CTMM Initiative

Jesse Alston
Justin M. Calabrese
Xianghui Dong
William F. Fagan
Christen H. Fleming
Elie Gurarie
Michael J. Noonan
Guillaume Péron
Ines Silva
Daniel Sheldon
Ben Wallberg
Kevin Winner

Continuous-Time Movement Modeling

ctmm graphs analyzing animal tracking data
ctmm is an R package for analyzing animal tracking data as a continuous-time stochastic processes. Package features include FFT variogram and Lomb-Scargle periodogram analysis, Kalman-filter maximum-likelihood estimation, Kriging, simulation, and autocorrelated kernel-density home-range estimation.

The above image depicts the variogram, periodogram, occurrence distribution, and range distribution of an African buffalo in Kruger National Park (DOI:10.5441/001/1.j900f88t/1).
 
CRAN package • Github project • Github reference • Google group • β packages
  • Silva, I., C. H. Fleming M. J. Noonan, W. F. Fagan, J. M. Calabrese, “movedesign: Shiny R app to evaluate sampling design for animal movement studies”, Methods in Ecology and Evolution 14:9 2216–2225 (2023)
  • Alston, J. M., C. H. Fleming, R. Kays, J. P. Streicher, C. T. Downs, T. Ramesh, B. Reineking, J. M. Calabrese, “Mitigating pseudoreplication and bias in resource selection functions with autocorrelation-informed weighting”, Methods in Ecology and Evolution 14:2 643–654 (2023)
  • Fleming, C. H., I. Deznabi, S. Alavi, M. C. Crofoot, B. T. Hirsch, E. P. Medici, M. J. Noonan, R. Kays, W. F. Fagan, D. Sheldon, J. M. Calabrese, “Population-level inference for home-range areas”, Methods in Ecology and Evolution 13:5 1027–1041 (2022)
  • Silva, I., C. H. Fleming, M. J Noonan, J. Alston, C. Folta, W. F. Fagan, J. M. Calabrese, “Autocorrelation-informed home range estimation: a review and practical guide”, Methods in Ecology and Evolution 13:3 534–544 (2021)
  • Noonan, M. J., R. Martinez-Garcia, G. H. Davis, M. C. Crofoot, R. Kays, B. T. Hirsch, D. Caillaud, E. Payne, A. Sih, D. L. Sinn, O. Spiegel, W. F. Fagan, C. H. Fleming, J M. Calabrese, “Estimating encounter
    location distributions from animal tracking data”, Methods in Ecology and Evolution, 12 1158–1173 (2021)
  • Calabrese, J. M., C. H. Fleming, M. J. Noonan, X. Dong, "ctmmweb: A Graphical User Interface for Autocorrelation‐Informed Home Range Estimation", Wildlife Society Bulletin, doi:10.1002/wsb.1154 (2021)
  • M. J. Noonan, C. H. Fleming, T. S. Akre, J. Dresher-Lehman, E. Gurarie, A.-L. Harrison, R. Kays, J. M. Calabrese, "Scale-insensitive estimation of speed and distance traveled from animal tracking data", Movement Ecology, 7:35 (2019)
  • C. H. Fleming, M. J. Noonan, E. P. Medici, J. M. Calabrese, "Overcoming the challenge of small effective sample sizes in home‐range estimation", Methods in Ecology and Evolution 10:10, 1679-1689 (2019)
