Files in mbjoseph/neuralecology
Fit Neural Hierarchical Models of Ecological Populations
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
Makefile
R/01-get-bbs-data.R
R/02-eda.R
R/03-extract-route-features.R
R/04-clean-data.R
R/05-single-species-models.R
R/06-compare-performance.R
R/07-test-set-checks.R
R/08-plot-embeddings.R
R/09-viterbi.R
R/10-analyze-states.R
R/s01-get-neon-data.R
R/s02-simulate-movement-trajectories.R
R/s03-momentuHMM-fits.R
R/s04-visualize-losses.R
R/s05-visualize-test-set.R
R/utils.R
README.md
binder/environment.yml
environment.yml
fig/.gitignore
fig/conv_hmm_edited.pdf
fig/conv_hmm_edited.png
fig/conv_hmm_edited.svg
fig/fig2.pdf
fig/fig2.svg
fig/figs1.pdf
fig/figs1.svg
fig/figs2.pdf
fig/figs2.svg
fig/hmm-general.pdf
fig/hmm-general.svg
notebooks/.gitignore
notebooks/dynamic-occupancy.ipynb
notebooks/hidden-markov-model.ipynb
notebooks/n-mixture-model.ipynb
notebooks/simple-occupancy.ipynb
paper/.gitignore
paper/appendix_s1.Rmd
paper/appendix_s2.Rmd
paper/appendix_s3.Rmd
paper/doc-prefix.tex
paper/ecology-letters.csl
paper/library.bib
paper/neural_ecology.Rmd
paper/neurips_2019.sty
paper/preprint-prefix.tex
paper/title.sty
python/bbs-occupancy-model.py
python/dataset.py
python/final-model-check.py
python/movement-model-comps.py
python/retrain-final-model.py
python/simutils.py
python/train-movement-models.py
python/utils.py
slides/tws2022/.gitignore
slides/tws2022/figs/.gitignore
slides/tws2022/figs/animal-detection.png
slides/tws2022/figs/auc_map.pdf
slides/tws2022/figs/badge_logo.pdf
slides/tws2022/figs/colonization-persistence-map.pdf
slides/tws2022/figs/conv_hmm_edited.pdf
slides/tws2022/figs/conv_hmm_edited.svg
slides/tws2022/figs/convhmm-perf.pdf
slides/tws2022/figs/dynamic-occ.pdf
slides/tws2022/figs/dynamic-occ.svg
slides/tws2022/figs/ex-assoc.pdf
slides/tws2022/figs/ex-gradient.pdf
slides/tws2022/figs/example-trajectory.pdf
slides/tws2022/figs/figs2-wide.pdf
slides/tws2022/figs/figs2-wide.svg
slides/tws2022/figs/goes-earth.jpg
slides/tws2022/figs/model-equations.pdf
slides/tws2022/figs/model-equations.svg
slides/tws2022/figs/occ-riecke.pdf
slides/tws2022/figs/occ-riecke.svg
slides/tws2022/figs/occ.png
slides/tws2022/figs/quad/empty-phase-space.pdf
slides/tws2022/figs/quad/empty-phase-space.svg
slides/tws2022/figs/quad/one-phase-space.pdf
slides/tws2022/figs/quad/one-phase-space.svg
slides/tws2022/figs/quad/partial-phase-space.pdf
slides/tws2022/figs/quad/partial-phase-space.svg
slides/tws2022/figs/quad/two-phase-space.pdf
slides/tws2022/figs/quad/two-phase-space.svg
slides/tws2022/figs/sketch.jpg
slides/tws2022/figs/top-prob-chips.png
slides/tws2022/notes.md
slides/tws2022/outline.md
slides/tws2022/preamble.tex
slides/tws2022/slides.Rmd
slides/visec2020/.gitignore
slides/visec2020/figs/.gitignore
slides/visec2020/figs/auc_map.pdf
slides/visec2020/figs/badge_logo.pdf
slides/visec2020/figs/colonization-persistence-map.pdf
slides/visec2020/figs/conv_hmm_edited.pdf
slides/visec2020/figs/conv_hmm_edited.svg
slides/visec2020/figs/convhmm-perf.pdf
slides/visec2020/figs/dynamic-occ.pdf
slides/visec2020/figs/dynamic-occ.svg
slides/visec2020/figs/ex-assoc.pdf
slides/visec2020/figs/ex-gradient.pdf
slides/visec2020/figs/example-trajectory.pdf
slides/visec2020/figs/figs2-wide.pdf
slides/visec2020/figs/figs2-wide.svg
slides/visec2020/figs/goes-earth.jpg
slides/visec2020/figs/model-equations.pdf
slides/visec2020/figs/model-equations.svg
slides/visec2020/figs/sketch.jpg
slides/visec2020/figs/top-prob-chips.png
slides/visec2020/notes.md
slides/visec2020/outline.md
slides/visec2020/preamble.tex
slides/visec2020/slides.Rmd
stan/.gitignore
stan/dynamic-occupancy.stan
