getCases: Get Case Data and aggregate per week and area

In AlertaDengue/AlertTools: utility functions for the Infodengue Alert System

Get Case Data and aggregate per week and area

Description

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

Usage

getCases(
  cities,
  lastday = Sys.Date(),
  firstday = as.Date("2018-01-01"),
  cid10 = "A90",
  dataini = "notific",
  completetail = NA,
  type = "notified",
  datasource = con
)

Arguments

cities	cities' geocode.
lastday	last day. Default is the last available. Format: "yyyy-mm-dd"
firstday	is the first date of the time series to be produced. 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.
type	case definition. Default = "notified". Other options: "probable", "lab_confirmed", "all". All means returning the three counts.
datasource	PostgreSQLConnection to project database.
returndata	TRUE if returns individual data as well.

Value

data.frame with the data aggregated per week according to disease onset date. Notice that the names of the columns and the number of columns will change according to type. To recover the original function behavior, use the default type.

Examples

NOT USE: con <- dbConnect(RSQLite::SQLite(), "../../AlertaDengueAnalise/mydengue.sqlite")
d <- getCases(cities =  3106200, dataini = "sinpri", type = "all") # 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 = 3304557, firstday = as.Date("2023-01-01"),dataini = "sinpri") 
tail(d)

AlertaDengue/AlertTools documentation built on Nov. 27, 2024, 11:55 p.m.