Navigating through the R packages

for movement

Rocıo Joo1, M.E. Boone 1, T.A. Clay 2,S.C. Patrick 2, S. Clusella-Trullas 3, M. Basille 1

1 University of Florida 2 University of Liverpool 3 Stellenbosch University

useR! - July 2019

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Movement

Tracking packages: created to process or analyze tracking data

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Movement

Tracking packages: created to process or analyze tracking data

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Tracking workflow

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Pre-processing

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Pre-processing

E.g. Light level geolocator data

Packages: GeoLight, probGLS, FlightR, trackit, TripEstimation/SGAT, Twilight Free, telemetr,

animalTrack, TrackReconstruction

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Pre-processing

E.g. Light level geolocator data

Packages: GeoLight, probGLS, FlightR, trackit, TripEstimation/SGAT, Twilight Free, telemetr,

animalTrack, TrackReconstruction

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Post-processing

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Post-processing

Cleaning (argosfilter, SDLfilter, T-LoCoH, TrajDataMining, trip)

Compression (adehabitatLT, amt, trajectories, trajr, TrajDataMining, rsMove)

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Analysis

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Path reconstruction

Purposes:

Correct errors

Finer data resolution

Regular time steps

Remember: model means assumptions!

Packages: HMMoce, kftrack, ukfsst/kfsst, ar-

gosTrack, bsam, crawl, ctmcmove, ctmm, Ba-

yesianAnimalTracker, TrackReconstruction

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Behavioral pattern identification

Purpose:

Proxy of behaviors through theobserved movement patterns

Remember: model means assumptions!

Packages: EMbC, m2b, adehabitatLT, seg-

clust2d, bcpa, marcher, migrateR, bsam, ls-

mnsd, momentuHMM, moveHMM

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Space use

Packages: adehabitatHR, adehabitatHS, amt, move, rhr, BBMM, ctmm, mkde, move,

movementAnalysis, T-LoCoH, hab, ctmcmove, feedr, VTrack, moveNT, recurse, rsMove

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Quality of a package

Usability

Quality

Style

Documentation

how and why of eachfunction‘statement of need’:gap/improvement

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Documentation

Survey: 225 users

11 pkgs over 75 % good/excellent documentation

adehabitatHR

adehabitatHSadehabitatLT

amtargosfilter

BBMM

bcpa bsam

crawl

ctmmEMbC

FLightR

GeoLight

hab

migrateR

momentuHMM

move

moveHMM

moveVis

recurse

rhr

SGAT/TripEstimation

T−LoCoH

trip

wildlifeDI

50

60

70

80

90

50 100 150

Number of respondents

Goo

d or

Exc

elle

nt R

atin

g

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Documentation

Survey: 225 users 11 pkgs over 75 % good/excellent documentation

adehabitatHR

adehabitatHSadehabitatLT

amtargosfilter

BBMM

bcpa bsam

crawl

ctmmEMbC

FLightR

GeoLight

hab

migrateR

momentuHMM

move

moveHMM

moveVis

recurse

rhr

SGAT/TripEstimation

T−LoCoH

trip

wildlifeDI

50

60

70

80

90

50 100 150

Number of respondents

Goo

d or

Exc

elle

nt R

atin

g

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Network

adehabitatHR

adehabitatHS

adehabitatLT

amt

animalTrack

anipaths

argosfilter

argosTrack

BayesianAnimalTracker

BBMM

bcpa

bsam

caribou

crawl

ctmcmove

ctmm

EMbC

feedr

FLightRGeoLight

hab

HMMocekftrack

lsmnsd

m2b

marcher

migrateR

mkde

momentuHMM

movemoveHMM

movementAnalysis

moveNT

moveVis

moveWindSpeed

probGLS

recurse

rhr

rpostgisLT

rsMove

SDLfilter

segclust2d

SGAT

SimilarityMeasures

SiMRiv

smam

T−LoCoH

telemetrtrackeR

trackit

TrackReconstruction

TrajDataMining

trajectories

trajr

trip

TwilightFree

ukfsst

VTrack

wildlifeDI

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Thanks for your attention

location

(x, y, z, t)

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