getCases: Get Case Data and aggregate per week and area
In claudia-codeco/AlertTools: utility functions for the Alerta Dengue System

Description Usage Arguments Value Examples

Create weekly time series from case data from server. The source is the SINAN.

getCases(
  cities,
  lastday = Sys.Date(),
  cid10 = "A90",
  dataini = "notific",
  completetail = NA,
  datasource = con
)

`cities`	cities' geocode.
`lastday`	last day. Default is the last available. Format: "yyyy-mm-dd"
`cid10`	cid 10 code. Dengue = "A90" (default), Chik = "A92.0", Zika = "A92.8",
`dataini`	"notific" if data aggregated by notification date or "sinpri" if data aggregated if aggregated by date of first symptoms
`completetail`	if sinan data is older than final_day, fill in the tail with NA (default) or 0.
`datasource`	PostgreSQLConnection to project database.

data.frame with the data aggregated per week according to disease onset date.

NOT USE: con <- dbConnect(RSQLite::SQLite(), "../../AlertaDengueAnalise/mydengue.sqlite")
d <- getCases(cities = 4314902, dataini = "sinpri") # dengue
d <- getCases(cities = 3300936, completetail = 0) # dengue
d <- getCases(cities = 3304557, cid10="A92.0") # chikungunya, until last day available
cid <- getCidades(regional = "Norte",uf = "Rio de Janeiro")
d <- getCases(cities = cid$municipio_geocodigo, datasource = con, dataini = "sinpri") 
tail(d)