R/fetch_datasus.R
In rfsaldanha/microdatasus: Download and preprocess DataSUS files
Defines functions
fetch_datasus
Documented in
fetch_datasus
#' Fetch and read microdata files from DataSUS
#'
#' \code{fetch_datasus} downloads microdata (DBC) files from DataSUS and reads them.
#'
#' This function downloads DBC files from DataSUS following parameters about start date, end date, UF and health information system abbreviation. After the download process, the files are merged into a unique \code{data.frame} object.
#'
#' 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", "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.
#' @param uf an optional string or a vector of strings. By default all UFs ("Unidades Federativas") are download. See \emph{Details}.
#' @param information_system string. The abbreviation of the health information system to be accessed. See \emph{Details}.
#' @param vars an optional string or a vector of strings. By default, all variables read and stored, unless a list of desired variables is informed by this parameter.
#' @param stop_on_error logical. If TRUE, the download process will be stopped if an error occurs.
#' @param timeout numeric (seconds). Sets a timeout tolerance for downloads, usefull on large files and/or slow connections. Defaults to 240 seconds.
#' @param track_source logical. If `TRUE`, adds a column called `source` with the downloaded file name.
#'
#' @section Warning:
#' A Internet connection is needed to use this function.
#'
#' The year and month used to download the files regards the processing month and year of the cases by DataSUS.
#'
#' The UF regards where the cases were processed by DataSUS.
#'
#' The files are downloaded to a temporary folder and deleted after the reading process.
#'
#' @examples \dontrun{
#' fetch_datasus(year_start = 2010, year_end = 2011,
#' information_system = "SIM-DO")
#'
#' fetch_datasus(year_start = 2014, year_end = 2014,
#' information_system = "SIM-DO",
#' vars = c("CODMUNRES", "DTOBITO", "CAUSABAS"))
#'
#' fetch_datasus(year_start = 2014, month_start = 1,
#' year_end = 2014, month_end = 2,
#' uf = c("RJ", "MG", "SP", "ES"),
#' information_system = "SIH-RD")
#' }
#' @export
fetch_datasus <- function(year_start, month_start = NULL, year_end, month_end = NULL, uf = "all", information_system, vars = NULL, stop_on_error = FALSE, timeout = 240, track_source = FALSE){
# Resets original timeout option on function exit
original_time_option <- getOption("timeout")
on.exit(options(timeout = original_time_option))
# Set new timeout
options(timeout = timeout)
# Assert arguments
# Health information system
sisSIH <- c("SIH-RD","SIH-RJ","SIH-SP","SIH-ER")
sisSIM <- c("SIM-DO", "SIM-DOFET","SIM-DOEXT","SIM-DOINF","SIM-DOMAT")
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", "SINAN-CHIKUNGUNYA", "SINAN-ZIKA", "SINAN-MALARIA")
available_information_system <- c(sisSIH, sisSIM, sisSINASC, sisCNES, sisSIA, sisSINAN)
checkmate::assert_choice(x = information_system, choices = available_information_system)
# Year and month
checkmate::assert_numeric(x = year_start, lower = 1996, null.ok = FALSE)
checkmate::assert_numeric(x = year_end, lower = 1996, null.ok = FALSE)
checkmate::assert_numeric(x = month_start, lower = 1, upper = 12, null.ok = TRUE)
checkmate::assert_numeric(x = month_end, lower = 1, upper = 12, null.ok = TRUE)
# 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" | information_system == "SINAN-CHIKUNGUNYA" | information_system == "SINAN-ZIKA" | information_system == "SINAN-MALARIA"){
date_start <- as.Date(paste0(year_start,"-01-01"))
date_end <- as.Date(paste0(year_end,"-01-01"))
}
# Check dates
if(date_start > date_end){
cli::cli_abort(message = "Start date must be greather than end date.")
}
# Check UF
ufs <- c("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")
checkmate::assert_choice(x = uf, choices = c("all",ufs))
# Check UF for SINAN files
if(information_system %in% sisSINAN & uf[1] != "all"){
cli::cli_alert_info("SINAN files are not available per UF. Ignoring argument 'uf' and downloading data.")
