Package: smam 0.7.2

smam: Statistical Modeling of Animal Movements

Animal movement models including Moving-Resting Process with Embedded Brownian Motion (Yan et al., 2014, <doi:10.1007/s10144-013-0428-8>; Pozdnyakov et al., 2017, <doi:10.1007/s11009-017-9547-6>), Brownian Motion with Measurement Error (Pozdnyakov et al., 2014, <doi:10.1890/13-0532.1>), Moving-Resting-Handling Process with Embedded Brownian Motion (Pozdnyakov et al., 2020, <doi:10.1007/s11009-020-09774-1>), Moving-Resting Process with Measurement Error (Hu et al., 2021, <doi:10.1111/2041-210X.13694>), Moving-Moving Process with two Embedded Brownian Motions.

Authors:Chaoran Hu [aut, cre], Vladimir Pozdnyakov [aut], Jun Yan [aut]

smam_0.7.2.tar.gz
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smam.pdf |smam.html✨
smam/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/chaoranhu/smam/issues

Uses libs:
  • gsl– GNU Scientific Library (GSL)
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

animal-movementbrownian-motionhidden-markov-modelhidden-statesmeasurement-errortelegraph-process

4.82 score 3 stars 11 scripts 281 downloads 37 exports 41 dependencies

Last updated 11 months agofrom:0d1164958a. Checks:OK: 3 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64OKNov 20 2024
R-4.5-linux-x86_64OKNov 20 2024
R-4.4-win-x86_64NOTENov 20 2024
R-4.4-mac-x86_64NOTENov 20 2024
R-4.4-mac-aarch64NOTENov 20 2024
R-4.3-win-x86_64NOTENov 20 2024
R-4.3-mac-x86_64NOTENov 20 2024
R-4.3-mac-aarch64NOTENov 20 2024

Exports:approxNormalOrderapproxNormalOrder2dtmdtrestimateestVarMMestVarMRME_GodambeestVarMRME_pBootstrapestVarMRMEnaive_GodambeestVarMRMEnaive_pBootstrapfitBmmefitBMMEfitMMfitMovResfitMRfitMRHfitMRMEfitMRME_naivefitMRMEapproxfitPartialViterbiMRfitPartialViterbiMRHfitStateMRfitStateMRHfitViterbiMRfitViterbiMRHintegr.controlrBBrBmmerBMMErMMrMovResrMRrMRBrMRHrMRMEseasonFiltertransfData

Dependencies:clicodetoolscolorspacedoParalleldoSNOWEnvStatsfansifarverforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmenloptrnortestnumDerivpillarpkgconfigR6RColorBrewerRcppRcppGSLRcppParallelrlangscalessnowtibbleutf8vctrsviridisLitewithr

Quick guide for 'smam'

Rendered fromquick_guide.pdf.asisusingR.rsp::asison Nov 20 2024.

Last update: 2018-05-22
Started: 2018-05-22

Readme and manuals

Help Manual

Help pageTopics
Auxiliary for Preparing Discrete Distribution used to approximating Standard Normal DistributionapproxNormalOrder approxNormalOrder2
Density for Time Spent in Moving or Restingdtm dtr
Estimate Result of smam Estimatorsestimate estimate.smam_bmme estimate.smam_mm estimate.smam_mr estimate.smam_mrh estimate.smam_mrme
Variance matrix of estimators from moving-resting process with measurement errorestVarMRMEnaive_Godambe estVarMRMEnaive_pBootstrap estVarMRME_Godambe estVarMRME_pBootstrap
GPS data of f109f109
GPS data of f109 (raw format)f109raw
Fit a Brownian Motion with Measurement ErrorfitBMME fitBmme
Fit a Moving-Moving Model with 2 Embedded Brownian MotionestVarMM fitMM
Fit a Moving-Resting Model with Embedded Brownian MotionfitMovRes fitMR
Fit a Moving-Resting-Handling Model with Embedded Brownian MotionfitMRH
Fit a Moving-Resting Model with Measurement ErrorfitMRME fitMRMEapprox fitMRME_naive
Estimation of states at each time point with Moving-Resting ProcessfitPartialViterbiMR fitStateMR fitViterbiMR
Estimation of states at each time point with Moving-Resting-Handling ProcessfitPartialViterbiMRH fitStateMRH fitViterbiMRH
Auxiliary for Controlling Numerical Integrationintegr.control
Sampling from a Brownian bridge path give a grid timerBB
Sampling from Brown Motion with Measurement ErrorrBMME rBmme
Sampling from a Moving-Moving Process with 2 Embedded Brownian MotionrMM
Sampling from a Moving-Resting Process with Embedded Brownian MotionrMovRes rMR rMRME
Sampling from a Moving-Resting bridgerMRB
Sampling from a Moving-Resting-Handling Process with Embedded Brownian MotionrMRH
Subsetting data during given season for each year (seasonal analysis toolbox)seasonFilter
smam: Statistical Modeling of Animal Movementssmam-package smam
Transfer raw dataset to the standard dataset (seasonal analysis toolbox)transfData
Variance-Covariance Matrix of smam Estimatorsvcov vcov.smam_bmme vcov.smam_mm vcov.smam_mr vcov.smam_mrh vcov.smam_mrme