Package: smam 0.7.3

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_0.7.3.tar.gz
smam_0.7.3.zip(r-4.7)smam_0.7.3.zip(r-4.6)smam_0.7.3.zip(r-4.5)
smam_0.7.3.tgz(r-4.6-x86_64)smam_0.7.3.tgz(r-4.6-arm64)smam_0.7.3.tgz(r-4.5-x86_64)smam_0.7.3.tgz(r-4.5-arm64)
smam_0.7.3.tar.gz(r-4.7-arm64)smam_0.7.3.tar.gz(r-4.7-x86_64)smam_0.7.3.tar.gz(r-4.6-arm64)smam_0.7.3.tar.gz(r-4.6-x86_64)
smam_0.7.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
smam/json (API)

# Install 'smam' in R:

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

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

Uses libs:

gsl– GNU Scientific Library (GSL)
c++– GNU Standard C++ Library v3

Datasets:

f109 - GPS data of f109
f109raw - GPS data of f109

On CRAN:

animal-movement brownian-motion hidden-markov-model hidden-states measurement-error telegraph-process gsl cpp

4.72 score 2 stars 13 scripts 407 downloads 37 exports 33 dependencies

Last updated from:a0d01ed295. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	159
linux-devel-x86_64	OK	149
source / vignettes	OK	255
linux-release-arm64	OK	157
linux-release-x86_64	OK	149
macos-release-arm64	OK	106
macos-release-x86_64	OK	269
macos-oldrel-arm64	OK	100
macos-oldrel-x86_64	OK	297
windows-devel	OK	164
windows-release	OK	180
windows-oldrel	OK	176
wasm-release	OK	172

Exports:approxNormalOrder approxNormalOrder2 dtm dtr estimate estVarMM estVarMRME_Godambe estVarMRME_pBootstrap estVarMRMEnaive_Godambe estVarMRMEnaive_pBootstrap fitBmme fitBMME fitMM fitMovRes fitMR fitMRH fitMRME fitMRME_naive fitMRMEapprox fitPartialViterbiMR fitPartialViterbiMRH fitStateMR fitStateMRH fitViterbiMR fitViterbiMRH integr.control rBB rBmme rBMME rMM rMovRes rMR rMRB rMRH rMRME seasonFilter transfData

Dependencies:cli codetools cpp11 doParallel doSNOW EnvStats farver foreach ggplot2 glue gtable isoband iterators labeling lattice lifecycle MASS Matrix nloptr nortest numDeriv R6 RColorBrewer Rcpp RcppGSL RcppParallel rlang S7 scales snow vctrs viridisLite withr

Quick guide for 'smam'

Fitting the MRME model to animal movement data | Simulation from for the MRME model | Other models implemented in smam | References

Rendered fromquick_guide.pdf.asisusingR.rsp::asis

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Auxiliary for Preparing Discrete Distribution used to approximating Standard Normal Distribution	approxNormalOrder approxNormalOrder2
Density for Time Spent in Moving or Resting	dtm dtr
Estimate Result of smam Estimators	estimate 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 error	estVarMRMEnaive_Godambe estVarMRMEnaive_pBootstrap estVarMRME_Godambe estVarMRME_pBootstrap
GPS data of f109	f109
GPS data of f109 (raw format)	f109raw
Fit a Brownian Motion with Measurement Error	fitBMME fitBmme
Fit a Moving-Moving Model with 2 Embedded Brownian Motion	estVarMM fitMM
Fit a Moving-Resting Model with Embedded Brownian Motion	fitMovRes fitMR
Fit a Moving-Resting-Handling Model with Embedded Brownian Motion	fitMRH
Fit a Moving-Resting Model with Measurement Error	fitMRME fitMRMEapprox fitMRME_naive
Estimation of states at each time point with Moving-Resting Process	fitPartialViterbiMR fitStateMR fitViterbiMR
Estimation of states at each time point with Moving-Resting-Handling Process	fitPartialViterbiMRH fitStateMRH fitViterbiMRH
Auxiliary for Controlling Numerical Integration	integr.control
Sampling from a Brownian bridge path give a grid time	rBB
Sampling from Brown Motion with Measurement Error	rBMME rBmme
Sampling from a Moving-Moving Process with 2 Embedded Brownian Motion	rMM
Sampling from a Moving-Resting Process with Embedded Brownian Motion	rMovRes rMR rMRME
Sampling from a Moving-Resting bridge	rMRB
Sampling from a Moving-Resting-Handling Process with Embedded Brownian Motion	rMRH
Subsetting data during given season for each year (seasonal analysis toolbox)	seasonFilter
smam: Statistical Modeling of Animal Movements	smam-package smam
Transfer raw dataset to the standard dataset (seasonal analysis toolbox)	transfData
Variance-Covariance Matrix of smam Estimators	vcov vcov.smam_bmme vcov.smam_mm vcov.smam_mr vcov.smam_mrh vcov.smam_mrme