Package: ctmm 1.2.1

Christen H. Fleming

ctmm: Continuous-Time Movement Modeling

Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic-process movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods 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>, Silva et al (2022) <doi:10.1111/2041-210X.13786>, Alston & Fleming et al (2023) <doi:10.1111/2041-210X.14025>.

Authors:Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Björn Reineking [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Chad J. Wilhite [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], Autumn-Lynn Harrison [dtc], Ronaldo G. Morato [dtc]

ctmm_1.2.1.tar.gz
ctmm_1.2.1.zip(r-4.5)ctmm_1.2.1.zip(r-4.4)ctmm_1.2.1.zip(r-4.3)
ctmm_1.2.1.tgz(r-4.4-any)ctmm_1.2.1.tgz(r-4.3-any)
ctmm_1.2.1.tar.gz(r-4.5-noble)ctmm_1.2.1.tar.gz(r-4.4-noble)
ctmm_1.2.1.tgz(r-4.4-emscripten)ctmm_1.2.1.tgz(r-4.3-emscripten)
ctmm.pdf |ctmm.html✨
ctmm/json (API)
NEWS

# Install 'ctmm' in R:
install.packages('ctmm', repos = c('https://ctmm-initiative.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ctmm-initiative/ctmm/issues

Datasets:
  • buffalo - African buffalo GPS dataset from Kruger National Park, South Africa.
  • coati - Coatis on Barro Colorado Island, Panama.
  • gazelle - Mongolian gazelle GPS dataset from the Mongolia's Eastern Steppe.
  • jaguar - Jaguar data from the Jaguar movement database.
  • pelican - Brown Pelican GPS and ARGOS data.
  • turtle - Wood turtle GPS and calibration dataset from Working Land and Seascapes.
  • wolf - Maned wolf GPS dataset from The Maned Wolf Conservation Program.

On CRAN:

82 exports 47 stars 4.80 score 39 dependencies 4 dependents 18 mentions 458 scripts 2.3k downloads

Last updated 2 days agofrom:1420c0bdaa. Checks:ERROR: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 16 2024
R-4.5-winERRORSep 16 2024
R-4.5-linuxWARNINGSep 16 2024
R-4.4-winERRORSep 16 2024
R-4.4-macERRORSep 16 2024
R-4.3-winERRORSep 16 2024
R-4.3-macERRORSep 16 2024

Exports:%#%agdeakdeannotateas.sfas.telemetrybandwidthcdecleaveclustercolorcompasscorrelogramctmmctmm.bootctmm.fitctmm.guessctmm.loglikectmm.selectdifferencedimfigdistancedistancesdt.plotemulateencounterExpextentfunnelheadhomerangeintensitylassoLogmagmarqueemedianmetamidpointnproccurrenceoptimizeroutlieoverlappd.logdetpd.solvepd.sqrtmperiodogrampkdeplotpredictprojectionprojection<-proximityrasterrevisitationrsf.fitrsf.selectsdm.fitsdm.integratesdm.selectsigfigsimulateSpatialPoints.telemetrySpatialPointsDataFrame.telemetrySpatialPolygonsDataFrame.telemetrySpatialPolygonsDataFrame.UDspeedspeedssuitabilitytailtbindtransitionuereuere.fituere<-variogramvariogram.fitvideowriteRasterwriteVectorzoom

Dependencies:BesselclassclassIntdata.tableDBIDEoptimRdigeste1071expmfasttimeGmediangmpgslKernSmoothlatticemagrittrmanipulateMASSMatrixnumDerivparsedatepbivnormpracmaproxyrasterRcppRcppArmadilloRcppEigenRmpfrrobustbaseRSpectras2sfshapespstatmodterraunitswk