  • M. J. Noonan, M. A. Tucker, C. H. Fleming, T. Akre, S. C. Alberts, A. H. Ali, J. Altmann, P. C. Antunes, J. L. Belant, D. Beyer, N. Blaum, K. Böhning‐Gaese, L. Cullen Jr., R. C. de Paula, J. Dekker, J. Drescher‐Lehman, N. Farwig, C. Fichtel, C. Fischer, A. Ford, J. R. Goheen, R. Janssen, F. Jeltsch, M. Kauffman, P. M. Kappeler, F. Koch, S. LaPoint, A. C. Markham, E. P. Medici, R. G. Morato, R. Nathan, L. G. R. Oliveira‐Santos, K. A. Olson, B. D. Patterson, A. Paviolo, E. E. Ramalho, S. Roesner, D. Schabo, N. Selva, A. Sergiel, M. X. da Silva, O. Spiegel, P. Thompson, W. Ullmann, F. Ziȩba, T. Zwijacz‐Kozica, W. F. Fagan, T. Mueller, J. M. Calabrese, "A comprehensive analysis of autocorrelation and bias in home range estimation", Ecological Monographs 89:2, e01344 (2019)
  • K. Winner, M. J. Noonan, C. H. Fleming, K. Olson, T. Mueller, D. Sheldon, J. M. Calabrese, "Statistical inference for home range overlap", Methods in Ecology and Evolution 9:7, 1679-1691 (2018)
  • C. H. Fleming, D. Sheldon, W. F. Fagan, P. Leimgruber, T. Mueller, D. Nandintsetseg, M. J. Noonan, K. A. Olson, E. Setyawan, A. Sianipar, J. M. Calabrese, "Correcting for missing and irregular data in home-range estimation", Ecological Applications 28:4, 1003-1010 (2018)
  • C. H. Fleming, D. Sheldon, E. Gurarie, W. F. Fagan, J. M. Calabrese, "Kálmán filters for continuous-time movement models", Ecological Informatics 40, 8-21 (2017)
  • G. Péron, C. H. Fleming, R. C. de Paula, N. Mitchell, M. Strohbach, P. Leimgruber, J. M. Calabrese, "Periodic continuous-time movement models uncover behavioral changes of wild canids along anthropization gradients", Ecological Monographs 87:3, 442-456 (2017)
  • C. H. Fleming, J. M. Calabrese, "A new kernel-density estimator for accurate home-range and species-range area estimation", Methods in Ecology and Evolution 8:5, 571-579 (2016)
  • G. Péron, C. H. Fleming, R. de Paula, J. M. Calabrese, “Uncovering periodic patterns of space use in animal tracking data with periodograms, including a new algorithm for the Lomb-Scargle periodogram and improved randomization tests”, Movement Ecology 4:19, 10.1186/s40462-016-0084-7 (2016)
  • J. M. Calabrese, C. H. Fleming, E. Gurarie, "ctmm: An R package for analyzing animal relocation data as a continuous-time stochastic process", Methods in Ecology and Evolution 7:9, 1124-1132 (2016)
  • C. H. Fleming, W. F. Fagan, T. Mueller, K. A. Olson, P. Leimgruber, J. M. Calabrese, "Estimating where and how animals travel: An optimal framework for path reconstruction from autocorrelated tracking data", Ecology, 97:3, 576-582 (2016)
  • C. H. Fleming, W. F. Fagan, T. Mueller, K. A. Olson, P. Leimgruber, J. M. Calabrese, "Rigorous home-range estimation with movement data: A new autocorrelated kernel-density estimator", Ecology 96:5, 1182-1188 (2015)
  • C. H. Fleming, Y. Subasi, J. M. Calabrese, "A maximum-entropy description of animal movement", Physical Review E 91, 032107 (2015)
  • C. H. Fleming, J. M. Calabrese, T. Mueller, K. A. Olson, P. Leimgruber, W. F. Fagan, "Non-Markovian maximum likelihood estimation of autocorrelated movement processes", Methods in Ecology and Evolution 5:5, 462-472 (2014)
  • C. H. Fleming, J. M. Calabrese, T. Mueller, K. A. Olson, P. Leimgruber, W. F. Fagan, "From fine-scale foraging to home ranges: A semi-variance approach to identifying movement modes across spatiotemporal scales", The American Naturalist 183:5, E154-E167 (2014)
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2019 NSF DBI #1915347

