Man pages for claudia-codeco/AlertTools
utility functions for the Alerta Dengue System
| adjustIncidence | Correct incidence data with notification delay (nowcasting). |
| AlertTools-package | utility functions for the Alerta Dengue System |
| applyGenTimeDist | Calculate matrix of generation time distribution for cities... |
| applymem | Get epidemic thresholds for a list of cities |
| bayesnowcasting | Correct incidence data with notification delay (nowcasting). |
| bestWU | Chooses the most updated meteorological data for a city from... |
| data2SE | Define Epidemiological Week. |
| daySEday | Return the first day of the Epidemiological Week and... |
| DenguedbConnect | Returns the connection to the database. |
| episem | Define Epidemiological Week. |
| epiYear | Define Epidemiological Year. |
| fouralert | Define conditions to issue a four level alert... |
| GenTimeDist | Calculates temperature dependent generation time distribution |
| geraMapa | Plot the alert map for any state. |
| getCases | Get Case Data and aggregate per week and area |
| getCasesinRio | Get cases from an APS in Rio de Janeiro and aggregate them... |
| getCidades | get list of cities. |
| getdelaydata | Get delay data for one or more cities for delay analysis |
| getRegionais | get list of regionais. |
| getTweet | Get Tweeter Data |
| getWU | Get Climate Data |
| getWUstation | get meteorological stations |
| infodengue_apply_mem | infodengue_apply_mem —– Function to apply MEM algorithm to... |
| insert_city_infodengue | Initial setup of a new city in the alerta system. Insert into... |
| lastDBdate | Returns the most recent date present in the database table. |
| lastepiweek | lastepiweek ——– |
| map_Rio | Plot the alert map for Rio de Janeiro city. |
| nafill | methods to substitute NAs. Use the function na.approx from... |
| pipe_infodengue | pipeline used by infodengue |
| pipe_infodengue_intra | 4 level alert Green-Yellow-Orange-Red for partitions within... |
| plot_alerta | Plot the time series of infodengue's alert levels for one or... |
| plot_alertaRio | Plot the time series of alerts for each APS. Specific for the... |
| read.cases | Function to extract case count for covered municipalities |
| read.parameters | Get city-level alert parameters for the infodengue pipeline. |
| Rt | Computes the effective reproductive number using alternative... |
| Rtoriginal | Computes the effective reproductive number using a Alerta's... |
| SE2date | Return the first day of the Epidemiological Week |
| seqSE | Sequence of epidemiological weeks. |
| setCriteria | Define rules to issue a four level alert... |
| setWUstation | set meteorological stations |
| sevendigitgeocode | convert 6 to 7 digits geocodes. |
| tabela_historico | Convert the alert object into a data.frame and calculate... |
| tabela_historico_intra | Convert the alert object into a data.frame and calculate... |
| temp.predict | Fit arima to fill in missing data at the end of temperature... |
| write_alerta | Write historico_alerta into the database. |
| write_alerta_local | Write historico_alerta into the local SQLite database. |
| write_alertaRio | Write the Rio de janeiro alert into the database. |
| write_parameters | City's parameterization. |
