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'.

Author
Ian Jonsen [aut, cre], Sophie Bestley [ctb], Simon Wotherspoon [ctb], Michael Sumner [ctb]
Date of publication
2016-11-17 14:34:35
Maintainer
Ian Jonsen <ian.jonsen@mq.edu.au>
License
GPL-2
Version
1.1.1
URLs

View on CRAN

Man pages

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

Files in this package

bsam
bsam/inst
bsam/inst/jags
bsam/inst/jags/DCRWS.txt
bsam/inst/jags/DCRW.txt
bsam/inst/jags/hDCRWS.txt
bsam/inst/jags/hDCRW.txt
bsam/inst/CITATION
bsam/NAMESPACE
bsam/NEWS.md
bsam/data
bsam/data/ellie.RData
bsam/R
bsam/R/plot_fit.R
bsam/R/fit_ssm.R
bsam/R/tpar.R
bsam/R/map_ssm.R
bsam/R/diag_ssm.R
bsam/R/dat4jags.R
bsam/R/ssm.R
bsam/R/simulate.r
bsam/R/bsam-deprecated.R
bsam/R/get_summary.R
bsam/R/hssm.R
bsam/R/bsam-package.R
bsam/README.md
bsam/MD5
bsam/DESCRIPTION
bsam/man
bsam/man/map_ssm.Rd
bsam/man/simulate.Rd
bsam/man/diag_ssm.Rd
bsam/man/bsam-deprecated.Rd
bsam/man/plot_fit.Rd
bsam/man/ellie.Rd
bsam/man/tpar.Rd
bsam/man/dat4jags.Rd
bsam/man/get_summary.Rd
bsam/man/bsam-package.Rd
bsam/man/ssm.Rd
bsam/man/fit_ssm.Rd
bsam/man/hssm.Rd