Files in reichlab/covidEnsembles
What the Package Does (One Line, Title Case)
.gitignore
.here
DESCRIPTION
NAMESPACE
R/QuantileForecastMatrix.R
R/covidEnsembles-package.R
R/data.R
R/date_management.R
R/download_zoltar_forecasts.R
R/math_utils.R
R/model_eligibility.R
R/plot_forecasts.R
R/qra_fit.R
R/qra_fit_convenience.R
R/retrospective_utils.R
R/truth.R
R/wis.R
README.md
code/application/baseline/fit_baseline_model.R
code/application/docker/Dockerfile
code/application/docker/README.md
code/application/docker/run-ensemble.sh
code/application/download_zoltar_forecasts.R
code/application/retrospective-qra-comparison/analyses/retrospective-eval-hosp-exclusions/calculate_scores.R
code/application/retrospective-qra-comparison/analyses/retrospective-eval-hosp-exclusions/plot_ensemble_forecasts.R
code/application/retrospective-qra-comparison/analyses/retrospective-eval-hosp-exclusions/plot_scores.R
code/application/retrospective-qra-comparison/analyses/retrospective-eval-hosp-exclusions/retrospective_scores-state_national-inc_hosp.rds
code/application/retrospective-qra-comparison/analyses/retrospective-peak-skill/retrospective_peak_skill_report.Rmd
code/application/retrospective-qra-comparison/analyses/retrospective-peak-skill/retrospective_peak_skill_report.html
code/application/retrospective-qra-comparison/analyses/retrospective-peak-skill/retrospective_peak_skill_report_with_incd.Rmd
code/application/retrospective-qra-comparison/analyses/retrospective-scores-report-inc-case-inc-death/retrospective_scores_report_inc_case_inc_death.Rmd
code/application/retrospective-qra-comparison/analyses/retrospective-scores-report-inc-case-inc-death/retrospective_scores_report_inc_case_inc_death.html
code/application/retrospective-qra-comparison/analyses/retrospective-scores-report-no-full-history/retrospective_scores_report_no_full_history.Rmd
code/application/retrospective-qra-comparison/analyses/retrospective-scores-report-no-full-history/retrospective_scores_report_no_full_history.html
code/application/retrospective-qra-comparison/analyses/retrospective-scores-report/retrospective_scores_report.Rmd
code/application/retrospective-qra-comparison/analyses/retrospective-scores-report/retrospective_scores_report.html
code/application/retrospective-qra-comparison/analyses/retrospective-scores/calculate_scores.R
code/application/retrospective-qra-comparison/analyses/retrospective-scores/retrospective_scores.rds
code/application/retrospective-qra-comparison/analyses/retrospective-weight-estimates/extract_weights.R
code/application/retrospective-qra-comparison/analyses/retrospective-weight-estimates/retrospective_weight_estimates.rds
code/application/retrospective-qra-comparison/analyses/retrospective-weight-exploration.R
code/application/retrospective-qra-comparison/commits_used.txt
code/application/retrospective-qra-comparison/data-anomalies/outliers-deaths.csv
code/application/retrospective-qra-comparison/fit_prospective_selection_model.R
code/application/retrospective-qra-comparison/fit_retrospective_model.R
code/application/retrospective-qra-comparison/identify_start_dates.R
code/application/retrospective-qra-comparison/misc_variations/hosp_selection/Hosp_Models_Locations with Thresholds Below SD_2020-12-23.csv
code/application/retrospective-qra-comparison/misc_variations/hosp_selection/build_ensembles_hosp_selection.R
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/calculate_scores.R
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/compare_covidhub_delphi.R
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/extract_weights.R
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/fit_retrospective_model_replicate_cmu.R
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/retrospective-fits/state/inc_death-forecast_week_2020-10-05-intercept_FALSE-combine_method_convex-missingness_impute-quantile_groups_3_groups-window_size_4-check_missingness_by_target_TRUE-do_standard_checks_FALSE-do_baseline_check_FALSE.rds
