Continuous-Time Movement Modeling

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) and its methods are based on those introduced in Fleming et al (2014) , Fleming et al (2014) , Fleming et al (2015) , Fleming et al (2016) , Péron & Fleming et al (2016) , Fleming & Calabrese (2016) , Péron et al (2017) , Fleming et al (2017) , Fleming et al (2018) , and Winner & Noonan et al (2018) .


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. First-time users can start with the Methods in Ecology and Evolution paper and then move on to the up-to-date vignettes vignette('variogram') and vignette('akde').

News

0.4.1 2017-08-30

  • projection method for ctmm objects

0.4.0 2017-08-29

  • periodigram vignette

  • New utility function %#% for unit conversions

  • New model-fit sampling function "emulate"

  • summary now works on lists of telemetry objects

  • new extent method for variogram objects

  • bugfixes in plot.variogram with fit UERE, tau==0

  • bugfixes with ctmm.fit/select/summary near boundaries

  • resetting Polak–Ribiere formula in weighted AKDE conjugate gradient routine

  • read.table fallback in as.telmetry

  • R 3.4 compatibility fixes

  • various improvements to plot.variogram

  • plot.UD & export can now accept multiple level.UD values

  • increased numerical precision in ctmm.loglike

  • SI speeds & diffusion fixed with units=FALSE

0.3.6 2017-04-23

  • AICc formulas updated from univariate to multivariate

  • ctmm.select more aggressive on small sample sizes where AICc >> AIC

  • new residuals and correlogram functions

  • ctmm.fit now has unified options controling optimization & differentiation

  • ctmm.fit Hessian and pREML calculations 2x faster

  • new writeRaster method for UD objects

  • Better UD plot boxes with new extent methods

  • variogram fast=TRUE less biased for irregular data with new res>1 option

  • variogram fast=FALSE more robust to irregularity

  • akde() can now handle duplicate times (with an error model)

  • plot.variogram bugfix for fixed error models [still not quite correct]

  • Column name preferences in as.telemetry

  • as.telemetry faster with fread & fastPOSIXct

  • new trace option for ctmm.fit

  • new labels option for plot.UD

  • more robust CIs for pREML, REML

  • chi-square CIs (area, semi-variance, etc.) more robust when DOF<1

0.3.5 2017-02-01

  • added a FAQ page to the documentation help("ctmm-FAQ")

  • bugfix in occurrence method for BM & IOU models

  • unit conversion can now be disabled in summary with units=FALSE argument

  • added trace option to ctmm.select & bandwidth/akde

  • improved telemetry error support in summary.ctmm and plot.variogram

  • as.telemetry more robust to alternative column label capitalizations

  • ctmm.loglike & ctmm.fit more robust when tau_velocity ~ tau_position

  • Kalman filter & smoother upgraded to Joseph form covariance updates

0.3.4 2016-11-28

  • weighted AKDE implemented, fast option, covered in vignette

  • overlap arguments & ouput changed/generalized

  • method akde.bandwidth renamed to bandwidth inline with S3 standards

  • predict now returns covariance estimates

  • occurrence distributions now exportable

  • AKDE overlap bugfixes

  • summary.ctmm now returns correct RMS speed

  • bugfix for eccentricity errors

  • variogram CIs fixed for odd dimensions

  • variogram.fit can now accept OU models

  • periodogram rare index bugfix

  • fixed missing lag in dt-argumented variogram

  • as.telemetry column identification more robust

  • as.telemetry defined for MoveStack objects

0.3.3 2016-09-05

  • improved import of 'move' objects

  • preliminary 3D AKDE support, debiased

  • new method predict for ctmm objects

  • akde now supports smoothing errors

  • variogram.fit and plot.variogram now support telemetry error

  • UERE fitting now possible simultaneous with tracking data

  • tag.local.identifier now used as backup to individual.local.identifier in as.telemetry

  • multiple bug fixes in uere

  • res.space fixed in occurrence

0.3.2 2016-05-12

  • new function overlap for stationary Gaussian distributions and KDEs

  • new function uere calculates UERE from calibration data

  • akde debias argument removes most bias from area estimtes, now default

  • akde CIs further improved

  • variogram, periodogram generalized to arbitrary dimensions

  • periodic mean function option for ctmm, ctmm.fit, ctmm.select, plot.variogram, summary (not yet documented)

  • new method residuals for ctmm objects

  • ctmm.select now only considers likely model modifications

  • DOFs now returned in summary

  • new methods [.telemetry, [.variogram, [.periodogram, subset.periodogram

  • methods for zoom, raster, writeShapefile now properly assigned to generics

  • new plot.periodogram option max

  • new periodogram option res.time (with Lagrange interpolation). Old option res renamed to res.freq.

