Runs a minimum-hypergeometric (mHG) test as described in: Eden, E. (2007). Discovering Motifs in Ranked Lists of DNA Sequences. Haifa.

Multilevel Hidden Markov Models Using Bayesian Estimation
person("Emmeke", "Aarts", email = "e.aarts@uu.nl",
role = c("aut", "cre"))
An implementation of the multilevel (also known as mixed or random
effects) hidden Markov model using Bayesian estimation in R. The multilevel
hidden Markov model (HMM) is a generalization of the well-known hidden
Markov model, for the latter see Rabiner (1989) <doi:10.1109/5.18626>. The
multilevel HMM is tailored to accommodate (intense) longitudinal data of
multiple individuals simultaneously, see e.g., de Haan-Rietdijk et al.
<doi:10.1080/00273171.2017.1370364>. Using a multilevel framework, we allow
for heterogeneity in the model parameters (transition probability matrix and
conditional distribution), while estimating one overall HMM. The model can
be fitted on multivariate data with a categorical distribution, and include
individual level covariates (allowing for e.g., group comparisons on model
parameters). Parameters are estimated using Bayesian estimation utilizing
the forward-backward recursion within a hybrid Metropolis within Gibbs
sampler. The package also includes various visualization options, a function
to simulate data, and a function to obtain the most likely hidden state
sequence for each individual using the Viterbi algorithm.
knitr, rmarkdown, alluvial, grDevices, RColorBrewer, testthat
(>= 2.1.0)

c(person("Emmeke", "Aarts", email = "e.aarts@uu.nl",
role = c("aut", "cre")),
person("Sebastian", "Mildiner Moraga", role = "ctb"))
Emmeke Aarts [aut, cre],
Sebastian Mildiner Moraga [ctb]

Processing of Accelerometry Data with 'GGIR' in mMARCH
c(
person(given = "Wei", family = "Guo",
role = c("aut", "cre"), email = "wei.guo3@nih.gov"),
person(given = "Andrew", family = "Leroux",
role = c("aut"), email = "andrew.leroux@cuanschutz.edu"),
person(given = "Vadim", family = "Zipunnikov",
role = c("aut"), email = "vzipunni@jhsph.edu"),
person(given = "Kathleen", family = "Merikangas",
role = c("aut"), email = "merikank@mail.nih.gov")
)
refund, denseFLMM, dplyr, xlsx, survival, stats, tidyr, zoo,
ineq, cosinor, cosinor2, abind, accelerometry, ActCR, ActFrag,
minpack.lm, kableExtra, GGIR
Wei Guo [aut, cre],
Andrew Leroux [aut],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]