}
# Check local Internet connection
local_internet <- curl::has_internet()
if(local_internet == TRUE){
cli::cli_alert_info("Your local Internet connection seems to be ok.")
} else {
cli::cli_alert_warning("It appears that your local Internet connection is not working. Can you check?")
return(NULL)
}
# Check DataSUS FTP server
datasus_ftp_connection <- RCurl::url.exists("ftp.datasus.gov.br", timeout.ms = 5000)
if(datasus_ftp_connection == TRUE){
cli::cli_alert_info("DataSUS FTP server seems to be up and reachable.")
cli::cli_alert_info("Starting download...")
} else {
cli::cli_alert_warning("It appears that DataSUS FTP is down or not reachable.")
return(NULL)
}
# Prepare sequence of dates
if(substr(information_system,1,3) == "SIH" | substr(information_system,1,4) == "CNES" | substr(information_system,1,3) == "SIA"){
dates <- seq(date_start, date_end, by = "month")
dates <- paste0(substr(lubridate::year(dates),3,4),formatC(lubridate::month(dates), width = 2, format = "d", flag = "0"))
} else if(substr(information_system,1,3) == "SIM" | information_system == "SINASC" | information_system == "SINAN-DENGUE" | information_system == "SINAN-CHIKUNGUNYA" | information_system == "SINAN-ZIKA" | information_system == "SINAN-MALARIA"){
dates <- seq(date_start, date_end, by = "year")
dates <- lubridate::year(dates)
}
# Prepare ufs
lista_uf <- vector()
if(uf[1] == "all"){
lista_uf <- ufs
} else {
lista_uf = uf
}
# Create files list for download
if(information_system == "SIM-DO") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DORES/"
avail_geral <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
avail_prelim <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_geral],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_prelim],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOFET") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOFET", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOFET", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOFET data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOFET", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOFET", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOEXT") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOEXT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOEXT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOEXT data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOEXT", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOEXT", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOINF") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOINF", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOINF", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOINF data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOINF", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOINF", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOMAT") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOMAT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOMAT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOMAT data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOMAT", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOMAT", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-RD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RD", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RD", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"RD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"RD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-RJ") {
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RJ", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RJ", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about preliminary data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"RJ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"RJ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-SP") {
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("SP", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("SP", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about preliminary data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"SP", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"SP", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-ER") {
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ER", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ER", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about preliminary data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ER", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ER", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINASC") {
# Available dates
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINASC/1994_1995/Dados/DNRES/"
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINASC/1996_/Dados/DNRES/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINASC/PRELIM/DNRES/"
avail_antigo <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 6, stop = 9))
avail_atual <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
avail_prelim <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_antigo, avail_atual, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_antigo, avail_atual, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_antigo, avail_atual, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates are from old folders and and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"DNR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"DN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list_3 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_prelim],".dbc")))
}
files_list <- c(files_list_1, files_list_2, files_list_3)
} else if(information_system == "CNES-LT"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/LT/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"LT", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-ST"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/ST/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"ST", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-DC"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/DC/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"DC", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EQ"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EQ/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EQ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-SR"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/SR/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"SR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-HB"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/HB/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"HB", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-PF"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/PF/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"PF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EP"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EP/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EP", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-RC"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/RC/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"RC", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-IN"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/IN/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"IN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EE"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EE/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EE", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EF"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EF/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-GM"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/GM/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"GM", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "SIA-AB"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AB", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AB", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AB", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AB", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-ABO"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