Files in reichlab/2018-2019-cdc-flu-contest
Code for Reich Lab entries in CDC flu contest 2018-2019

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/cdcFlu20182019-package.R R/data.R R/get-partially-revised-data.R R/kcde-utils.R R/kde-prediction-utils.R R/kde-utils.R R/make_one_kde_prediction_file.R R/my_plot_weekahead.R R/sarima-utils.R R/stacking-utils.R R/utils.R README.md

data-raw/flu_data.csv

data-raw/flu_onset_baselines.csv

data-raw/hosp_data.csv

data-raw/region-prediction-template-EW53.csv

data-raw/region-prediction-template.csv

data-raw/state_flu_data.csv

data/e

data/flu_data.rdata

data/flu_data_with_backfill.rds

data/flu_onset_baselines.rdata

data/hosp_data.rdata

data/state_flu_data.rdata

inst/data-processing/create-clean-flu-data-for-test-phase-prospective-predictions.R inst/data-processing/create-clean-flu-data-hosp.R inst/data-processing/create-clean-flu-data-state-level.R inst/data-processing/create-clean-flu-data.R inst/data-processing/create-flu-baseline-file.R inst/data-processing/save-unrevised-data.R

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-0-4 y-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-0-4 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2017_2018.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-0-4 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-18-49 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2017_2018.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-18-49 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-18-49-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-5-17 -seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-5-17 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2017_2018.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-5-17 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-50-64 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2017_2018.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-50-64 yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-50-64-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-65+ y-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-65+ yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2017_2018.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-65+ yr-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-Overa-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-Overall-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2017_2018.rds

inst/estimation/hosp-sarima/fits-seasonal-differencing/sarima-Entire_Network-age-Overall-seasonal_difference_FALSE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/hosp-sarima/sarima-hosp-estimation.R inst/estimation/region-kcde/copula-estimation-step.R inst/estimation/region-kcde/kcde-estimation-step.R inst/estimation/region-kcde/submit-cluster-job-kcde-estimation-step.R inst/estimation/region-kde/check-2018-2019-files.R inst/estimation/region-kde/create-current-season-kde-entry-files.R

inst/estimation/region-kde/fits/kde-National-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region1-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region10-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region2-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region3-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region4-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region5-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region6-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region7-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region8-fit-prospective-2018-2019.rds

inst/estimation/region-kde/fits/kde-Region9-fit-prospective-2018-2019.rds

inst/estimation/region-sarima/sarima-region-estimation-loso.R

inst/estimation/region-stacking/readme.txt

inst/estimation/region-stacking/scores-with-20172018.csv

inst/estimation/region-stacking/stacking_estimation.R inst/estimation/region-stacking/submit-cluster-job-stacking-estimation-step.R

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Alabama-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Alaska-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Arizona-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Arkansas-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-California-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Colorado-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Connecticut-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Delaware-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-District_of_Columbia-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Georgia-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Hawaii-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Idaho-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Illinois-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Indiana-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Iowa-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Kansas-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Kentucky-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Louisiana-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Maine-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Maryland-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Massachusetts-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Michigan-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Minnesota-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Mississippi-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Missouri-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Montana-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Nebraska-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Nevada-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-New_Hampshire-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-New_Jersey-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-New_Mexico-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-New_York-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-New_York_City-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-North_Carolina-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-North_Carolina-seasonal_difference_TRUE-transformation_none-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-North_Dakota-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Ohio-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Oklahoma-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Oregon-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Pennsylvania-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Puerto_Rico-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Rhode_Island-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-South_Carolina-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-South_Dakota-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Tennessee-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Texas-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Utah-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Vermont-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Virgin_Islands-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Virginia-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Washington-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-West_Virginia-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Wisconsin-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/fits-seasonal-differencing/sarima-Wyoming-seasonal_difference_TRUE-transformation_box-cox-first_test_season_2018_2019.rds

inst/estimation/state-sarima/sarima-state-estimation.R inst/forecast-reports/MA/forecast-report-template.Rmd inst/forecast-reports/MA/forecast-report-template.pdf

inst/guidance/FluSurv_Submission_Template_1819.csv

inst/guidance/Flu_Challenge_2018-19_final.docx

inst/guidance/Hosp_Guidance_2018-19_final.docx

inst/guidance/Long_Flu_Submission_Template_1819.csv

inst/guidance/Model_Methodology_Form_final.docx

inst/guidance/StateILI_Submission_Template_1819.csv

inst/guidance/State_ILI_Guidance_final.docx

inst/make-submission-files/make-regional-ensemble-submission-file.R inst/make-submission-files/make-regional-kcde-submission-files.R inst/make-submission-files/make-regional-sarima-seasonal-false-submission-files.R inst/make-submission-files/make-regional-sarima-seasonal-true-submission-files.R inst/make-submission-files/make-sarima-hosp-submission-files.R inst/make-submission-files/make-sarima-state-submission-files.R

