Files in ha0ye/portalDS
Compute Dynamic Stability for Rodents at Portal
.Rbuildignore
.gitignore
.lintr
.pre-commit-config.yaml
.travis.yml
.zenodo.json
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
R/analysis-workflow.R
R/calculations-ccm.R
R/calculations-jacobian-metrics.R
R/calculations-simplex.R
R/calculations-smap.R
R/data-portal.R
R/data-sim-3sp-food-chain.R
R/data-sim-flour-beetle.R
R/data-sim-resource-competition.R
R/plotting_functions.R
R/plotting_helpers.R
R/portalDS-package.R
R/utils-data-transformations.R
R/utils-pipe.R
README.Rmd
README.md
analysis/intertidal_analysis.Rmd
analysis/intertidal_analysis.md
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-3-1.png
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-4-1.png
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-5-1.png
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-6-1.png
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-7-1.png
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-8-1.png
analysis/intertidal_analysis_files/figure-gfm/unnamed-chunk-9-1.png
analysis/maizuru_analysis.R
analysis/portal_analysis.Rmd
analysis/portal_analysis.md
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-10-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-12-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-13-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-14-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-3-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-4-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-5-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-6-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-7-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-8-1.png
analysis/portal_analysis_files/figure-gfm/unnamed-chunk-9-1.png
analysis/simulation_testing.Rmd
analysis/supplemental_analyses.R
analysis/talk_figures.R
analysis/temp_figures.R
codecov.yml
data/maizuru_block.rda
env_copy.sh
figures/maizuru_ds.pdf
figures/maizuru_ds_blank.pdf
figures/maizuru_ds_threshold.pdf
figures/maizuru_network.pdf
figures/maizuru_network_subset.pdf
figures/maizuru_time_series.pdf
figures/maizuru_time_series_subset.pdf
figures/multisurface.pdf
figures/portal_eigenvalues_50.pdf
figures/portal_eigenvalues_50_a.pdf
figures/portal_eigenvalues_50_aa.pdf
figures/portal_eigenvalues_50_b.pdf
figures/portal_eigenvalues_50_bb.pdf
figures/portal_eigenvalues_50_complex.pdf
figures/portal_eigenvalues_50_dom.pdf
figures/portal_eigenvector_a.pdf
figures/portal_eigenvector_b.pdf
figures/portal_eigenvector_c.pdf
figures/portal_eigenvector_null.pdf
figures/portal_eigenvectors_50.pdf
figures/portal_network_50.pdf
figures/portal_time_series.pdf
figures/portal_time_series_highlight.pdf
inst/extdata/maizuru_ccm_links.RDS
inst/extdata/maizuru_ccm_results.RDS
inst/extdata/maizuru_smap_matrices.RDS
inst/extdata/portal_block.RDS
inst/extdata/portal_block_50.RDS
man/add_regime_shift_highlight.Rd
man/compute_ccm.Rd
man/compute_ccm_links.Rd
man/compute_dynamic_stability.Rd
man/compute_eigen_decomp.Rd
man/compute_simplex.Rd
man/compute_smap_coeffs.Rd
man/compute_smap_matrices.Rd
man/compute_svd_decomp.Rd
man/compute_total_variance.Rd
man/compute_volume_contraction.Rd
man/extract_matrix_values.Rd
man/get_smap_coefficients.Rd
man/maizuru_block.Rd
man/make_portal_block.Rd
man/make_surrogate_annual_spline.Rd
man/norm_rescale.Rd
man/pipe.Rd
man/plot_eigenvalues.Rd
man/plot_eigenvectors.Rd
man/plot_indicator_values.Rd
man/plot_network.Rd
man/plot_smap_coeffs.Rd
man/plot_time_series.Rd
man/simulate_3sp_food_chain.Rd
man/simulate_LPA_flour_beetles.Rd
man/simulate_resource_competition.Rd
portalDS.Rproj
tests/figs/deps.txt
tests/figs/plotting-functions/maizuru-eigenvalues-complex.svg
tests/figs/plotting-functions/maizuru-eigenvalues.svg
tests/figs/plotting-functions/maizuru-eigenvectors-highlight.svg
tests/figs/plotting-functions/maizuru-eigenvectors-ipr.svg
tests/figs/plotting-functions/maizuru-eigenvectors.svg
tests/figs/plotting-functions/maizuru-interaction-network.svg
tests/figs/plotting-functions/maizuru-s-map-coefficients.svg
tests/figs/plotting-functions/maizuru-svd-values.svg
tests/figs/plotting-functions/maizuru-svd-vectors.svg
tests/figs/plotting-functions/maizuru-time-series-winters.svg
tests/figs/plotting-functions/maizuru-time-series.svg
tests/testthat.R
tests/testthat/test-01-datasets.R
tests/testthat/test-02-get_data.R
tests/testthat/test-03-data-simulations.R
tests/testthat/test-04-data_utils.R
tests/testthat/test-05-analysis_functions.R
tests/testthat/test-06-dynamic_stability_workflow.R
tests/testthat/test-07-dynamic_stability_drake_plan.R
tests/testthat/test-08-plotting_helpers.R
tests/testthat/test-09-plotting_functions.R
vignettes/maizuru-dynamic-stability.Rmd
vignettes/my_lib.bib
vignettes/parallelization.Rmd