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/retrospective-fits/state/inc_death-forecast_week_2020-10-05-intercept_FALSE-combine_method_convex-missingness_impute-quantile_groups_3_groups-window_size_8-check_missingness_by_target_TRUE-do_standard_checks_FALSE-do_baseline_check_FALSE.rds
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/retrospective_scores.rds
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/retrospective_weight_estimates.rds
code/application/retrospective-qra-comparison/misc_variations/replicate_cmu/run_fit_retrospective_model_replicate_cmu.R
code/application/retrospective-qra-comparison/rel_wis_weighted_median_proof_of_concept.r
code/application/retrospective-qra-comparison/run_fit_prospective_selection_model.R
code/application/retrospective-qra-comparison/run_fit_prospective_selection_model_ensemble_variations_locally.R
code/application/retrospective-qra-comparison/run_fit_retrospective_model.R
code/application/retrospective-qra-comparison/run_fit_retrospective_model_hosp_exclusions.R
code/application/weekly-ensemble/build_4_week_ensembles.R
code/application/weekly-ensemble/build_ensembles.R
code/application/weekly-ensemble/build_trained_ensembles.R
code/application/weekly-ensemble/build_trained_ensembles_step2.R
code/application/weekly-ensemble/exclusion-inputs/Hosp_Models_Locations with Thresholds Below SD_2020-12-29.csv
code/application/weekly-ensemble/exclusion-inputs/Hosp_Models_Locations with Thresholds Below SD_2021-01-05.csv
code/application/weekly-ensemble/exclusion-inputs/Hosp_Models_Locations with Thresholds Below SD_updated_2021-01-12.csv
code/application/weekly-ensemble/exclusion-inputs/Hosp_Models_Locations with Thresholds Below SD_updated_2021-01-19.csv
code/application/weekly-ensemble/exclusion-inputs/Hosp_Models_Locations with Thresholds Below SD_updated_2021-01-26.csv
code/application/weekly-ensemble/fig-ensemble_weight.Rmd
code/application/weekly-ensemble/inc_vs_cum.R
code/application/weekly-ensemble/makefile
code/application/weekly-ensemble/plot_losses.R
code/application/weekly-ensemble/plot_median_vs_trained_ensemble_forecasts.R
code/application/weekly-ensemble/plot_submissions.R
code/application/weekly-ensemble/thetas-2021-11-15
code/application/weekly-ensemble/thetas-2021-11-22
code/application/weekly-ensemble/thetas-2021-11-29
code/application/weekly-ensemble/thetas-2021-12-06
code/application/weekly-ensemble/thetas-2021-12-13
code/application/weekly-ensemble/thetas-2021-12-20
code/application/weekly-ensemble/thetas-2021-12-27
code/application/weekly-ensemble/thetas-2022-01-03
code/application/weekly-ensemble/thetas-2022-01-10
code/application/weekly-ensemble/thetas-2022-01-17
code/application/weekly-ensemble/thetas-2022-01-24
code/application/weekly-ensemble/thetas-2022-01-31
code/application/weekly-ensemble/thetas-2022-02-07
code/application/weekly-ensemble/thetas-2022-02-14
code/application/weekly-ensemble/thetas-2022-02-21
code/simulation/gen-sim-data/get-truth-data.py
code/simulation/gen-sim-data/models.Rmd
code/simulation/gen-sim-data/models.pdf
code/simulation/gen-sim-data/step1-per-location/bsplines.stan
code/simulation/gen-sim-data/step1-per-location/explore_sird_one_location.Rmd
code/simulation/gen-sim-data/step1-per-location/predictive_sird_one_location.stan
code/simulation/gen-sim-data/step1-per-location/run_sird_one_location_spline_beta.R
code/simulation/gen-sim-data/step1-per-location/seird_one_location.stan
code/simulation/gen-sim-data/step1-per-location/sird_one_location.stan
code/simulation/gen-sim-data/step1-per-location/sird_one_location_spline_beta.stan
code/simulation/gen-sim-data/step1-per-location/validate_bsplines.R
covidEnsembles.sublime-workspace
data-raw/location_traits.csv
data-raw/readme.md
data/baseline_forecasts.rdata
data/fips_codes.rdata
man/as.data.frame.QuantileForecastMatrix.Rd
man/baseline_forecasts.Rd
man/build_covid_ensemble.Rd
man/calc_baseline_check.Rd
man/calc_forecast_missingness.Rd
