0025-x.


Michael Kemp, a former PhD student in our CGE-group, has created a fantastic R package to process NCEP/NCAR reanalysis (weather) data for use in our bird migration models.
We did describe the package in: Kemp M.U., E.E. van Loon, J. Shamoun-Baranes, W. Bouten (2011) RNCEP: global weather and climate data at your fingertips. Methods in Ecology and Evolution. doi: 10.1111/j.2041-210X.2011.00138.x
For anyone using weather data in ecological models, the RNCEP package may contain very useful functions.


I lecture in the BSc and MSc programs of the earth and biological sciences, beta-gamma and future planet studies (see the link below for an overview). These courses cover statistics and research methods in the natural sciences. In addition, I supervise MSc students during their thesis work. If you are interested in statistical or methodological issues, especially when these relate to biogeography or spatio-temporal dynamics, you may consider to conduct an MSc thesis under my supervision.



  • Yang, S., Cammeraat, E., Jansen, B., den Haan, M., van Loon, E., & Recharte, J. (2018). Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena, 171, 11-21. DOI: 10.1016/j.catena.2018.06.038  [details] 
  • McLaren, J. D., Buler, J. J., Schreckengost, T., Smolinsky, J. A., Boone, M., van Loon, E. E., ... Walters, E. L. (2018). Artificial light at night confounds broad-scale habitat use by migrating birds. Ecology Letters, 21(3), 356-364. DOI: 10.1111/ele.12902  [details] 
  • Golding, N., August, T. A., Lucas, T. C. D., Gavaghan, D. J., van Loon, E. E., & Mcinerny, G. (2018). The zoon r package for reproducible and shareable speciesdistribution modelling. Methods in Ecology and Evolution, 9(2), 260-268. DOI: 10.1111/2041-210X.12858  [details] 
  • Konzack, M., Gijsbers, P., Timmers, F., Loon, E. V., Westenberg, M. A., & Buchin, K. (2018). Visual exploration of migration patterns in gull data. Information Visualization, 1473871617751245. DOI: 10.1177/1473871617751245 
  • Overbeek, C. C., van der Geest, H. G., van Loon, E. E., & Admiraal, W. (Accepted/In press). Decomposition of Standing Litter Biomass in Newly Constructed Wetlands Associated with Direct Effects of Sediment and Water Characteristics and the Composition and Activity of the Decomposer Community Using Phragmites australis as a Single Standard Substrate. Wetlands. DOI: 10.1007/s13157-018-1081-y 


  • Muluneh, A., van Loon, E., Bewket, W., Keesstra, S., Stroosnijder, L., & Burka, A. (2017). Effects of long-term deforestation and remnant forests on rainfall and temperature in the Central Rift Valley of Ethiopia. Forest Ecosystems, 4, [23]. DOI: 10.1186/s40663-017-0109-8  [details] 
  • Tyson, C., Kirk, H., Fayet, A., Van Loon, E. E., Shoji, A., Dean, B., ... Guilford, T. (2017). Coordinated provisioning in a dual-foraging pelagic seabird. Animal Behaviour, 132, 73-79. DOI: 10.1016/j.anbehav.2017.07.022  [details] 
  • Dokter, A. M., van Loon, E. E., Fokkema, W., Lameris, T. K., Nolet, B. A., & van der Jeugd, H. P. (2017). Analyzing time-ordered event data with missed observations. Ecology and Evolution, 7(18), 7362-7369. DOI: 10.1002/ece3.3281  [details] 
  • Dokter, A. M., van Loon, E. E., Rappoldt, C., Oosterbeek, K., Baptist, M. J., Bouten, W., & Ens, B. J. (2017). Balancing food and density-dependence in the spatial distribution of an interference-prone forager. Oikos, 126(8), 1184-1196. DOI: 10.1111/oik.04139  [details] 
  • Simaiakis, S. M., Rijsdijk, K. F., Koene, E. F. M., Norder, S. J., Van Boxel, J. H., Stocchi, P., ... Tjørve, E. (2017). Geographic changes in the Aegean Sea since the Last Glacial Maximum: Postulating biogeographic effects of sea-level rise on islands. Palaeogeography, Palaeoclimatology, Palaeoecology, 471, 108-119. DOI: 10.1016/j.palaeo.2017.02.002  [details] 
  • van Loon, E. E., Bos, D., van Hellenberg Hubar, C. J., & Ydenberg, R. C. (2017). A historical perspective on the effects of trapping and controlling the muskrat (Ondatra zibethicus) in the Netherlands. Pest Management Science, 73(2), 305-312. DOI: 10.1002/ps.4270  [details] 
  • Shamoun-Baranes, J., Burant, J. B., van Loon, E. E., Bouten, W., & Camphuysen, C. J. (2017). Short distance migrants travel as far as long distance migrants in lesser black‐backed gulls Larus fuscus. Journal of Avian Biology, 48(1), 49-57. DOI: 10.1111/jav.01229  [details] 
  • Norder, S. J., Seijmonsbergen, A. C., Rughooputh, S. D. D. V., van Loon, E. E., Tatayah, V., Kamminga, A. T., & Rijsdijk, K. F. (2017). Assessing temporal couplings in social–ecological island systems: historical deforestation and soil loss on Mauritius (Indian Ocean). Ecology and Society, 22(1), [29]. DOI: 10.5751/ES-09073-220129  [details] 
  • Serna-Chavez, H. M., Swenson, N. G., Weiser, M. D., van Loon, E. E., Bouten, W., Davidson, M. D., & van Bodegom, P. M. (2017). Strong biotic influences on regional patterns of climate regulation services. Global Biogeochemical Cycles, 31(5), 787-803. DOI: 10.1002/2017GB005627  [details] 