Readme and manuals

Help Manual

Help pageTopics
Continuous-time movement modelingctmm-package
Calculate an autocorrelated kernel density estimateakde akde.list akde.telemetry pkde
Import, coerce, summarize, and combine MoveBank dataas.telemetry as.telemetry.character as.telemetry.data.frame as.telemetry.Move head head.telemetry summary.telemetry tail tail.telemetry tbind
Calculate the optimal bandwidth matrix of movement databandwidth
African buffalo GPS dataset from Kruger National Park, South Africa.buffalo
Clustering of movement-model parameterscluster
Coatis on Barro Colorado Island, Panama.coati
Color telemetry objects by timeannotate color
Specify, fit, and select continuous-time movement modelsctmm ctmm.fit ctmm.loglike ctmm.select
ctmm FAQctmm-FAQ ctmm-faq
Parametric bootstrap continuous-time movement modelsctmm.boot
Estimate the proximity of two individualsdifference distances midpoint proximity
Calculate the square distance between two distributions or location estimatesdistance
Functions for diagnosing sampling schedulesdt.plot
Draw a random model-fit from the sampling distributionemulate emulate.ctmm emulate.telemetry
Encounter statisticscde encounter
Export ctmm data formatsas.sf export raster,UD-method SpatialPoints.telemetry SpatialPointsDataFrame.telemetry SpatialPolygonsDataFrame.telemetry SpatialPolygonsDataFrame.UD writeRaster,UD,character-method writeVector writeVector,list,character-method writeVector,list,missing-method writeVector,telemetry,character-method writeVector,telemetry,missing-method writeVector,UD,character-method writeVector,UD,missing-method
Extentextent extent,ctmm-method extent,data.frame-method extent,list-method extent,matrix-method extent,telemetry-method extent,UD-method extent,variogram-method
Scientific formatting of numbersdimfig sigfig
Mongolian gazelle GPS dataset from the Mongolia's Eastern Steppe.gazelle
Calculate a range distribution estimateagde homerange suitability
Compare empirical and theoretical intensity (resource-selection) functions [IN DEVELOPMENT]intensity
Jaguar data from the Jaguar movement database.jaguar
Log transformation of parameter estimates and their uncertaintiesExp Log
Average movement models and autocorrelated kernel density estimatesmean.ctmm mean.UD
Compute a number-weighted average of variogram objectsmean.variogram
Meta-analysis of movement-model parametersfunnel meta
Calculate a non-parametric regression surfacenpr
Calculate a Kriged occurrence distribution estimateoccurrence
Minimize a functionoptimizer
Methods to facilitate outlier detection.outlie outlier plot.outlie
Calculate the overlap between two stationary distributionsoverlap
Postive-definite matrix operationspd.logdet pd.solve pd.sqrtm
Brown Pelican GPS and ARGOS data.pelican
Calculate the Lomb-Scargle periodogram of animal-tracking dataperiodogram plot.periodogram
Plotting methods for telemetry objectsplot plot.telemetry zoom,list-method zoom,telemetry-method zoom,UD-method
Plotting methods for variogram objects.plot.variogram zoom,variogram-method
Projectioncompass median median.telemetry projection projection,ctmm-method projection,list-method projection,NULL-method projection,telemetry-method projection,UD-method projection<-,ctmm-method projection<-,list-method projection<-,telemetry-method
Calculate model fit residuals and assess their autocorrelationcorrelogram mag mag.telemetry residuals residuals.ctmm residuals.telemetry
Calculate an revisitation distribution estimaterevisitation
Fit integrated resource selection functions (iRSFs) with autocorrelation-adjusted weighted likelihoodrsf.fit rsf.select
Fit species distribution models (SDMs) [IN DEVELOPMENT]sdm.fit sdm.integrate sdm.select
Spatial selection methods for telemetry objects.cleave lasso marquee
Predict or simulate from a continuous-time movement modelpredict predict.ctmm predict.telemetry simulate simulate.ctmm simulate.telemetry
Estimate the average speed of a tracked animalspeed speed.ctmm speed.telemetry speeds speeds.ctmm speeds.telemetry
Summarize a continuous-time movement modelsummary.ctmm
Summarize a range distributionsummary.UD
Make a sequence of transition slide figurestransition
Wood turtle GPS and calibration dataset from Working Land and Seascapes.turtle
Estimate RMS UERE from calibration datasummary.UERE uere uere.fit uere<-
Convert dimensionful quantities to and from SI units%#%
Calculate an empirical variogram from movement datavariogram
Visually fit a movement model to a variogramctmm.guess variogram.fit
Video record animated telemetry objects.video
Maned wolf GPS dataset from The Maned Wolf Conservation Program.wolf