Dr. Christen H. Fleming

Dr. Christen H. Fleming (curriculum vitae)

Associate research scientist, University of Maryland, College Park
Smithsonian Institution Fellow under Justin M. Calabrese
Phd from the University of Maryland, College Park under Bei-Lok Hu
B.S. from the University of South Alabama in Physics, Mathematics and Statistics under Justin M. Sanders and Vasiliy A. Prokhorov

Contact Information

Continuous-Time Movement Modeling

An overview of the ctmm R package. [1]
How important is autocorrelation in home-range estimation? [2,3]
How do we properly estimate the home range of an animal, given that tracking data are necessarily autocorrelated? [4]
- How do we correct for bias in the kernel-density area estimates? [5]
- How do we correct for sampling bias/irregularity? [6]
How do we estimate home-range overlap, correcting for bias and accounting for uncertainty? [7]
How do we estimate where an animal has been from a sparse set of tracking data? [8]
- How do we estimate how fast and how far the animal was traveling? [9]
What is the general framework to estimating autocorrelation in animal tracking data? [10]

How do we estimate efficiently with large datasets? [11]
How do we correct for bias in these estimates? [12]

What is the best way to visualize the autocorrelation structure in animal tracking data? [13]
What is the best way to visualize periodicities in animal tracking data? [14]

What is the best way to fit periodicities to animal tracking data? [15]

What justifies our class of movement models? [16]

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)
M. J. Noonan, M. A. Tucker, C. H. Fleming, et al, "A comprehensive analysis of autocorrelation and bias in home range estimation", Ecological Monographs, 89:2, e01344 (2019)
M. J. Noonan, C. H. Fleming, et al, "Bodysize-dependent underestimation of mammalian area requirements", Conservation Biology, 34:4 1017-1028 (2020)
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, J. M. Calabrese, "A new kernel-density estimator for accurate home-range and species-range area estimation", Methods in Ecology and Evolution 8, 571-579 (2016)
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, 9:7, 1679-1691 (2018)
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)
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, 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, D. Sheldon, E. Gurarie, W. F. Fagan. S. LaPoint, J. M. Calabrese, "Kalman filters for continuous-time movement models", Ecological Informatics 40, 8-21 (2017)
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)
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)
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 10.1186/s40462-016-0084-7 (2016)
G. Péron, C. H. Fleming, R. C. de Paula, N. Mitchell, M. Stronbach, 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, Y. Subasi, J. M. Calabrese, "A maximum-entropy description of animal movement", Physical Review E 91, 032107 (2015)

`ctmm R` package (Initiative/CRAN/Github/Reference/Group)

This CRAN package has most everything you need to estimate the home ranges of range-resident animals: from variogram movement-model visualization, to maxmimum-likelihood movement-model estimation, to autocorrelated kernel-density home-range estimation and Kriged occurrence estimation. In the future, more analyses will be rolled into this package.

Here I archive different versions of the package and (on request) host development verions for users that cannot install via devtools.

Version	Release Date	Updates
0.5.10	2020-05-04	location class improvements, ...
0.5.9	2020-03-23	exact variogram CIs option, mean.UD weights option, ...
0.5.8	2019-12-09	ctmm.select improvements, R version 4 compatibility, ...
0.5.7	2019-08-07	pHREML estimator, pNewton optimizer, grid argument, ...
0.5.6	2019-05-14	lasso, marquee, cleave, annotate, color, ...
0.5.5	2019-02-11	summary.ctmm bugfix for timescale CIs, ...
0.5.4	2019-02-07	ctmm.select issue fix for OUO/OUf models
0.5.3	2019-01-31	oscillatory and critically dampled OUF models, speeds, ...
0.5.2	2018-09-10	error model selection, uere.fit,...
0.5.1	2018-08-14	micro unit support, ctmm.select feature building, uere residuals,...
0.5.0	2018-05-15	ARGOS error ellipse support, outlie, median,...
0.4.2	2018-02-15	AIC bugfix for circular covariance, speed, ctmm.boot,...
0.4.1	2017-08-30	projection method, CRAN compliance.
0.4.0	2017-08-29	periodogram vignette, unit conversion method `%#%`, parameter boundary bugfixes, ...
0.3.6	2017-04-23	correlogram (acf), extent, writeRaster, multivariate AICc, ...
0.3.5	2017-02-01	unit conversion options, progress tracing, occurrence bugfix, ...
0.3.4	2016-11-28	AKDE weights, overlap bugfix, ...
0.3.3	2016-09-05	UERE bugfixes, improved `move` compatibility, ...
0.3.2	2016-05-12	overlap estimator, UERE estimator, area-corrected AKDE, further improved AKDE CIs, ...
0.3.1	2016-02-23	oscillatory and circulation models, improved AKDE CIs, various bugfixes, ...
0.3.0	2015-11-26	Kriged occurrence distribution, basic model selection, AKDE & HR methods and options cleanups, ...
0.2.9	2015-10-13	FFT Lomb-Scargle periodogram, multiscale variogram, import fix, ...
0.2.8	2015-08-25	Import, variogram fixes, ...
0.2.7	2015-07-27	CRAN compliant and published. Methods and options cleanups.
0.2.6	2015-07-17	Export fixes
0.2.5	2015-07-14	IOU fixes
0.2.4	2015-06-28	various usability features, ...
0.2.3	2015-06-19	import fix, likelihood underflow fix, BM & IOU model support, ...
0.2.2	2015-05-21	minimal periodogram functionality, ...
0.2.1	2015-05-08	export functions, timezone fix, ...
0.2.0	2015-04-27	vignettes "variogram" and "akde", contour fix, ...

Dr. Christen H. Fleming (curriculum vitae)

Contact Information

Continuous-Time Movement Modeling

ctmm R package (Initiative/CRAN/Github/Reference/Group)

`ctmm R` package (Initiative/CRAN/Github/Reference/Group)