Man pages for CBDRH/covidrecon
Pulls and Analyses COVID data
| add_country_hit_limit | Add a column that indicates when a country hits a limit of... |
| add_country_label | Add a country label for plotting |
| add_country_row_id | Add row ID for each country from start date |
| add_covid_change_point | Adds changepoint date based on 'changepoint.np::cpt.np' |
| add_days_since_limit | Add a column of the days since some limit of cumulative cases... |
| add_instant_reproduction | Add instant reproduction number measures to provided covid19... |
| add_weekly_avg | Add Weekly average summary, for each country |
| augment_estimate_repro | Tidies output of 'estimate_repro_all' |
| country_repro_errors | Extract (any) errors from 'estimate_repro_all' |
| covid_change_point | Calculate changepoint date using 'changepoint::cpt.meanvar' |
| covid_ecdc | Download raw COVID19 data from European CDC |
| covid_estimate_repro | Fit EpiEstim::estimate_R to covid19 data |
| covid-estimate-repro | Fits instant reproduction for each country |
| covid_high_incidence | Return only countries that have more than some limit |
| covid_highlight_australia_plus | Add alpha column which will highlight australia foremost,... |
| covid_jhu | Pulls and tidies the latest covid19 data |
| covid_jhu_clean_names | clean variable names of covid19 raw data (from 'covid_read') |
| covid_jhu_filter_countres | Filter covid countries to provided countries |
| covid_jhu_pivot_longer | pivots the covid19 data into longer form |
| covid_jhu_read | read in raw covid19 data |
| covid_latest | Pull latest covid19 data from European CDC |
| covid_prepare_estimate_repro | Prepare covid19 data for estimating instant repro number |
| covid_summarise_doubling | Calculate the time to double covid19 data |
| diff_days | Difference in days between two dates |
| effective-repro | Plot effective reproduction number |
| extract_change_point_mean_var | Extract changepoint |
| extract_first_np_change_point | Extract non-parametric changepoint |
| filter_country_over_limit | Filter data to only include countries that have more than a... |
| geom_covid_country_label | Adds nice country labels to ggplot, based on... |
| gg-covid | misc-ggplot funs for covid19 |
| gg_covid_cumulative_cases_deaths_exceed_limit | Base plot for creating cumulative cases vs deaths of covid19... |
| gg_covid_cumulative_exceed_limit | Base plot for creating cumulative cases of covid19 data |
| gg_covid_incidence_exceed_limit | Base plot for creating incident cases chart of covid19 data |
| gg_effective_repro_incidence_patchwork | Effective Reproductive pathwork |
| gt-zero | Determine when all numbers in a vector are greater than zero |
| patch_data | Patch the case records for China and Italy |
| pipe | Pipe operator |
| pluck_latest_ecdc | Pluck the latest ecdc data |
| summarise_country_over_limit | Create a summary for each country, and a flag of whether they... |
| summarise_covid_global | Summarise covid19 data to cases over time globally |
| tidy_repro_estimate | Tidies up output from 'EpiEstim::estimate_R' |
| try_ecdc | Downloads both yesterday and today's COVID19 data |
