Fit Hidden Markov Models using Template Model Builder

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Documentation for package ‘hmmTMB’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

as_character_formula	Read formula with as.character without splitting
as_sparse	Transforms matrix to dgTMatrix
bdiag_check	Create block diagonal matrix (safe version)
cov_grid	Grid of covariates
Dist	R6 class for probability distribution
find_re	Find s(, bs = "re") terms in formula
HMM	R6 class for hidden Markov model
hmmTMB_cols	hmmTMB colour palette
invmlogit	Multivarite inverse logit function
is_whole_number	Check if number of whole number
logLik.HMM	logLik function for SDE objects
logsumexp	Log of sum of exponentials
make_formulas	Process formulas and store in nested list
make_matrices	Create model matrices
MarkovChain	R6 class for HMM hidden process model
mlogit	Multivariate logit function
mvnorm_invlink	Multivariate Normal inverse link function
mvnorm_link	Multivariate Normal link function
na_fill	Fill in NAs
Observation	R6 class for HMM observation model
prec_to_cov	Get covariance matrix from precision matrix
quad_pos_solve	Solve for positive root of quadratic ax^2 + bx + c = 0 when it exists
strip_comments	Strip comments marked with a hash from a character vector
update.HMM	Update a model to a new model by changing one formula