  • Kemp, M. U., Shamoun-Baranes, J., van Loon, E. E., McLaren, J. D., Dokter, A. M., & Bouten, W. (2012). Quantifying flow-assistance and implications for movement research. Journal of Theoretical Biology, 308, 56-67. DOI: 10.1016/j.jtbi.2012.05.026  [details] 
  • Kemp, M. U., van Loon, E. E., Shamoun-Baranes, J., & Bouten, W. (2012). RNCEP: global weather and climate data at your fingertips. Methods in Ecology and Evolution, 3, 65-70. DOI: 10.1111/j.2041-210X.2011.00138.x  [details] 
  • Klotzbücher, T., Kaiser, K., Stepper, C., van Loon, E., Gerstberger, P., & Kalbitz, K. (2012). Long-term litter input manipulation effects on production and properties of dissolved organic matter in the forest floor of a Norway spruce stand. Plant and Soil, 355(1-2), 407-416. DOI: 10.1007/s11104-011-1123-1  [details] 
  • Shamoun-Baranes, J., Bom, R., van Loon, E. E., Ens, B. J., Oosterbeek, K., & Bouten, W. (2012). From sensor data to animal behaviour: an oystercatcher example. PLoS One, 7(5), e37997. [e37997]. DOI: 10.1371/journal.pone.0037997  [details] 
  • Shamoun-Baranes, J., van Loon, E. E., Purves, R. S., Speckmann, B., Weiskopf, D., & Camphuysen, C. J. (2012). Analysis and visualization of animal movement. Biology Letters, 8, 6-9. DOI: 10.1098/rsbl.2011.0764  [details] 
  • Veen, L. E., van Reenen, G. B. A., Sluiter, F. P., van Loon, E. E., & Bouten, W. (2012). A semantically integrated, user-friendly data model for species observation data. Ecological Informatics, 8, 1-9. DOI: 10.1016/j.ecoinf.2011.11.002  [details] 


  • Shamoun-Baranes, J., Dokter, A. M., van Gasteren, H., van Loon, E. E., van Leijnse, H., & Bouten, W. (2011). Birds flee en mass from New Year's Eve fireworks. Behavioral Ecology, 22(6), 1173-1177. DOI: 10.1093/beheco/arr102  [details] 
  • van Loon, E. E., Shamoun-Baranes, J., Bouten, W., & Davis, S. L. (2011). Understanding soaring bird migration through interactions and decisions at the individual level. Journal of Theoretical Biology, 270(1), 112-126. DOI: 10.1016/j.jtbi.2010.10.038  [details] 
  • van Strien, A. J., Dekker, J. J. A., Straver, M., van der Meij, T., Soldaat, L. L., Ehrenburg, A., & van Loon, E. (2011). Occupancy dynamics of wild rabbits (Oryctolagus cuniculus) in the coastal dunes of the Netherlands with imperfect detection. Wildlife Research, 38(8), 717-725. DOI: 10.1071/WR11050  [details] 


  • Hengl, T., Heuvelink, G. B. M., & van Loon, E. E. (2010). On the uncertainty of stream networks derived from elevation data: the error propagation approach. Hydrology and Earth System Sciences, 14(7), 1153-1165. DOI: 10.5194/hess-14-1153-2010  [details] 
  • Jansen, B., van Loon, E. E., Hooghiemstra, H., & Verstraten, J. M. (2010). Improved reconstruction of palaeo-environments through unravelling of preserved vegetation biomarker patterns. Palaeogeography, Palaeoclimatology, Palaeoecology, 285(1-2), 119-130. DOI: 10.1016/j.palaeo.2009.10.029  [details] 
  • Kemp, M. U., Shamoun-Baranes, J., van Gasteren, H., Bouten, W., & van Loon, E. E. (2010). Can wind help explain seasonal differences in avian migration speed? Journal of Avian Biology, 41(6), 672-677. DOI: 10.1111/j.1600-048X.2010.05053.x  [details] 
  • Shamoun-Baranes, J., Leyrer, J., van Loon, E., Bocher, P., Robin, F., Meunier, F., & Piersma, T. (2010). Stochastic atmospheric assistance and the use of emergency staging sites by migrants. Proceedings of the Royal Society B-Biological Sciences, 277, 1505-1511. DOI: 10.1098/rspb.2009.2112  [details] 
  • Shamoun-Baranes, J., Bouten, W., & van Loon, E. E. (2010). Integrating meteorology into research on migration. Integrative and Comparative Biology, 50(3), 280-292. DOI: 10.1093/icb/icq011  [details] 
  • Sheikh, V., van Loon, E., Hessel, R., & Jetten, V. (2010). Sensitivity of LISEM predicted catchment discharge to initial soil moisture content of soil profile. Journal of Hydrology, 393(3-4), 174-185. DOI: 10.1016/j.jhydrol.2010.08.016  [details] 