man/calc_forecast_week_end_date.Rd
man/calc_model_eligibility_for_ensemble.Rd
man/calc_nondecreasing_quantile_check.Rd
man/calc_q10_check.Rd
man/calc_relative_horizon.Rd
man/calc_relative_target.Rd
man/calc_retrospective_ensemble_scores.Rd
man/calc_sd_check.Rd
man/calc_target_string_end_date.Rd
man/calc_target_week_end_date.Rd
man/covidEnsembles.Rd
man/date_to_week_end_date.Rd
man/estimate_qra.Rd
man/estimate_qra_ew.Rd
man/estimate_qra_optimized.Rd
man/estimate_qra_qenspy.Rd
man/estimate_qra_quantgen.Rd
man/extract_weights_qenspy_qra_fit.Rd
man/fips_codes.Rd
man/get_all_project_forecasts.Rd
man/get_all_wis_components.Rd
man/get_by_location_group_ensemble_fits_and_predictions.Rd
man/get_candidate_models.Rd
man/get_ensemble_fit_and_predictions.Rd
man/get_imputed_ensemble_fits_and_predictions.Rd
man/get_observed_by_location_target_end_date.Rd
man/get_one_project_forecast.Rd
man/grid_search_rel_wis_weights.Rd
man/impute_missing_per_quantile.Rd
man/init_par_constructor_convex_per_model.Rd
man/init_par_constructor_rel_wis_weighted_mean.Rd
man/init_par_constructor_rel_wis_weighted_median.Rd
man/init_par_constructor_rescaled_convex_per_model.Rd
man/init_par_constructor_unconstrained_per_model.Rd
man/interval_score.Rd
man/is.QuantileForecastMatrix.Rd
man/is.median_qra_fit.Rd
man/is.qenspy_qra_fit.Rd
man/is.qra_fit.Rd
man/is.rescaled_qra_fit.Rd
man/is.weighted_median_qra_fit.Rd
man/load_covid_forecasts_relative_horizon.Rd
man/load_retrospective_ensemble_forecasts.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/model_constructor_convex_per_model.Rd
man/model_constructor_rel_wis_weighted_mean.Rd
man/model_constructor_rel_wis_weighted_median.Rd
man/model_constructor_rescaled_convex_per_model.Rd
man/model_constructor_unconstrained_per_model.Rd
man/new_QuantileForecastMatrix.Rd
man/new_QuantileForecastMatrix_from_df.Rd
man/new_median_qra_fit.Rd
man/new_qenspy_qra_fit.Rd
man/new_qra_fit.Rd
man/new_rescaled_qra_fit.Rd
man/new_weighted_median_qra_fit.Rd
man/par_grid_constructor_rel_wis_weighted_mean.Rd
man/par_grid_constructor_rel_wis_weighted_median.Rd
man/parse_model_case.Rd
man/plot_forecasts_single_model.Rd
man/predict.median_qra_fit.Rd
man/predict.qenspy_qra_fit.Rd
man/predict.qra_fit.Rd
man/predict.rescaled_qra_fit.Rd
man/predict.weighted_median_qra_fit.Rd
man/print.qfm.Rd
man/qfm_data.Rd
man/quantile_score.Rd
man/softmax_matrix_rows.Rd
man/sort.QuantileForecastMatrix.Rd
man/str.QuantileForecastMatrix.Rd
man/sub-.QuantileForecastMatrix.Rd
man/validate_QuantileForecastMatrix.Rd
man/validate_qra_fit.Rd
man/validate_quantile_crossing.Rd
man/validate_rescaled_qra_fit.Rd
man/weighted_interval_penalty.Rd
man/weighted_interval_width.Rd
man/wip.Rd
man/wis.Rd
man/wis_loss.Rd
man/wis_loss_rel_wis_weights.Rd
man/wiw.Rd
src/Makevars
src/Makevars.win
src/utility.c
src/utility.h
tests/.gitignore
tests/testthat/run-tests.R
tests/testthat/test-QuantileForecastMatrix.R
tests/testthat/test-data/data-processed-test-get_candidate_models/COVIDhub-baseline/metadata-COVIDhub-baseline.txt
tests/testthat/test-data/data-processed-test-get_candidate_models/COVIDhub-ensemble/metadata-COVIDhub-ensemble.txt
tests/testthat/test-data/data-processed-test-get_candidate_models/model-A/metadata-model-A.txt
tests/testthat/test-data/data-processed-test-get_candidate_models/model-B/metadata-model-B.txt
tests/testthat/test-data/data-processed-test-get_candidate_models/model-C/metadata-model-C.txt
tests/testthat/test-data/data-processed-test-get_candidate_models/model-D/metadata-model-D.txt
tests/testthat/test-date-management.R
tests/testthat/test-impute.R
tests/testthat/test-load_covid_forecasts_relative_horizon.R
tests/testthat/test-math-utils.R
tests/testthat/test-model-eligibility.R
tests/testthat/test-qra_fit_common.R
tests/testthat/test-qra_fit_convex_per_model.R
tests/testthat/test-qra_fit_ew.R
tests/testthat/test-wis.R
vignettes/qra_fit.Rmd
vignettes/qra_fit.pdf
writing/manuscript/calibration.R
writing/weighted_median/weighted_median_ensemble.Rmd