2015 NSF ABI #1458748

  • Attias N., L. G. R. Oliveira-Santos, W. F. Fagan, G. de Miranda Mourão, "Effects of air temperature on habitat selection and activity patterns of two tropical imperfect homeotherms", Animal Behaviour, 140 129-140 (2018)
  • Calabrese, J. M., Fleming, C. H., W. F. Fagan, M. Rimmler, P. Kaczensky, S. Bewick, P. Leimgruber, and T. Mueller, "Disentangling social interactions and environmental drivers in multi-individual wildlife tracking data", Philosophical Transactions of the Royal Society of London: B, 373:1746, 10.1098/rstb.2017.0007 (2018)
  • Cheraghi F, M Delavar, F Amiraslani, K Alavipanah, E Gurarie, and WF Fagan, "Statistical analysis of Asiatic cheetah movement and its spatio-temporal drivers", Journal of Arid Environments, v.151, 2018, p. 141
  • Delgado MdM, M Miranda, SJ Alvarez, E Gurarie, WF Fagan, V Penteriani, A di Virgilio, and JM Morales, "The importance of individual variation in the dynamics of animal collective movements", Philosophical Transactions of the Royal Society of London: B, v.373, 2018, p. 20170008.
  • Fagan, W.F., E. Gurarie, S. Bewick, A. Howard, S. Cantrell, and C. Cosner, "Perceptual ranges, information gathering, and foraging success in dynamic landscapes", American Naturalist, v.189, 2017, p. 474. doi:10.1086/691099
  • Fleming CH, D Sheldon, WF Fagan, T Mueller, D Nandintsetseg, MJ Noonan, KA Olson, P Leimgruber, E Setyawan, A Sianipar, and JM Calabrese, "Correcting for missing and irregular data in home-range estimation", Ecological Applications, v.28, 2018, p. 1003
  • Horton, KG; Van Doren, BM; La Sorte, FA; Fink, D; Sheldon, D; Farnsworth, A; Kelly, JF, "Navigating north: how body mass and winds shape avian flight behaviours across a North American migratory flyway", Ecology Letters, v.21, 2018, p. 1055
  • Tucker MA, K Böhning-Gaese, WF Fagan, JM Fryxell, B van Moorter, ?JM Calabrese,? CH Fleming,?E Gurarie,?107 other coauthors ?, and T. Mueller, "Moving in the Anthropocene: Global reductions in terrestrial mammalian movements", Science, v.359, 2018, p. 446.
  • Winner, Kevin, Michael J Noonan, Chris H Fleming, Kirk A Olson, Thomas Mueller, Dan Sheldon, Justin M Calabrese, "Statistical inference for home range overlap", Methods in Ecology and Evolution, 2018
  • Fleming C.H. and J.M. Calabrese, "A new kernel-density estimator for accurate home-range and species-range area estimation", Methods in Ecology and Evolution, v.8, 2017, p. 571. doi:10.1111/2041-210X.12673
  • Fleming, C.H., D. Sheldon, E. Gurarie, S. La Point, W.F. Fagan, and J.M. Calabrese, "Kalman filters for continuous-time movement models", Ecological Informatics, v.40, 2017, p. 8. doi:10.1016/j.ecoinf.2017.04.008
  • Gurarie, E., C.H. Fleming, W.F. Fagan, K. Laidre, J. Hernández-Pliego, O. Ovaskainen, "Correlated velocity models as a fundamental unit of animal movement: synthesis and applications", Movement Ecology, v.5, 2017, p. 13. doi:10.1186/s40462-017-0103-3
  • Gurarie, E., W. Peters, C.H. Fleming, F. Cagnacci, J.M. Calabrese, T. Mueller, and W.F. Fagan, "A framework for modeling range shifts and migrations: asking when, whither, whether and will it return", Journal of Animal Ecology, v.86, 2017, p. 943. doi:10.1111/1365-2656.12674
  • Martinez-Garcia, R, J.M. Calabrese, and C. Lopez, "Online games: a novel approach to explore how partial information influences random search processes", Scientific Reports, v.7, 2017, p. 40029. doi:10.1038/srep40029
  • Meckley TD, E Gurarie, JR Miller, and CM Wagner, "How do fishes find the shore? Evidence for orientation to bathymetry from the non-homing sea lamprey", Canadian Journal of Fisheries and Aquatic Sciences, v.74, 2017, p. 2045.
