pipe_infodengue: pipeline used by infodengue
In claudia-codeco/AlertTools: utility functions for the Alerta Dengue System

Description Usage Arguments Value Examples

wrap of functions used by Infodengue.

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

`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.
`nowcasting`	"fixedprob" for static model, "bayesian" for the dynamic model. "none" for not doing nowcast (default)
`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"

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

cidades <- getCidades(uf = "Paraná",datasource = con)
res <- pipe_infodengue(cities = cidades$municipio_geocodigo, cid10 = "A90",
nowcasting="none", dataini= "sinpri", completetail = 0, datarelatorio = 202124)
tail(tabela_historico(res))
# User's parameters (not working)
dd <- read.parameters(cities = c(3200300)) %>% mutate(limiar_epidemico = 100)
res <- pipe_infodengue(cities = dd, cid10 = "A90", 
finalday= "2018-08-12",nowcasting="none")
restab <- tabela_historico(res)