inst/submissions/hosp-sarima/EW1-KoT-Hosp-2019-01-14.csv

inst/submissions/hosp-sarima/EW10-KoT-Hosp-2019-03-18.csv

inst/submissions/hosp-sarima/EW11-KoT-Hosp-2019-03-25.csv

inst/submissions/hosp-sarima/EW12-KoT-Hosp-2019-04-01.csv

inst/submissions/hosp-sarima/EW13-KoT-Hosp-2019-04-08.csv

inst/submissions/hosp-sarima/EW14-KoT-Hosp-2019-04-15.csv

inst/submissions/hosp-sarima/EW15-KoT-Hosp-2019-04-22.csv

inst/submissions/hosp-sarima/EW16-KoT-Hosp-2019-04-29.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-10-27.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-10-28.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-10-30.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-11-02.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-11-03.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-11-05.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-11-09.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-11-15.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2018-11-30.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2019-05-06.csv

inst/submissions/hosp-sarima/EW17-KoT-Hosp-2019-05-13.csv

inst/submissions/hosp-sarima/EW2-KoT-Hosp-2019-01-21.csv

inst/submissions/hosp-sarima/EW3-KoT-Hosp-2019-01-28.csv

inst/submissions/hosp-sarima/EW4-KoT-Hosp-2019-02-04.csv

inst/submissions/hosp-sarima/EW5-KoT-Hosp-2019-02-11.csv

inst/submissions/hosp-sarima/EW50-KoT-Hosp-2018-12-25.csv

inst/submissions/hosp-sarima/EW50-KoT-Hosp-2018-12-26.csv

inst/submissions/hosp-sarima/EW51-KoT-Hosp-2019-01-02.csv

inst/submissions/hosp-sarima/EW52-KoT-Hosp-2019-01-07.csv

inst/submissions/hosp-sarima/EW6-KoT-Hosp-2019-02-18.csv

inst/submissions/hosp-sarima/EW7-KoT-Hosp-2019-02-25.csv

inst/submissions/hosp-sarima/EW8-KoT-Hosp-2019-03-04.csv

inst/submissions/hosp-sarima/EW9-KoT-Hosp-2019-03-11.csv

inst/submissions/region-KoT/EW01-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW01-2019-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW01-2019-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW02-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW02-2019-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW02-2019-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW03-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW03-2019-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW03-2019-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW04-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW04-2019-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW04-2019-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW05-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW06-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW07-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW08-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW09-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW10-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW11-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW12-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW13-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW14-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW15-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW16-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW17-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW18-2019-ReichLab_KoT.csv

inst/submissions/region-KoT/EW42-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW42-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW42-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW43-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW43-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW43-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW44-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW44-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW44-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW45-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW45-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW45-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW46-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW46-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW46-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW47-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW47-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW47-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW48-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW48-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW48-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW49-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW49-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW49-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW50-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW50-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW50-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW51-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW51-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW51-2018-ReichLab_KoT_stable.csv

inst/submissions/region-KoT/EW52-2018-ReichLab_KoT.csv

inst/submissions/region-KoT/EW52-2018-ReichLab_KoT_dev.csv

inst/submissions/region-KoT/EW52-2018-ReichLab_KoT_stable.csv

inst/submissions/region-kcde/EW01-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW02-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW03-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW04-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW05-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW06-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW07-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW08-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW09-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW10-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW11-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW12-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW13-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW14-2019-ReichLab_kcde.csv

inst/submissions/region-kcde/EW15-2019-ReichLab_kcde.csv

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inst/submissions/region-kcde/EW42-2018-ReichLab_kcde.csv

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inst/submissions/region-kde/EW01-2019-ReichLab_kde.csv

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inst/submissions/region-kde/EW40-2018-ReichLab_kde.csv

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inst/submissions/region-sarima_seasonal_difference_FALSE/EW01-2019-ReichLab_sarima_seasonal_difference_FALSE.csv

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inst/submissions/region-sarima_seasonal_difference_FALSE/EW16-2019-ReichLab_sarima_seasonal_difference_FALSE.csv

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inst/submissions/region-sarima_seasonal_difference_FALSE/EW18-2019-ReichLab_sarima_seasonal_difference_FALSE.csv

inst/submissions/region-sarima_seasonal_difference_FALSE/EW42-2018-ReichLab_sarima_seasonal_difference_FALSE.csv

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inst/submissions/region-sarima_seasonal_difference_TRUE/EW08-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

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inst/submissions/region-sarima_seasonal_difference_TRUE/EW11-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

inst/submissions/region-sarima_seasonal_difference_TRUE/EW12-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

inst/submissions/region-sarima_seasonal_difference_TRUE/EW13-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

inst/submissions/region-sarima_seasonal_difference_TRUE/EW14-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

inst/submissions/region-sarima_seasonal_difference_TRUE/EW15-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

inst/submissions/region-sarima_seasonal_difference_TRUE/EW16-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

inst/submissions/region-sarima_seasonal_difference_TRUE/EW17-2019-ReichLab_sarima_seasonal_difference_TRUE.csv