  • Péron, G., C.H. Fleming, R.C. de Paula, N. Mitchell, M. Strohbach, P. Leimgruber, and J.M. Calabrese, "Periodic continuous-time movement models uncover behavioral changes of wild canids along anthropization gradients", Ecological Monographs, v.87, 2017, p. 442
  • Péron G, CH Fleming, O Duriez, J Fluhr, C Itty, S Lambertucci, K Safi, ELC Shepard, and JM Calabrese, "The energy landscape predicts flight height and wind turbine collision hazard in three species of soaring raptor", Journal of Applied Ecology, v.54, 2017, p. 1895. doi:10.1111/1365-2664.12909
  • Calabrese, J.M., C.H. Fleming, and E Gurarie, "ctmm: An R package for analyzing animal relocation data as a continuous-time stochastic process", Methods in Ecology and Evolution, v.7, 2016, p. 1124. doi:DOI: 10.1111/2041-210X.12559
  • Fleming, C.H., W.F. Fagan, T. Mueller, K.A. Olson, P. Leimgruber, J.M. Calabrese, "Estimating where and how animals travel: An optimal framework for path reconstruction from autocorrelated tracking data", Ecology, v.97, 2016, p. 576. doi:10.1890/15-1607
  • Kojola, I., V. Hallikainen, K. Mikkola, E. Gurarie, S. Heikkinen, S. Kaartinen, A. Nikula, V. Nivala, "Wolf visitations close to human residences in Finland: The role of age, residence density, and time of day", Biological Conservation, v.198, 2016, p. 9. doi:10.1016/j.biocon.2016.03.025
  • Morato, R., J. Stabach, C.H. Fleming, J.M. Calabrese, R. de Paula, K. Ferraz, D. Kantek, S. Miyazaki, T. Pereira, G. Araujo, A. Paviolo, C. De Angelo, M. Di Bitetti, P. Cruz, F. Lima, L. Cullen, D. Sana, E. Ramalho, M. Carvalho, F. Soares, B. Zimbres, M., "Space Use and Movement of a Neotropical Top Predator: The Endangered Jaguar", PLoS ONE, v.11, 2016, p. e0168176. doi:10.1371/journal.pone.0168176
  • Moßbrucker AM, CH Fleming, MA Imron, and S Pudyatmoko, "AKDEc home range size and habitat selection of Sumatran elephants", Wildlife Research, v.43, 2016, p. 566. doi:10.1071/WR16069
  • Péron, G., C.H. Fleming, R.C. de Paula, and J.M. Calabrese, "Uncovering periodic patterns of space use in animal tracking data with periodograms, including a new algorithm for the Lomb-Scargle periodogram and improved randomization tests", Movement Ecology, v.4, 2016, p. 19. doi:10.1186/s40462?016?0084?7
  • Shamoun-Baranes J, A Farnsworth, B Aelterman, JA Alves, K Azijn, G Bernstein, S Branco, P Desmet, AM Dokter, K Horton, S Kelling, S Kelling, JF Kelly, H Leijnse, J Rong, D Sheldon, W Van den Broeck, JK Van Den Meersche, BM Van Doren, and Hans van Gasteren, "Innovative visualizations shed light on avian nocturnal migration", PLoS-ONE, v.11, 2016, p. e0160106. doi:10.1371/journal.pone.0160106
  • Stoffels, R.J., R.A. Rehwinkel, A.E. Price, and W.F. Fagan, "Dynamics of fish dispersal during river-floodplain connectivity", Aquatic Sciences, v.78, 2016, p. 355. doi:10.?1007/?s00027-015-0437-0
  • Teitelbaum, C., S. Converse, W.F. Fagan, K. Boehning-Gaese, R. O?Hara, A. Lacey, and T. Mueller, "Experience drives innovation of new migration patterns in response to global change", Nature Communications, v.7, 2016, p. 12793. doi:10.1038/ncomms12793
  • Jenks, K.E., E.O. Aikens, N. Songsassen, J.M. Calabrese, C.H. Fleming, N. Bhumpakphan, S. Wanghongsa, B. Kanchanasaka, M. Songer, P. Leimgruber, "Comparative movement analysis of a sympatric dhole and golden jackal in a human-dominated landscape", Raffles Bulletin of Zoology, v.63, 2015, p. 546. ISSN 2345-7600
  • Rakhimberdiev, E., D.W. Winkler, E. Bridge, N.E. Seavy, D. Sheldon, T. Piersma, A. Saveliev, "A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity", Movement Ecology, v.3, 2015, p. 1. doi:10.1186/s40462-015-0062-5

2011 NSF ABI #1062411