Package: bsam 1.1.3

bsam: Bayesian State-Space Models for Animal Movement

Tools to fit Bayesian state-space models to animal tracking data. Models are provided for location filtering, location filtering and behavioural state estimation, and their hierarchical versions. The models are primarily intended for fitting to ARGOS satellite tracking data but options exist to fit to other tracking data types. For Global Positioning System data, consider the 'moveHMM' package. Simplified Markov Chain Monte Carlo convergence diagnostic plotting is provided but users are encouraged to explore tools available in packages such as 'coda' and 'boa'.

Authors:Ian Jonsen [aut, cre], Sophie Bestley [ctb], Simon Wotherspoon [ctb], Michael Sumner [ctb], Joanna Mills Flemming [ctb]

bsam_1.1.3.tar.gz
bsam_1.1.3.zip(r-4.7)bsam_1.1.3.zip(r-4.6)bsam_1.1.3.zip(r-4.5)
bsam_1.1.3.tgz(r-4.6-any)bsam_1.1.3.tgz(r-4.5-any)
bsam_1.1.3.tar.gz(r-4.7-any)bsam_1.1.3.tar.gz(r-4.6-any)
bsam_1.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
bsam/json (API)
NEWS

# Install 'bsam' in R:

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

Bug tracker:https://github.com/ianjonsen/bsam/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.
c++– GNU Standard C++ Library v3

Datasets:

ellie1 - Elephant seal Argos satellite data
ellie2 - Elephant seal Argos satellite data

On CRAN:

cran-downloads jags cpp

5.45 score 19 stars 30 scripts 669 downloads 12 mentions 13 exports 38 dependencies

Last updated from:7d191f532d. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	131
source / vignettes	OK	178
linux-release-x86_64	NOTE	150
macos-release-arm64	NOTE	173
macos-oldrel-arm64	NOTE	211
windows-devel	NOTE	111
windows-release	NOTE	105
windows-oldrel	NOTE	121
wasm-release	OK	104

Exports:dat4jags diag_ssm diagSSM fit_ssm fitSSM get_summary hssm map_ssm plot_fit plotSSM simulate ssm tpar

Dependencies:cli coda cpp11 dplyr expm farver generics ggplot2 glue gridExtra gtable isoband labeling lattice lifecycle lubridate magrittr Matrix msm mvtnorm pillar pkgconfig R6 RColorBrewer rjags rlang rworldxtra S7 scales sp survival tibble tidyselect timechange utf8 vctrs viridisLite withr

Help page	Topics
Fit Bayesian state-space models to animal tracking data	bsam-package bsam
Correlated Random Walk Filter	dat4jags
Plot standard McMC convergence diagnostics to help determine lack of model convergence.	diag_ssm
Elephant seal Argos satellite data (1 individual)	ellie1
Elephant seal Argos satellite data (2 individuals)	ellie2
Fit Bayesian state-space models to animal movement data	fit_ssm
Deprecated functions.	diagSSM fitSSM plotSSM
Extract summary output and optionally export as a .csv file.	get_summary
Fits hierarchical state-space models to Argos data	hssm
Plot estimated track, behavioural states and observations on a map.	map_ssm
Plot the 1-D time-series of estimated location and behavioural states	plot_fit
Simulate from the DCRW model with Argos location errors	simulate
Fits state-space models to Argos data	ssm
ARGOS Error Fixed Parameters	tpar

Package: bsam 1.1.3

bsam: Bayesian State-Space Models for Animal Movement

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Help Manual

Usage by other packages (reverse dependencies)