├── LICENSE ├── README.md ├── module_clustering ├── .ipynb_checkpoints │ └── clustering_tutorial-checkpoint.ipynb ├── README.md ├── TESTDATA_DIEL18S.RData ├── clustering_tutorial.ipynb └── clustering_tutorial.r ├── module_inference ├── equilibrium.m ├── generate_parameters.m ├── infer_network.m ├── inference_error.m ├── mod3_inference.png ├── plot_network.m ├── plot_one2one.m ├── plot_recons.m ├── plot_timeseries.m ├── simulate_dynamics.m └── tutorial.mlx ├── module_introduction ├── figure_autoregression.jpg ├── figure_autoregression.m ├── helper_functions │ ├── label_ax.m │ ├── plot_correlation.m │ ├── plot_correlation_example.m │ ├── plot_distribution.m │ └── redbluecmap.mat ├── randomwalk_ensemble │ ├── randomwalk_ensemble.m │ ├── randomwalk_ensemble_originals.mat │ └── randomwalk_ensemble_residuals.mat ├── readme.txt ├── tutorial_autoregression.mlx └── tutorial_autoregression_octave.m ├── module_periodicity ├── README.md ├── TESTDATA_DIEL18S.RData ├── periodicity_tutorial.ipynb └── periodicity_tutorial.r └── module_regression ├── code ├── MASTER.m ├── autoregression.m ├── figure_autoregression.m ├── figure_autoregression_summary.m ├── figure_casttimes.m ├── figure_partialautocorrelation.m ├── figure_partialautocorrelation_summary.m ├── figure_regression.m ├── figure_regression_summary.m ├── figure_replicates.m ├── figure_timeseries.m ├── figure_timeseries_summary.m ├── figure_uniformsampling.m ├── figure_uniformsampling_error.m ├── generate_manuscript_figures.m ├── importdata.m ├── interpolatenans.m ├── label_figure.m ├── partialautocorrelation.m ├── print_manuscript_fig.m ├── redblue.m ├── regression.m ├── splitdepths.m └── uniformsampling.m ├── data_mat ├── aloha_clean.mat ├── aloha_clean_uniform.mat ├── aloha_raw.mat ├── aloha_replicates.mat ├── aloha_uniformsampling.mat ├── ar_depth1.mat ├── ar_depth2.mat ├── ar_depth3.mat ├── ar_depth4.mat ├── ar_depth5.mat ├── ar_depth6.mat ├── ar_depth7.mat ├── pac_depth1.mat ├── pac_depth2.mat ├── pac_depth3.mat ├── pac_depth4.mat ├── pac_depth5.mat ├── pac_depth6.mat ├── pac_depth7.mat ├── reg_depth1.mat ├── reg_depth2.mat ├── reg_depth3.mat ├── reg_depth4.mat ├── reg_depth5.mat ├── reg_depth6.mat ├── reg_depth7.mat ├── ts_depth1.mat ├── ts_depth2.mat ├── ts_depth3.mat ├── ts_depth4.mat ├── ts_depth5.mat ├── ts_depth6.mat └── ts_depth7.mat ├── data_raw ├── Suppl_Table_2_HOT_2010_11_metadata_4.xlsx └── merged.relativeabundances.129alohaviralcontigs.txt ├── figures ├── autoregression │ ├── depth1.png │ ├── depth2.png │ ├── depth3.png │ ├── depth4.png │ ├── depth5.png │ ├── depth6.png │ ├── depth7.png │ ├── summary_coefficients.png │ └── summary_residuals.png ├── casttimes.png ├── partialautocorrelation │ ├── depth1.png │ ├── depth2.png │ ├── depth3.png │ ├── depth4.png │ ├── depth5.png │ ├── depth6.png │ ├── depth7.png │ ├── summary_fraction.png │ └── summary_value.png ├── regression │ ├── depth1.png │ ├── depth2.png │ ├── depth3.png │ ├── depth4.png │ ├── depth5.png │ ├── depth6.png │ ├── 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