A gentle tutorial of accelerated parameter and confidence interval estimation for Hidden Markov Models using Template Model Builder

Contributors: Timothee Bacri¹, Geir Drage Berentsen², Jan Bulla¹ and Sondre Hølleland³.

This repository contains the code to produce the R-bookdown website found here.

The folders (code/, data/, functions/) related to the analysis code and results of the paper https://doi.org/10.1002/bimj.202100256 are described in Directory structure.

The folders inside (paper2-github-preprint/) follow a similar structure, but concern a (second) paper https://doi.org/10.1080/00949655.2023.2226788.

Author’s github account

Timothee Bacri - timothee-bacri

Sondre Hølleland - holleland

Geir Berentsen - gberentsen

This project is licensed under the GPL v2 License - see LICENSE for details.

Name		Name	Last commit message	Last commit date
Latest commit History 114 Commits
Data-supplements_files		Data-supplements_files
code		code
data		data
docs		docs
functions		functions
img		img
paper2-github-preprint		paper2-github-preprint
.gitignore		.gitignore
02-principles.Rmd		02-principles.Rmd
03-estimation.Rmd		03-estimation.Rmd
04-using-tmb.Rmd		04-using-tmb.Rmd
05-confidence-intervals.Rmd		05-confidence-intervals.Rmd
06-application.Rmd		06-application.Rmd
07-normal-hmm.Rmd		07-normal-hmm.Rmd
08-multivariate-normal-hmm.Rmd		08-multivariate-normal-hmm.Rmd
09-guide-code.Rmd		09-guide-code.Rmd
10-local-decoding-cis.Rmd		10-local-decoding-cis.Rmd
11-references.Rmd		11-references.Rmd
404.html		404.html
Data supplements.Rproj		Data supplements.Rproj
LICENSE		LICENSE
README.md		README.md
_bookdown.yml		_bookdown.yml
_output.yml		_output.yml
american-statistical-association.csl		american-statistical-association.csl
apa.csl		apa.csl
hide_code.html		hide_code.html
index.Rmd		index.Rmd
index.md		index.md
packages.bib		packages.bib
paper.bib		paper.bib
preamble.tex		preamble.tex
style.css		style.css
summary.html		summary.html
width.css		width.css