Skip to content

Commit

Permalink
Fetch SINAN-Malaria data
Browse files Browse the repository at this point in the history
  • Loading branch information
@rfsaldanha
rfsaldanha committed Sep 14, 2021
1 parent 81b3e33 commit bf00c94
Show file tree
Hide file tree
Showing 2 changed files with 12 additions and 6 deletions.
16 changes: 11 additions & 5 deletions R/fetch_datasus.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
#'
#' A specific UF or a vector of UFs can be informed using the following abbreviations: "AC", "AL", "AP", "AM", "BA", "CE", "DF", "ES", "GO", "MA", "MT", "MS", "MG", "PA", "PB", "PR", "PE", "PI", "RJ", "RN", "RS", "RO", "RR", "SC", "SP", "SE", "TO".
#'
#' The following systems are implemented: "SIH-RD", "SIH-RJ", "SIH-SP", "SIH-ER", "SIM-DO", "SIM-DOFET", "SIM-DOEXT", "SIM-DOINF", "SIM-DOMAT", "SINASC", "CNES-LT", "CNES-ST", "CNES-DC", "CNES-EQ", "CNES-SR", "CNES-HB", "CNES-PF", "CNES-EP", "CNES-RC", "CNES-IN", "CNES-EE", "CNES-EF", "CNES-GM", "SIA-AB", "SIA-ABO", "SIA-ACF", "SIA-AD", "SIA-AN", "SIA-AM", "SIA-AQ", "SIA-AR", "SIA-ATD", "SIA-PA", "SIA-PS", "SIA-SAD", "SINAN-DENGUE-FINAL", "SINAN-DENGUE-PRELIMINAR", "SINAN-CHIKUNGUNYA-FINAL", "SINAN-CHIKUNGUNYA-PRELIMINAR", "SINAN-ZIKA-FINAL", "SINAN-ZIKA-PRELIMINAR".
#' The following systems are implemented: "SIH-RD", "SIH-RJ", "SIH-SP", "SIH-ER", "SIM-DO", "SIM-DOFET", "SIM-DOEXT", "SIM-DOINF", "SIM-DOMAT", "SINASC", "CNES-LT", "CNES-ST", "CNES-DC", "CNES-EQ", "CNES-SR", "CNES-HB", "CNES-PF", "CNES-EP", "CNES-RC", "CNES-IN", "CNES-EE", "CNES-EF", "CNES-GM", "SIA-AB", "SIA-ABO", "SIA-ACF", "SIA-AD", "SIA-AN", "SIA-AM", "SIA-AQ", "SIA-AR", "SIA-ATD", "SIA-PA", "SIA-PS", "SIA-SAD", "SINAN-DENGUE-FINAL", "SINAN-DENGUE-PRELIMINAR", "SINAN-CHIKUNGUNYA-FINAL", "SINAN-CHIKUNGUNYA-PRELIMINAR", "SINAN-ZIKA-FINAL", "SINAN-ZIKA-PRELIMINAR", "SINAN-MALARIA-FINAL", "SINAN-MALARIA-PRELIMINAR".
#'
#' @param year_start,year_end numeric. Start and end year of files in the format yyyy.
#' @param month_start,month_end Numeric. Start and end month in the format mm. Those parameters are only used with the healh information systems SIH, CNES and SIA. There parameter are ignored if the information health system is SIM or SINASC.
Expand Down Expand Up @@ -45,15 +45,15 @@ fetch_datasus <- function(year_start, month_start, year_end, month_end, uf="all"
sisSINASC <- c("SINASC")
sisCNES <- c("CNES-LT", "CNES-ST", "CNES-DC", "CNES-EQ", "CNES-SR", "CNES-HB","CNES-PF","CNES-EP","CNES-RC","CNES-IN","CNES-EE","CNES-EF","CNES-GM")
sisSIA <- c("SIA-AB", "SIA-ABO", "SIA-ACF", "SIA-AD", "SIA-AN", "SIA-AM", "SIA-AQ", "SIA-AR", "SIA-ATD", "SIA-PA", "SIA-PS", "SIA-SAD")
sisSINAN <- c("SINAN-DENGUE-FINAL", "SINAN-DENGUE-PRELIMINAR", "SINAN-CHIKUNGUNYA-FINAL", "SINAN-CHIKUNGUNYA-PRELIMINAR", "SINAN-ZIKA-FINAL", "SINAN-ZIKA-PRELIMINAR")
sisSINAN <- c("SINAN-DENGUE-FINAL", "SINAN-DENGUE-PRELIMINAR", "SINAN-CHIKUNGUNYA-FINAL", "SINAN-CHIKUNGUNYA-PRELIMINAR", "SINAN-ZIKA-FINAL", "SINAN-ZIKA-PRELIMINAR", "SINAN-MALARIA-FINAL", "SINAN-MALARIA-PRELIMINAR")
available_information_system <- c(sisSIH, sisSIM, sisSINASC, sisCNES, sisSIA, sisSINAN)
if(!(information_system %in% available_information_system)) stop("Health informaton system unknown.")