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inst/submissions/region-sarima_seasonal_difference_TRUE/EW39-2018-ReichLab_sarima_seasonal_difference_TRUE.csv

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inst/submissions/region-sarima_seasonal_difference_TRUE/EW51-2018-ReichLab_sarima_seasonal_difference_TRUE.csv

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inst/submissions/state-sarima/EW1-KoT-StateILI-2019-01-14.csv

inst/submissions/state-sarima/EW10-KoT-StateILI-2019-03-18.csv

inst/submissions/state-sarima/EW11-KoT-StateILI-2019-03-25.csv

inst/submissions/state-sarima/EW12-KoT-StateILI-2019-04-01.csv

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inst/submissions/state-sarima/EW14-KoT-StateILI-2019-04-15.csv

inst/submissions/state-sarima/EW15-KoT-StateILI-2019-04-22.csv

inst/submissions/state-sarima/EW16-KoT-StateILI-2019-04-29.csv

inst/submissions/state-sarima/EW17-KoT-Hosp-2018-11-03.csv

inst/submissions/state-sarima/EW17-KoT-StateILI-2019-05-06.csv

inst/submissions/state-sarima/EW18-KoT-StateILI-2019-05-13.csv

inst/submissions/state-sarima/EW2-KoT-StateILI-2019-01-21.csv

inst/submissions/state-sarima/EW3-KoT-StateILI-2019-01-28.csv

inst/submissions/state-sarima/EW4-KoT-StateILI-2019-02-05.csv

inst/submissions/state-sarima/EW4-KoT-StateILI-2019-02-06.csv

inst/submissions/state-sarima/EW42-KoT-StateILI-2018-10-26.csv

inst/submissions/state-sarima/EW42-KoT-StateILI-2018-11-02.csv

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inst/submissions/state-sarima/EW43-KoT-StateILI-2018-11-09.csv

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inst/submissions/state-sarima/EW45-KoT-StateILI-2018-11-19.csv

inst/submissions/state-sarima/EW46-KoT-StateILI-2018-11-28.csv

inst/submissions/state-sarima/EW47-KoT-StateILI-2018-12-03.csv

inst/submissions/state-sarima/EW48-KoT-StateILI-2018-12-10.csv

inst/submissions/state-sarima/EW5-KoT-StateILI-2019-02-11.csv

inst/submissions/state-sarima/EW50-KoT-StateILI-2018-12-26.csv

inst/submissions/state-sarima/EW51-KoT-StateILI-2019-01-02.csv

inst/submissions/state-sarima/EW52-KoT-StateILI-2019-01-07.csv

inst/submissions/state-sarima/EW6-KoT-StateILI-2019-02-18.csv

inst/submissions/state-sarima/EW7-KoT-StateILI-2019-02-25.csv

inst/submissions/state-sarima/EW8-KoT-StateILI-2019-03-04.csv

inst/submissions/state-sarima/EW9-KoT-StateILI-2019-03-11.csv

inst/templates/65_template.csv

inst/templates/FluSurv_Submission_Template_1819.csv

inst/templates/hosp-prediction-template.csv

inst/templates/region-prediction-template-EW53.csv

inst/templates/region-prediction-template.csv

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man/assemble_predictions.Rd man/assemble_stacking_inputs.Rd man/calc_median_from_binned_probs.Rd man/cdcFlu20182019.Rd man/compute_competition_log_score.Rd man/download_and_preprocess_flu_data.Rd man/download_and_preprocess_state_flu_data.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_num_MMWR_weeks_in_first_season_year.Rd man/get_num_MMWR_weeks_in_year.Rd man/get_observed_seasonal_quantities.Rd man/get_official_observed_seasonal_quantities.Rd man/get_onset_baseline.Rd man/get_onset_week.Rd man/get_partially_revised_ilinet.Rd man/get_rng_substream.Rd man/get_submission_one_region_via_trajectory_simulation.Rd man/get_submission_via_trajectory_simulation.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_one_kde_prediction_file.Rd man/make_predictions_dataframe.Rd man/make_predictions_plots.Rd man/my_plot_weekahead.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_wrapper.Rd man/season_week_to_year_week.Rd man/simulate_trajectories_kcde.Rd man/state_flu_data.Rd man/weighted_combine_predictions.Rd man/year_week_to_season_week.Rd

src/Makevars

src/Makevars.win

src/utility.c

src/utility.h

travis-push.sh

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reichlab/2018-2019-cdc-flu-contest
Code for Reich Lab entries in CDC flu contest 2018-2019

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Code for Reich Lab entries in CDC flu contest 2018-2019

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reichlab/2018-2019-cdc-flu-contest Code for Reich Lab entries in CDC flu contest 2018-2019

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