  • Fillinger, U., Sombroek, H., Majambere, S., van Loon, E., Takken, W., & Linsay, S. W. (2009). Identifying the most productive breeding sites for malaria mosquitoes in The Gambia. Malaria Journal, 8, 62. DOI: 10.1186/1475-2875-8-62  [details] 
  • Raes, N., Roos, M. C., Slik, J. W. F., van Loon, E. E., & ter Steege, H. (2009). Botanical richness and endemicity patterns of Borneo derived from species distribution models. Ecography, 32(1), 180-192. DOI: 10.1111/j.1600-0587.2009.05800.x  [details] 


  • Hengl, T., van Loon, E. E., Shamoun-Baranes, J., & Bouten, W. (2008). Geostatistical analysis of GPS trajectory data: Space-time densities. In J. Zhang, & M. F. Goodchild (Eds.), Proceedings of the 8th International Symposium on Spatial Accuracy Assessment in Natural Resources and Environmental Sciences: Shanghai, China, June 25-27, 2008: Volume 1: Spatial uncertainty (pp. 17-24). Liverpool: World Academic Press. [details] 
  • Hengl, T., van Loon, E., Sierdsema, H., & Bouten, W. (2008). Advancing spatio-temporal analysis of ecological data: Examples in R. Lecture Notes in Computer Science, 5072, 692-707. DOI: 10.1007/978-3-540-69839-5_51  [details] 
  • Marijnissen, S. A. E., Michel, E., Kamermans, M., Olaya-Bosch, K., Kars, M., Cleary, D. F. R., ... Menken, S. B. J. (2008). Ecological correlates of species differences in the Lake Tanganyika crab radiation. Hydrobiologia, 615(1), 81-94. DOI: 10.1007/s10750-008-9566-y  [details] 
  • Shamoun-Baranes, J., Bouten, W., Buurma, L., DeFusco, R., Dekker, A., Sierdsema, H., ... van Loon, E. (2008). Avian information systems: Developing web-based bird avoidance models. Ecology and Society, 13(2), 38. [details] 
  • Sierdsema, H., & van Loon, E. E. (2008). Filling the gaps: Using count survey data to predict bird density distribution patterns and estimate population sizes. Revista Catalana d’Ornitologia, 24, 88-99. [details] 
  • van Gasteren, H., Holleman, I., Bouten, W., van Loon, E., & Shamoun-Baranes, J. (2008). Extracting bird migration information from C-band Doppler weather radars. Ibis, 150(4), 674-686. DOI: 10.1111/j.1474-919X.2008.00832.x  [details] 
  • van Meeteren, M. J. M., Tietema, A., van Loon, E. E., & Verstraten, J. M. (2008). Microbial dynamics and litter decomposition under a changed climate in a Dutch heathland. Applied Soil Ecology, 38(2), 119-127. DOI: 10.1016/j.apsoil.2007.09.006  [details] 
  • Zaugg, S., Saporta, G., van Loon, E., Schmaljohann, H., & Liechti, F. (2008). Automatic identification of bird targets with radar via patterns produced by wing flapping. Journal of the Royal Society Interface, 5(26), 1041-1053. DOI: 10.1098/rsif.2007.1349  [details] 


  • Ordóñez, A., van Loon, E., & Bouten, W. (2011). Effects of population variability on the accuracy of detection probability estimates. Anales de Biología, 33, 149-160. [details] 


  • van Boxel, J. H., Brandts, E. B., Grimm, E., Flantua, S. G. A., Hooghiemstra, H., & van Loon, E. E. (2017). Kleine Data Projecten - Eindrapportage: Ontsluiting van paleoecologische datasets van IBED, FNWI, UvA. Den Haag: DANS. [details] 
  • van Boxel, J. H., Brandts, E. B., Flantua, S. G. A., Grimm, E. C., Hooghiemstra, H., & van Loon, E. E. (2017). Data description for the DANS project: Disclosure of paleoecological datasets of IBED, FNWI, UvA. Den Haag: DANS. DOI: 10.17026/dans-zg3-b2jf  [details] 


  • Sterk, H. P., Seijmonsbergen, A. C., de Jong, M. G. G., & van Loon, E. E. (2016). Progress in digital mapping of shallow mass movements by using a combination of orthophotos, LiDAR- and UAV-derived information. 319. Abstract from GeoTirol 2016, Innsbruck, Austria.


  • Whatley, M. H., van Loon, E. E., van Dam, H., Vonk, J. A., van der Geest, H. G., & Admiraal, W. (2012). Vegetation governs aquatic invertebrate composition in agricultural peatlands. Paper presented at New Zealand Freshwater Sciences Society Conference, .

Journal editor

  • van Loon, E. (reviewer) (2016). Scientific Data (Journal).
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