# Create dates for verification
if(substr(information_system,1,3) == "SIH" | substr(information_system,1,4) == "CNES" | substr(information_system,1,3) == "SIA"){
date_start <- as.Date(paste0(year_start,"-",formatC(month_start, width = 2, format = "d", flag = "0"),"-","01"))
date_end <- as.Date(paste0(year_end,"-",formatC(month_end, width = 2, format = "d", flag = "0"),"-","01"))
} else if(substr(information_system,1,3) == "SIM" | information_system == "SINASC" | information_system == "SINAN-DENGUE-FINAL" | information_system == "SINAN-DENGUE-PRELIMINAR" | information_system == "SINAN-CHIKUNGUNYA-FINAL" | information_system == "SINAN-CHIKUNGUNYA-PRELIMINAR" | information_system == "SINAN-ZIKA-FINAL" | information_system == "SINAN-ZIKA-PRELIMINAR"){
} else if(substr(information_system,1,3) == "SIM" | information_system == "SINASC" | information_system == "SINAN-DENGUE-FINAL" | information_system == "SINAN-DENGUE-PRELIMINAR" | information_system == "SINAN-CHIKUNGUNYA-FINAL" | information_system == "SINAN-CHIKUNGUNYA-PRELIMINAR" | information_system == "SINAN-ZIKA-FINAL" | information_system == "SINAN-ZIKA-PRELIMINAR" | information_system == "SINAN-MALARIA-FINAL" | information_system == "SINAN-MALARIA-PRELIMINAR"){
date_start <- as.Date(paste0(year_start,"-01-01"))
date_end <- as.Date(paste0(year_end,"-01-01"))
}
Expand All @@ -68,7 +68,7 @@ fetch_datasus <- function(year_start, month_start, year_end, month_end, uf="all"
} else if(substr(information_system,1,3) == "SIM" | information_system == "SINASC"){
dates <- seq(date_start, date_end, by = "year")
dates <- lubridate::year(dates)
} else if(information_system == "SINAN-DENGUE-FINAL" | information_system == "SINAN-DENGUE-PRELIMINAR" | information_system == "SINAN-CHIKUNGUNYA-FINAL" | information_system == "SINAN-CHIKUNGUNYA-PRELIMINAR" | information_system == "SINAN-ZIKA-FINAL" | information_system == "SINAN-ZIKA-PRELIMINAR"){
} else if(information_system == "SINAN-DENGUE-FINAL" | information_system == "SINAN-DENGUE-PRELIMINAR" | information_system == "SINAN-CHIKUNGUNYA-FINAL" | information_system == "SINAN-CHIKUNGUNYA-PRELIMINAR" | information_system == "SINAN-ZIKA-FINAL" | information_system == "SINAN-ZIKA-PRELIMINAR" | information_system == "SINAN-MALARIA-FINAL" | information_system == "SINAN-MALARIA-PRELIMINAR"){
dates <- seq(date_start, date_end, by = "year")
dates <- lubridate::year(dates)
dates <- substr(dates, 3, 4)
Expand Down Expand Up @@ -223,6 +223,12 @@ fetch_datasus <- function(year_start, month_start, year_end, month_end, uf="all"
} else if(information_system == "SINAN-ZIKA-PRELIMINAR"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
files_list <- paste0(url,"ZIKA", file_extension)
} else if(information_system == "SINAN-MALARIA-FINAL"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
files_list <- paste0(url,"MALA", file_extension)
} else if(information_system == "SINAN-MALARIA-PRELIMINAR"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
files_list <- paste0(url,"MALA", file_extension)
}

# Dowload files
Expand All @@ -244,7 +250,7 @@ fetch_datasus <- function(year_start, month_start, year_end, month_end, uf="all"

# Merge files
if(nrow(partial) > 0){
if(!all(vars %in% names(partial))) stop("One or more variables names are unknow. Typo?")
if(!all(vars %in% names(partial))) stop("One or more variables names are unknown. Typo?")
if(is.null(vars)){
data <- dplyr::bind_rows(data, partial)
} else {
Expand Down
2 changes: 1 addition & 1 deletion man/fetch_datasus.Rd
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

0 comments on commit bf00c94

Please sign in to comment.