ctmm-package: Continuous-time movement modeling

ctmm-packageR Documentation

Continuous-time movement modeling

Description

Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic-process movement models to animal tracking data. The package is described in Calabrese & Fleming (2016) <doi:10.1111/2041-210X.12559> and its models and methods are based on those introduced and detailed in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>, Fleming et al (2019) <doi:10.1111/2041-210X.13270>, Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>, Fleming et al (2020) <doi:10.1101/2020.06.12.130195>, Noonan et al (2021) <doi:10.1111/2041-210X.13597>, Fleming et al (2022) <doi:10.1111/2041-210X.13815>, and and Silva et al (2022) <doi:10.1111/2041-210X.13786>.

Details

Package: ctmm
Type: Package
Version: 1.1.0
Date: 2022-11-03
License: GPL-3

Author(s)

Christen H. Fleming and Justin M. Calabrese

Maintainer: Christen H. Fleming <flemingc@si.edu>

References

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) doi: 10.1086/675504.

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) doi: 10.1111/2041-210X.12176.

C. H. Fleming, Y. Subaşı, J. M. Calabrese, “A maximum-entropy description of animal movement”, Physical Review E 91 032107 (2015) doi: 10.1103/PhysRevE.91.032107.

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) doi: 10.1890/14-2010.1.

J. M. Calabrese, C. H. Fleming, “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) doi: 10.1111/2041-210X.12559.

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) doi: 10.1890/15-1607.1.

G. Péron, C. H. Fleming, R. C. 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 (2016) doi: 10.1186/s40462-016-0084-7.

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 (2017) doi: 10.1111/2041-210X.12673.

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) doi: 10.1002/ecm.1260

C. H. Fleming, D. Sheldon, E. Gurarie, W. F. Fagan, S. LaPoint, J. M. Calabrese, “Kálmán filters for continuous-time movement models”, Ecological Informatics 40 8-21 (2017) doi: 10.1016/j.ecoinf.2017.04.008.

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) doi: 10.1002/eap.1704.

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) doi: 10.1111/2041-210X.13027.

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) doi: 10.1111/2041-210X.13270.

M. J. Noonan, C. H. Fleming, T. S. Akre, J. Drescher-Lehman, E. Gurarie, A.-L. Harrison, R. Kays, Justin Calabrese, “Scale-insensitive estimation of speed and distance traveled from animal tracking data”, Movement Ecology 7:35 (2019) doi: 10.1186/s40462-019-0177-1.

C. H. Fleming et al, “A comprehensive framework for handling location error in animal tracking data”, bioRxiv (2020) doi: 10.1101/2020.06.12.130195.

M. J. Noonan R. Martinez-Garcia, G. H. Davis, M. C. Crofoot, R. Kays, B. T. Hirsch, D. Caillaud, E. Payne, A. Sihm, 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 12:7 1158-1173 (2021) doi: 10.1111/2041-210X.13597.

C. H. Fleming, 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 1027-1041 (2022) doi: 10.1111/2041-210X.13815.

I. Silva, 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 13 534-544 (2022) doi: 10.1111/2041-210X.13786.


ctmm documentation built on Nov. 4, 2022, 5:06 p.m.