Man pages for Skomim/COVID_trajectory_Madison
Used to calculate sub-state metrics relating to the COVID-19 pandemic
| calc_num_tests | INTERNAL function to calculate total tests per county per day |
| calc_pos_neg | INTERNAL function to calculate ingredients for percent... |
| check_nonneg | Checks that input values are non-negative, non-missing... |
| class_burden | Classify population adjusted burden |
| class_trajectory | Classify Trajectory Measure for County Data |
| clean_cli | Clean ESSENCE data for CLI metrics |
| clean_histTable | INTERNAL function to clean case data for metrics |
| clean_hospital | Clean Hospital Data for metric calculation |
| clean_ili | Clean ESSENCE data for ILI metrics |
| clean_reversals | Clean up reversals in daily count time series |
| clean_testing | Internal function to clean testing data |
| clean_total_ed | Clean ESSENCE data for Total ED metrics |
| confirmed_case_composite | Calculate the confirmed case composite summary |
| county_data | County Level Data to Facilitate Metric Calculation and... |
| essence_data | Call ESSENCE API and ingest response as data.frame |
| essence_query | Customize ESSENCE API query |
| fdr_trajectory | Calculates the False Discovery Rate for trajectory p-values |
| fill_dates | Ensure that all units of observation have all dates within... |
| hosp_sim | Fake hospitalization data inspired by the source data for... |
| merge_metric_files | Combine metric data into a single output file |
| OLD_process_confirmed_cases | OBSOLETE - VERSION Process the shaped confirmed case... |
| process_cli | Process the shaped CLI data into a Tableau ready format |
| process_confirmed_cases | Process the shaped confirmed case data.frame into a Tableau... |
| process_hospital | Process the shaped hospital data into a Tableau ready format |
| process_ili | Process the shaped ILI data into a Tableau ready format |
| process_testing | Process the shaped hospital data into a Tableau ready format |
| process_total_ed | Process the shaped Total Emergency Department Visit data into... |
| pull_essence | Pulls Essence Data for 3 metrics: CLI, ILI, Total ED Visits |
| pull_histTable | Pull down DHS COVID-19 Historical Data Table |
| pull_hospital | Imports Hospitalization file produced from EM Resource |
| pull_testing | Pull data from WEDSS for Testing Metrics |
| pull_wedss | Pull Confirmed Case data from WEDSS |
| pval_trajectory | Calculate p-value of trajectory current counts vs prior... |
| rev_cusum_lcl | Calculates lower control limits for the reverse cusum control... |
| rev_cusum_ucl | Calculates upper control limits for the reverse cusum control... |
| rolling_week | Calculates rolling weeks backward from the end_date. |
| score_burden | calculate the burden |
| score_trajectory | Trajectory Measure for Count Data |
| shape_case_data | Reshape confirmed case data for producing Tableau extracts |
| shape_cli_data | Shape CLI data |
| shape_hospital_data | Shape EM Resource summary data for metric calculations |
| shape_ili_data | Shape ILI data |
| shape_testing_data | Shape Testing summary data for metric calculations |
| shape_total_ed_data | Shape Total Emergency Department Visits data |
