Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018)
An R package for Maximum likelihood analysis Of animal MovemENT behavior Using multivariate Hidden Markov Models
Get started with the vignette: Guide to using momentuHMM
The package is available on CRAN. To install it:
install.packages("momentuHMM")
To install the latest (stable) version of the package from Github:
library(devtools)install_github("bmcclintock/momentuHMM")
To install the latest (unstable) version of the package from Github:
library(devtools)install_github("bmcclintock/momentuHMM", ref="develop")
McClintock, B.T., Michelot, T. (2018) momentuHMM: R package for generalized hidden Markov models of animal movement. Methods in Ecology and Evolution, 9(6), 1518-1530.
McClintock, B.T., King R., Thomas L., Matthiopoulos J., McConnell B.J., Morales J.M. (2012) A general discrete-time modeling framework for animal movement using multistate random walks. Ecological Monographs, 82(3), 335-349.
McClintock, B.T. (2017) Incorporating telemetry error into hidden Markov models of animal movement using multiple imputation. Journal of Agricultural, Biological, and Environmental Statistics, 22(3), 249-269.
NEW FEATURES
Northern fulmar example of Pirotta et al (2018) added to vignette
retrySD argument added to crawlWrap for additional flexibility when exploring the likelihood surface using retryFits
shape argument added to plotSat and plotSpatialCov functions
projargs argument added to plotSat function (for handling projected data coordinates)
stateNames argument added to plotSpatialCov function
data argument of plotSat function can now be a data frame, momentuHMMData, momentuHMM, miHMM, or miSum object
data argument of plotSpatialCov function can now be a data frame, momentuHMMData, momentuHMM, miHMM, or miSum object
CHANGES
'angleStrength' special function name changed to 'angleFormula'
strength argument in 'angleFormula' special function is now optional
when theta and/or fixPar arguments are missing in crawlWrap, crawl::crwMLE default values are now used
bug fix in crawlWrap when retryFits>0 and control argument is NULL. This bug caused additional model fitting attempts to fail
modified B-spline examples in fitHMM and simData to accommodate bug fixes in splines2 (>= 0.2.8)
NEW FEATURES
special function 'toState' can now be used in formula argument for modelling transitions to specific states
timeInStates function added for calculating activity budgets
modelName argument added to fitHMM and MIfitHMM
added setModelName and setStateNames functions
added stationary and plotStationary functions for calculating and visualizing stationary state probabilities as a function of covariates
plotStationary argument added to plot.momentuHMM, plot.miHMM, and plot.miSum
added summary.momentuHMMData function
CHANGES
bug fix when a pseudo-design matrix formula includes interactions with >1 factor variable
check and print package version upon loading
unit tests no longer included in CRAN build because they were taking too long
updated citation info
NEW FEATURES
von Mises consensus distribution of Rivest et al. (2016) can now be specified for angular data streams
angleStrength function can now be used in circular-circular regression models. This allows each angular covariate (e.g. wind direction) to be weighted by an additional positive real covariate (e.g. wind speed) as in Rivest et al. (2016).
checkPar0 function added to aid users with initial parameter (e.g. Par0, beta0, delta0) specification
centroids argument added to MIfitHMM
useInitial argument added to MIfitHMM for using parameter estimates of first model fit as initial values for all subsequent model fits
retrySD argument added to fitHMM and MIfitHMM for specifying standard deviation of random normal perturbations when using retryFits
alternative optimization methods (Nelder-Mead'' andSANN'') can now be specified in fitHMM and MIfitHMM using the optMethod and control arguments
prior argument added to fitHMM and MIfitHMM for specifying prior distributions on working parameters
AICweights function added for calculating AIC weights across a set of candidate models
sample size (n) argument added to AIC.momentuHMM for calculating small sample corrected AIC (i.e. AICc)
crawlPlot argument added to plot.crwData as a wrapper for crawl::crwPredictPlot
various graphical parameters added to plot.momentuHMM for plot customization
CHANGES
For multiple imputation analyses, pseudoRes (and plotPR) can now calculate (and plot) pseudo-residuals individually for each model fit
cons and workcons arguments are now deprecated; please use workBounds instead
verbose argument in fitHMM and MIfitHMM is now deprecated; please use nlmPar instead
NEW FEATURES
Dynamic activity centers (i.e., those with coordinates that can change over time) can now be handled via the centroids argument in prepData and simData. An example based on the group dynamic model of Langrock et al. (2014) has been added to the vignette.
initialPosition argument in simData can now be specified as a list indicating the initial position for each individual
CHANGES
multinomial logit link now used on zeroInflation and oneInflation parameters
bug fix in calculation of pseudo-residuals (pseudoRes) with zeroInflation and/or oneInflation
bug fix in CIreal when natural scale delta estimates are near boundary
bug fix in crawlWrap when predTime is of length one
bug fix in MIpool when initial distribution includes covariates
splines and splines2 package dependencies changed to Suggests in DESCRIPTION file
NEW FEATURES
CHANGES
If step length is zero at time t or t+1, simData and prepData now return NA for turning angle at time step t
bug fix in pseudoRes such that pseudo-residuals now "reset" for each individual
bug fix in fitHMM when using fixPar to fix initial distribution (delta)
bug fix in fitHMM when nbStates=1 and circularAngleMean=TRUE
bug fix in fitHMM when nbStates=1 and retryFits>0
NEW FEATURES
Normal (Gaussian) and Bernoulli distributions can now be specified for data streams
Harbour seal example of McClintock et al (2013) added to vignette
Changes
NEW FEATURES
fixPar argument in fitHMM and MIfitHMM now specified on the same scale as the initial parameters (Par0, beta0, and delta0 arguments)
Factor-level covariates (e.g. 'sexM', `sexF') can now be included in pseudo design matrix DM arguments of fitHMM, MIfitHMM, and simData
obsPerAnimal argument in simData can now be specified as a list indicating the number of observations for each individual
CHANGES
vignette now built using knitr
bug fix in crawlWrap when predTimes argument includes times that are before the time of first observation
bug fix in plot.miSum calculation of natural scale parameters when cons and/or workcons MIfitHMM arguments are used
NEW FEATURES
CHANGES
turning angles for lat/long coordinates (type='LL') now calculated based on initial bearings using geosphere::bearing in turnAngle
bug fix when calculating activity center distances from lat/long coordinates (type='LL') in distAngle
bug fix in prepData when successive pairs of coordinates are NA
Initial CRAN posting