Files in reichlab/adaptively-weighted-ensemble

Adaptively Weighted Ensembles via Stacking

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/awes-package.R R/data.R R/kcde-utils.R R/kde-prediction-utils.R R/kde-utils.R R/sarima-utils.R R/stacking-utils.R R/utils.R README.md

data-raw/allflu-cleaned.csv

data-raw/cdc-baselines.csv

data/flu_data.rdata

data/flu_onset_baselines.rdata

inst/AWE-workflow.Rmd inst/data-processing/create-clean-flu-data.R inst/data-processing/create-flu-baseline-file.R inst/estimation/em-stacking/em-stacking-estimation.R inst/estimation/em-stacking/em-stacking-plots.R

inst/estimation/em-stacking/fits/em_weights.rds

inst/estimation/em-stacking/plots/em-stacking-plots-all-regions-all-targets.pdf inst/estimation/kcde/check-kcde-predictions-onset.pdf inst/estimation/kcde/check-kcde-predictions-peak_inc.pdf inst/estimation/kcde/check-kcde-predictions-peak_week.pdf inst/estimation/kcde/check-kcde-predictions-ph_1_inc.pdf inst/estimation/kcde/check-kcde-predictions-ph_2_inc.pdf inst/estimation/kcde/check-kcde-predictions-ph_3_inc.pdf inst/estimation/kcde/check-kcde-predictions-ph_4_inc.pdf inst/estimation/kcde/check-kcde-predictions.pdf inst/estimation/kcde/check-loso-predictions.R inst/estimation/kcde/check_dists_sum_to_1.R inst/estimation/kcde/copula-estimation-step-none-left-out.R inst/estimation/kcde/copula-estimation-step.R

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2000-2001.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2001-2002.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2002-2003.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2003-2004.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2004-2005.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2005-2006.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2006-2007.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2007-2008.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2008-2009.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 1-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_2008-2009.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 10-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 2-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 2-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 2-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 2-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 2-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 2-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_2007-2008.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_2008-2009.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 3-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_2007-2008.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_2008-2009.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 4-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_2008-2009.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 5-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2000-2001.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2001-2002.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2004-2005.rds

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inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2007-2008.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2008-2009.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2009-2010.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_2010-2011.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 6-max_lag_1-seasonality_TRUE-season_left_out_none.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 7-max_lag_1-seasonality_TRUE-season_left_out_1997-1998.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 7-max_lag_1-seasonality_TRUE-season_left_out_1998-1999.rds

inst/estimation/kcde/copula-fits/kcde-copula-fits-Region 7-max_lag_1-seasonality_TRUE-season_left_out_1999-2000.rds

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inst/evaluation/test-predictions/xgb_stacking_unregularized-Region7-2013-2014-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region7-2014-2015-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region7-2015-2016-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region8-2011-2012-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region8-2012-2013-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region8-2013-2014-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region8-2014-2015-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region8-2015-2016-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region9-2011-2012-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region9-2012-2013-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region9-2013-2014-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region9-2014-2015-test-predictions.rds

inst/evaluation/test-predictions/xgb_stacking_unregularized-Region9-2015-2016-test-predictions.rds

inst/evaluation/xgb-stacking-unregularized/xgb-stacking-unregularized-prediction-test.R inst/evaluation/xgb-stacking/xgb-stacking-prediction-test.R

inst/manuscript/GrandMacros.tex

inst/manuscript/awes-manuscript.Rmd inst/manuscript/awes-manuscript.pdf

inst/manuscript/feature-weighted-ensembles.bib

inst/manuscript/get-permutations-season-diff-from-median.R

inst/manuscript/plos2015.bst

inst/presentations/20170429_NESS/20170429_NESS_Ray_AWES.Rmd

inst/presentations/20170429_NESS/20170429_NESS_Ray_AWES.html

inst/presentations/20170429_NESS/Ray and Reich - NESS 2017 - Ensemble Methods for Flu Prediction.pdf

inst/presentations/20170429_NESS/manual-styles.css

inst/presentations/20170801_JSM_poster/GrandMacros.tex

inst/presentations/20170801_JSM_poster/JSM2017_poster_ensembles.Rnw

inst/presentations/20170801_JSM_poster/JSM2017_poster_ensembles.pdf

inst/presentations/20170801_JSM_poster/UMass_logo.png

inst/presentations/20170801_JSM_poster/beamerposter.sty

inst/presentations/20170801_JSM_poster/beamerthemeconfposter.sty

inst/presentations/20170801_JSM_poster/knit_poster.R inst/presentations/20170801_JSM_slides/20170801_JSM_Ray_Model_Averaging.Rmd

inst/presentations/20170801_JSM_slides/20170801_JSM_Ray_Model_Averaging.html

inst/presentations/20170801_JSM_slides/Model Averaging for Probabilistic Time Series Forecasts.pdf

inst/presentations/20170801_JSM_slides/manual-styles.css

inst/presentations/misc_plots/KDE_peak_inc_demo_plot.R inst/presentations/misc_plots/ew-and-cw-plots.R

inst/supplement/GrandMacros.tex

inst/supplement/awes-supplement.Rmd inst/supplement/awes-supplement.pdf inst/supplement/experimental-analysis.R

inst/supplement/feature-weighted-ensembles.bib

man/assemble_predictions.Rd man/assemble_stacking_inputs.Rd man/awes.Rd man/calc_median_from_binned_probs.Rd man/compute_competition_log_score.Rd man/fit_kde_log_peak_week_inc.Rd man/fit_kde_onset_week.Rd man/fit_kde_peak_week.Rd man/fit_kde_weekly_inc.Rd man/fit_kernel_smoothed_stacked_model_fixed_bw.Rd man/fit_region_kdes.Rd man/fit_region_sarima.Rd man/fit_stacked_model.Rd man/fit_unregularized_stacked_model.Rd man/flu_data.Rd man/flu_onset_baselines.Rd man/get_inc_bin.Rd man/get_initial_rng_substream.Rd man/get_log_scores_via_direct_simulation.Rd man/get_log_scores_via_trajectory_simulation.Rd man/get_observed_seasonal_quantities.Rd man/get_onset_baseline.Rd man/get_onset_week.Rd man/get_rng_substream.Rd man/logspace_add.Rd man/logspace_sub.Rd man/logspace_sub_matrix_rows.Rd man/logspace_sum.Rd man/logspace_sum_matrix_rows.Rd man/make_predictions_dataframe.Rd man/predict_kde_log_peak_week_inc.Rd man/predict_kde_log_weekly_inc.Rd man/predict_kde_onset_week.Rd man/predict_kde_peak_week.Rd man/predict_region_kde.Rd man/sample_predictive_trajectories_arima.Rd man/sample_predictive_trajectories_arima_wrapper.Rd man/season_week_to_year_week.Rd man/simulate_trajectories_kcde.Rd man/weighted_combine_predictions.Rd man/year_week_to_season_week.Rd

src/Makevars

src/Makevars.win

src/utility.c

src/utility.h

reichlab/adaptively-weighted-ensemble documentation built on May 27, 2019, 4:53 a.m.