Files in jrgant/FluHospPrediction
Code for Flu Hospital Prediction Paper
.Rbuildignore
.Rprofile
.gitattributes
.gitignore
DESCRIPTION
FluHospPrediction.Rproj
LICENSE.md
Makefile
NAMESPACE
R/calendar_mgmt.R
R/loss_absolute_error.R
R/simcrv_funs.R
R/sl_procedure.R
R/summaries.R
README.Rmd
README.md
data/cleaned/empdat.csv
data/cleaned/empdat_weeksum.csv
data/cleaned/hypothetical-curves_lambda-1se.Rds
data/cleaned/hypothetical-curves_lambda-min.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_01.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_02.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_03.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_04.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_05.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_06.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_07.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_08.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_09.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_10.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_11.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_12.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_13.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_14.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_15.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_16.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_17.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_18.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_19.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_20.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_21.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_22.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_23.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_24.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_25.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_26.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_27.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_28.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_29.Rds
data/cleaned/sim_dataset_analytic_lambda-1se_week_30.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_01.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_02.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_03.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_04.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_05.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_06.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_07.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_08.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_09.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_10.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_11.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_12.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_13.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_14.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_15.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_16.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_17.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_18.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_19.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_20.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_21.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_22.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_23.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_24.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_25.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_26.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_27.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_28.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_29.Rds
data/cleaned/sim_dataset_analytic_lambda-min_week_30.Rds
data/cleaned/sim_dataset_long_lambda-1se.csv
data/cleaned/sim_dataset_long_lambda-min.csv
data/cleaned/sim_dataset_wide_lambda-1se.csv
data/cleaned/sim_dataset_wide_lambda-min.csv
data/raw/flu/FluSurveillance_EIP_Entire Network_Data.csv
data/raw/flu/FluSurveillance_FluSurv-NET_Entire Network_Data.csv
data/raw/flu/Weekly_Data_Counts.csv
data/raw/flu/Weekly_Data_Percent.csv
inst/01_data_cleaning_empdat.R
inst/02_simulate_hospcurves.R
inst/03_create_analysis_dataset.R
inst/04_run_superlearner.R
inst/05_run_sqerrloss_sensitivity.R
inst/06.1_tables-figures-setup.R
inst/06.2_tables-figures-simul.R
inst/06.3_tables-figures-main.R
inst/06.4_tables-figures-sens-1se.R
inst/06.5_tables-figures-sens-elastrf.R
inst/06.6_tables-figures-sens-sqerrloss.R
inst/06.7_tables-figures-sens-comb.R
inst/07_run_sl_prospective.R
inst/08_run_sl_observed.R
inst/09_tables-figures-sub-prosp-obs.R
inst/10_ensemble-cv.R
inst/11_ensemble-cv-sqerrloss.R
inst/12_ensemble-cv-1se.R
inst/13_ensemble_optimism.R
inst/14_run_sl_observed_allseasons.R
inst/15_extract-obstrain-preds.R
inst/16_tables-figures-obstrain.R
inst/17_figure-peakrate-week16.R
inst/99_test-script.R
inst/fmt_emp_season.R
man/calendar_mgmt.Rd
man/loss_absolute_error.Rd
man/predcurves.Rd
man/simcrv.Rd
man/simdist.Rd
man/summary_functions.Rd
man/super_learner_proc.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
renv/settings.json
results/00_paper_output/2023-03-21_cumhosp_lrnr_selection_1se.csv
results/00_paper_output/2023-03-21_cumhosp_lrnr_selection_erf.csv
results/00_paper_output/2023-03-21_cumhosp_lrnr_selection_sqe.csv
results/00_paper_output/2023-03-21_pkrate_lrnr_selection_1se.csv
results/00_paper_output/2023-03-21_pkrate_lrnr_selection_erf.csv
results/00_paper_output/2023-03-21_pkrate_lrnr_selection_sqe.csv
results/00_paper_output/2023-03-21_pkweek_lrnr_selection_1se.csv
results/00_paper_output/2023-03-21_pkweek_lrnr_selection_erf.csv
results/00_paper_output/2023-03-21_pkweek_lrnr_selection_sqe.csv
results/00_paper_output/FIG_Boxplot_H01-W16-Risks_PeakRate-LambdaMin_2023-03-21.pdf
results/00_paper_output/FIG_Boxplot_H01-W16-Risks_PeakRate-LambdaMin_2023-03-21.png
results/00_paper_output/FIG_Ensemble-Summary_All-Targets-Panel-A_2023-03-21.eps
results/00_paper_output/FIG_Ensemble-Summary_All-Targets-Panel-A_2023-03-21.pdf
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results/00_paper_output/FIG_Ensemble-Summary_All-Targets-SQE_2023-03-21.pdf
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results/00_paper_output/FIG_Ensemble-Summary_All-Targets_Reg-Scale-Components_2023-03-21.pdf
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results/create_output_directories.r
results/prune_prosp_components.R
results/rerun_missing_cv_weeks.R
results/rerun_missing_cv_weeks_search_results.r
results/rerun_missing_cv_weeks_search_results_bigmem.r
scripts/RUN_ENSEMBLE_CV.sh
scripts/RUN_ENSEMBLE_CV_1se.sh
scripts/RUN_ENSEMBLE_CV_ElastNetRF.sh
scripts/RUN_ENSEMBLE_CV_SqErrLoss.sh
scripts/RUN_OBS_AllSeasons.sh
scripts/RUN_OBS_AllTargets.sh
scripts/RUN_PROSPECTIVE_AllTargets.sh
scripts/RUN_TARGET-cumhosp_LAMBDA-lambda-1se.sh
scripts/RUN_TARGET-cumhosp_LAMBDA-lambda-min.sh
scripts/RUN_TARGET-cumhosp_LAMBDA-lambda-min_SENS-ElastNetRF.sh
scripts/RUN_TARGET-cumhosp_LAMBDA-lambda-min_SENS-SqErrLoss.sh
scripts/RUN_TARGET-pkrate_LAMBDA-lambda-1se.sh
scripts/RUN_TARGET-pkrate_LAMBDA-lambda-min.sh
scripts/RUN_TARGET-pkrate_LAMBDA-lambda-min_SENS-ElastNetRF.sh
scripts/RUN_TARGET-pkrate_LAMBDA-lambda-min_SENS-SqErrLoss.sh
scripts/RUN_TARGET-pkweek_LAMBDA-lambda-1se.sh
scripts/RUN_TARGET-pkweek_LAMBDA-lambda-min.sh
scripts/RUN_TARGET-pkweek_LAMBDA-lambda-min_SENS-ElastNetRF.sh
scripts/RUN_TARGET-pkweek_LAMBDA-lambda-min_SENS-SqErrLoss.sh
scripts/make_ensemble_cv.R
scripts/make_sens-elastrf_analyses.sh
scripts/make_sens-sqerrloss.sh
scripts/make_standard_analyses.sh
scripts/make_standard_analyses_NoLoess.sh
scripts/submit_jobs.sh
scripts/submit_jobs_1se.sh
scripts/submit_script_template.sh
scripts/submit_script_template_sens-elastrf.sh
scripts/submit_script_template_sens-sqerrloss.sh
scripts/submit_sens-elastnetrf.sh
scripts/submit_sens-sqerrloss.sh
