ctmm-package: Continuous-time movement modeling

Description Details Author(s) References

Description

Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese & Fleming (2016) <doi:10.1111/2041-210X.12559> and its methods are based on those introduced in Fleming et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, 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 (2016) <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>, and Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>.

Details

Package: ctmm
Type: Package
Version: 0.5.2
Date: 2018-08-28
License: GPL-3

Author(s)

Christen H. Fleming and Justin M. Calabrese

Maintainer: Christen H. Fleming <[email protected]>

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).

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, Y. Subasi, J. M. Calabrese. A maximum-entropy description of animal movement. Physical Review E, 91, 032107 (2015).

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).

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).

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).

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, DOI:10.1186/s40462-016-0084-7 (2016).

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. 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, 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).

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).

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, DOI:10.1111/2041-210X.13027 (2018).


ctmm-initiative/ctmm documentation built on Aug. 31, 2018, 9:23 p.m.