Man pages for claudia-codeco/AlertTools
utility functions for the Alerta Dengue System

adjustIncidenceAdjust incidence data correcting for the notification delay.
alertaRio4 level alert Green-Yellow-Orange-Red for Rio de Janeiro.
AlertTools-packageutility functions for the Alerta Dengue System
applymemGet epidemic thresholds for a list of cities
data2SEDefine Epidemiological Week
delaycalcOrganize delay data for analysis and produce a nice plot.
DenguedbConnectReturns the connection to the database.
episemDefine Epidemiological Week
fitDelay.inlaFit INLA model to notification delay.
fitDelayModelFit lognormal model to the notification delay
fouralertDefine conditions to issue a four level alert...
geraMapaPlot the alert map for any state.
getCasesGet Case Data and aggregate per week and area
getCasesinRioGet cases from an APS in Rio de Janeiro and aggregate them...
getCidadesget list of cities.
getdelaydataGet delay data for one or more cities for delay analysis
getmergeInfodataGet and merge cases, tweets and climate data.
getRegionaisget list of regionais.
getTweetGet Tweeter Data
getWUGet Climate Data
info.dengue.apply.memFunction to apply MEM algorithm to generate pre-epidemic,...
insertCityinAlertaInitial setup of a new city in the alerta system.
isOrangeRaise orange alert if sustained transmission is detected.
isRedRaise red alert if incidence reaches above a threshold.
lastDBdateReturns the most recent date present in the database table.
lastepiweeklastepiweek ——–
map.RioPlot the alert map for Rio de Janeiro city.
mergedataMerge cases, tweets and climate data.
mergedata2Define conditions to issue a 4 level alert...
nafillmethods to substitute NAs.Use the function na.approx from...
plot.alertaPlot the time series of warnings.
plot.inla.replot delay and time random effects
prob.incposterior distribution of the incidence
read.casesFunction to extract case count for covered municipalities
read.parametersGet city alert parameters.
RtComputes the effective reproductive number using alternative...
RtoriginalComputes the effective reproductive number using a Alerta's...
SE2dateReturn the first day of the Epidemiological Week
seqSESequence of epidemiological weeks
sevendigitgeocodeconvert 6 to 7 digits geocodes.
temp.predictFit arima to fill in missing data at the end of temperature...
twoalertDefine conditions to issue a 2 level alert Green/Yellow.
update.alertaDefine conditions to issue a 4 level alert...
updateDelayModelUpdate notification delay model.
write.alertaWrite the alert object into the database.
write.alertaRioWrite the Rio de janeiro alert into the database.
write.parametersCity's parameterization.
claudia-codeco/AlertTools documentation built on June 21, 2018, 7:15 p.m.