  • akde res argument is now relative to the bandwidth

  • occurrence res.space argument is now relative to the average diffusion

  • plot.telemetry with data error now uses level.UD for error radius instead of one standard deviation

  • gridding function for fast=TRUE variogram and periodogram now always fast

  • bad location removed from buffalo "Pepper"

0.3.1 2016-02-23

  • variogram.fit now stores global variables of any name

  • variogram.fit sliders now use pretty units

  • variogram.fit range argument depreciated in favor of a more general CTMM prototype argument

  • akde UD CIs significantly improved for high quality datasets

  • akde bugfix: subscript out of bounds

  • circulatory model introduced via circle ctmm argument

  • oscillatory CPF model introduced via CPF ctmm argument

  • as.telemetry now imports GPS.HDOP columns with a UERE argument

  • summary now works on arbitrary lists of ctmm objects

  • ctmm.fit now tries to make sense of ML parameters that lie on boundaries

  • occurrence() now works when some timesteps are tiny

0.3.0 2015-11-26

  • new function "occurrence" to estimate occurrence distributions

  • "akde" & "occurrence" class objects generalized to "UD" class

  • alpha & alpha.HR arguments simplified and generalized to level & level.UD

  • AKDE= and *.HR= arguments generalized to UD= and *.UD=

  • new basic telemetry error functionality in ctmm, ctmm.fit

  • new function ctmm.select

  • new methods subset.telemetry and subset.variogram

  • fixed a bug in the uncertainty report of uncorrelated processes

  • ctmm.fit is now much faster by specifying a reasonable parscale for optim

  • ctmm.fit now has a backup for when Brent fails

0.2.9 2015-10-13

  • fixed a rare condition in ctmm.fit where solve would fail on correlated errors

  • multiscale variogram and mean variogram example in vignette

  • new data example Mongolian gazelle

  • new fast option for periodogram

  • improvements in plot.periodogram

  • bugfix in as.telemetry for numeric indentifiers

  • bugfix in dt array option of variogram

  • new resolution option and better estimation algorithms in akde

  • alpha, alpha.HR, res arguments made consistent across all functions

0.2.8 2015-08-25

  • efficiency gains in as.telemetry with multiple animals

  • bugfix in plot.telemetry for multiple Gaussian PDFs

  • bugfix in variogram for rare condition when fast=TRUE

0.2.7 2015-07-27

  • CRAN check compliance achieved.

  • all methods (plot, mean, summary, simulate) can and must be run without class extensions

  • argument names no longer clash with function names and are more explicit about their object class

0.2.6 2015-07-17

  • export bugfixes

0.2.5 2015-07-14

  • IOU bug fixes in ctmm.fit and plot.variogram

0.2.4 2015-06-28

  • cleaned up and labeled tau parameter arrays

  • implemented Workaround for when subset demotes S4 objects to S3 objects

  • plot.telemetry now enforces asp=1 even with xlim/ylim arguments

0.2.3 2015-06-19

  • new function summary.telemetry

  • bugfix in as.telemetry for data$t

  • bugfix in ctmm.loglike for some cases with numeric underflow

  • periodogram and plot.periodogram can now check for spurious periodicities

  • minimal support for BM and IOU motion

0.2.2 2015-05-21

  • new functions periodogram, plot.periodogram

0.2.1 2015-05-08

  • new function SpatialPoints.telemetry returns SpatialPoints object from telemetry data

  • new function SpatialPolygonsDataFrame.akde returns akde home-range contour SpatialPolygons objects from akde object

  • new function writeShapefile.akde writes akde home-range contours to ESRI shapefile

  • new function raster.akde returns akde pdf raster object

  • new function summary.akde returns HR area of AKDE

  • fixed bad CI in plot.telemetry model option

  • as.telemetry now takes a timezone argument for as.POSIXct and defaults to UTC

  • telemetry, ctmm, and akde objects now have idenification and projection information slotted, with consistent naming throughout

0.2.0 2015-04-27

  • vignettes "variogram" and "akde"

  • new function as.telemetry imports MoveBank formatted csv data and returns telemetry objects

  • new function variogram.zoom plots a variogram with zoom slider

  • variogram.fit and variogram.zoom default to a logarithmic-scale zoom slider, which requires much less fiddling

  • plot.variogram now takes multiple variogram, model, and color options

  • plot.telemetry now takes multiple data, model, akde, and color options

  • plot.telemetry can now make probability density plots for both Gaussian model and akde data

  • ctmm.fit no longer screws up results with initial sigma guesstimates. ML parameter estimates now match closely with published Mathematica results. CIs are improved.

  • ks-package was producing incorrect home-range contours and has been replaced with custom code. ML home ranges now match published Mathematica results. CIs should be improved.

Reference manual

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install.packages("ctmm")

0.5.0 by Christen H. Fleming, 2 months ago


https://github.com/ctmm-initiative/ctmm, http://biology.umd.edu/movement.html


Browse source code at https://github.com/cran/ctmm


Authors: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc]


Documentation:   PDF Manual  


Task views: Handling and Analyzing Spatio-Temporal Data


GPL-3 license


Imports data.table, expm, fasttime, Gmedian, graphics, grDevices, manipulate, MASS, Matrix, methods, numDeriv, pbivnorm, pracma, raster, rgdal, scales, shape, stats, utils

Suggests bit64, fftw, knitr, move, parallel, sp


Suggested by amt.


See at CRAN