pipe_infodengue: pipeline used by infodengue

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

pipeline used by infodengue

Description

wrap of functions used by Infodengue.

Usage

pipe_infodengue(
  cities,
  cid10 = "A90",
  datarelatorio,
  finalday = Sys.Date(),
  iniSE = 201001,
  nowcasting = "none",
  narule = NULL,
  writedb = FALSE,
  datasource = con,
  completetail = NA,
  dataini = "notific"
)

Arguments

cities	In general, a vector of 7-digit geocodes. If it is a data.frame containing geocodes and all parameters, these will replace the database's parameters.
cid10	default is A90 (dengue). Chik = A92.0, Zika = A92.8
datarelatorio	epidemiological week
finalday	if provided, uses only disease data reported up to that day
iniSE	first date of the disease data. Default = 201501. Minimum = 201001.
narule	how to treat missing climate data. Do nothing (default), "zero" fills with zeros, "linear" for linear interpolation, "arima" for inter and extrapolation.
writedb	TRUE if it should write into the database, default is FALSE.
datasource	posgreSQL connection to project's database
completetail	if sinan data is older than final_day, fill in the tail with NA (default) or 0.
dataini	"notif" (default) or "sinpri"
"bayesian"	for the dynamic model, "none" for not doing nowcast (default)

Value

data.frame with the week condition and the number of weeks within the last lag weeks with conditions = TRUE.

Examples

cidades <- getCidades(uf = "Rio de Janeiro",datasource = con)
t1 <- Sys.time()
res <- pipe_infodengue(cities = 3304557, cid10 = "A90",
nowcasting="bayesian", dataini= "sinpri", completetail = 0, datarelatorio = 202419)
tail(tabela_historico(res))
t2 <- Sys.time()
message(paste("total time was", t2-t1))
tail(tabela_historico(res))
res <- pipe_infodengue(cities = 4209102 , cid10 = "A90",
nowcasting="none", dataini= "sinpri", completetail = 0,
datarelatorio = 202408)

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