Man pages for reichlab/2017-2018-cdc-flu-contest
code for cdc flu contest 2017-2018

assemble_predictionsAssemble leave-one-season-out or test phase predictions made...
assemble_stacking_inputsAssemble a data frame of inputs to stacking
calc_median_from_binned_probsCalcluation of median value from binned probability...
cdcFlu20172018cdcFlu20172018 - Code and submissions for 2017-2018 CDC flu...
compute_competition_log_scoreCalculate "log scores" for the purpose of the competition -...
download_and_preprocess_flu_dataDownload and preprocess the latest CDC flu data, both...
download_and_preprocess_state_flu_dataDownload and preprocess the latest CDC flu data, state-level
fit_kde_log_peak_week_incEstimate KDE for LOG peak week incidence
fit_kde_onset_weekEstimate KDE for onset week
fit_kde_peak_weekEstimate KDE for peak week
fit_kde_weekly_incFit a GAM for weekly incidence
fit_kernel_smoothed_stacked_model_fixed_bwEstimate weights for a linear combination of predictive...
fit_region_kdesFits and saves KDE models for all region-year combinations
fit_region_sarimaEstimate SARIMA model using data up to but not including...
fit_stacked_modelFit a stacking model that assigns weights to component models...
fit_unregularized_stacked_modelEstimate "optimal" unregularized weights for a linear...
flu_dataInfluenza incidence in the US (1997 - 2016)
flu_onset_baselinesFlu season "onset thresholds" from the US CDC.
get_inc_binreturn the bin name for a given incidence
get_initial_rng_substreamGet the initial rng substream for an rstream object. Should...
get_log_scores_via_direct_simulationGet log scores and full predictive distributions for each...
get_log_scores_via_trajectory_simulationGet log scores and full predictive distributions for each...
get_num_MMWR_weeks_in_first_season_yearreturn integer that's either 52 or 53: number of weeks in the...
get_num_MMWR_weeks_in_yearreturn integer that's either 52 or 53: number of MMWR weeks...
get_observed_seasonal_quantitiesCompute season onset, peak week, and peak incidence
get_official_observed_seasonal_quantitiesCompute season onset, peak week, and peak incidence
get_onset_baselineGet the onset baseline for a combination of region and season
get_onset_weekUtility function to compute onset week based on a trajectory...
get_partially_revised_ilinetWrapper function around epiforecast::mimicPastEpidataDF to...
get_rng_substreamGet the rng substream for an rstream object corresponding to...
get_submission_one_region_via_trajectory_simulationGet log scores and full predictive distributions for each...
get_submission_via_trajectory_simulationGet log scores and full predictive distributions for each...
logspace_addCalculate log(exp(logx) + exp(logy)) in a somewhat...
logspace_subCalculate log(exp(logx) - exp(logy)) in a somewhat...
logspace_sub_matrix_rowsCalculate logspace difference of matrix rows in a somewhat...
logspace_sumCalculate log(sum(exp(logx))) in a somewhat numerically...
logspace_sum_matrix_rowsCalculate logspace summation of matrix rows in a somewhat...
make_one_kde_prediction_fileWrapper for prediction of a single time-point from KDE fits
make_predictions_dataframeHelper function to standardize creation of empty prediction...
make_predictions_plotsMake plots of prediction submissions for flu contest: so far,...
my_plot_weekaheadPlots Week Ahead Forecasts
predict_kde_log_peak_week_incCompute predictive distribution for peak week incidence from...
predict_kde_log_weekly_incCompute predictive distribution for weekly incidence from GAM...
predict_kde_onset_weekFunctions for predicting from KDE fits
predict_kde_peak_weekCompute predictive distribution for peak week from KDE fit
predict_region_kdeWrapper for prediction and evaluation of KDE fits
sample_predictive_trajectories_arimaSimulate predictive trajectories from an ARIMA model
sample_predictive_trajectories_arima_wrapperA wrapper around sample_predictive_trajectories_arima...
season_week_to_year_weekConvert season week to year week
simulate_trajectories_kcdeSimulate predictive distributions from KCDE/copulas model;...
weighted_combine_predictionsCompute a weighted combination of prediction results
year_week_to_season_weekConvert year week to season week
reichlab/2017-2018-cdc-flu-contest documentation built on April 23, 2018, 2:23 a.m.