ABO", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ABO", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ABO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ABO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-ACF"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ACF", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ACF", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ACF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ACF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AD", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AD", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AN"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AN", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AN", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AM"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AM", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AM", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AM", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AM", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AQ"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AQ", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AQ", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AQ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AQ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AR"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AR", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AR", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-ATD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ATD", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ATD", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ATD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ATD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-PA"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PA", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 9))
avail_atual <- gsub(pattern = "\\.", replacement = "", x = avail_atual)
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PA", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 9))
avail_antigo <- gsub(pattern = "\\.", replacement = "", x = avail_antigo)
# Check if required dates are available
if(!all(dates %in% c(substr(x = avail_atual, start = 0, stop = 4), substr(x = avail_antigo, start = 0, stop = 4)))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(substr(x = avail_atual, start = 0, stop = 4), substr(x = avail_antigo, start = 0, stop = 4))], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- c(avail_atual, avail_antigo)[substr(x = c(avail_atual, avail_antigo), start = 0, stop = 4) %in% dates]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"PA", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"PA", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-PS"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PS", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 9))
avail_atual <- gsub(pattern = "\\.", replacement = "", x = avail_atual)
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PS", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 9))
avail_antigo <- gsub(pattern = "\\.", replacement = "", x = avail_antigo)
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"PS", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"PS", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-SAD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^SAD", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 9))
avail_atual <- gsub(pattern = "\\.", replacement = "", x = avail_atual)
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^SAD", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 9))
avail_antigo <- gsub(pattern = "\\.", replacement = "", x = avail_antigo)
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"SAD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"SAD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-DENGUE"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DENGBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DENGBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DENGUE data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DENGBR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DENGBR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-CHIKUNGUNYA"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("CHIKBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("CHIKBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("CHIKUNGUNYA data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"CHIKBR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"CHIKBR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-ZIKA"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ZIKABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ZIKABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("ZIKA data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"ZIKABR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"ZIKABR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-MALARIA"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("MALABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("MALABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("MALARIA data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"MALABR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"MALABR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
}
# Dowload files
data <- NULL
for(file in files_list){
# Temporary file
temp <- tempfile()
# Empty data.frame
partial <- data.frame()
# Try to download file
tryCatch({
utils::download.file(file, temp, mode = "wb", method = "libcurl")
partial <- read.dbc::read.dbc(temp, as.is = TRUE)
file.remove(temp)
},
error=function(cond) {
cli::cli_alert_info(paste("Something went wrong with this URL:", file))
cli::cli_alert("This can be a problem with the Internet or the file does not exist yet.")
cli::cli_alert("If the file is too big, try to increase the timeout argument value.")
if(stop_on_error == TRUE){
cli::cli_abort("Stopping download.")
}
})
# Merge files
if(nrow(partial) > 0){
if(track_source == TRUE){
partial$source <- basename(file)
}
if(!all(vars %in% names(partial))) cli::cli_abort("One or more variables names are unknown. Typo?")
if(is.null(vars)){
data <- dplyr::bind_rows(data, partial)
} else {
data <- dplyr::bind_rows(data, subset(partial, select = vars))
}
}
}
# Return
return(data)
}
rfsaldanha/microdatasus documentation built on April 13, 2024, 2:25 p.m.
R Package Documentation
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Defines functions fetch_datasus
Documented in fetch_datasus
#' Fetch and read microdata files from DataSUS
#'
#' \code{fetch_datasus} downloads microdata (DBC) files from DataSUS and reads them.
#'
#' This function downloads DBC files from DataSUS following parameters about start date, end date, UF and health information system abbreviation. After the download process, the files are merged into a unique \code{data.frame} object.
#'
#' 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", "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.
#' @param uf an optional string or a vector of strings. By default all UFs ("Unidades Federativas") are download. See \emph{Details}.
#' @param information_system string. The abbreviation of the health information system to be accessed. See \emph{Details}.
#' @param vars an optional string or a vector of strings. By default, all variables read and stored, unless a list of desired variables is informed by this parameter.
#' @param stop_on_error logical. If TRUE, the download process will be stopped if an error occurs.
#' @param timeout numeric (seconds). Sets a timeout tolerance for downloads, usefull on large files and/or slow connections. Defaults to 240 seconds.
#' @param track_source logical. If `TRUE`, adds a column called `source` with the downloaded file name.
#'
#' @section Warning:
#' A Internet connection is needed to use this function.
#'
#' The year and month used to download the files regards the processing month and year of the cases by DataSUS.
#'
#' The UF regards where the cases were processed by DataSUS.
#'
#' The files are downloaded to a temporary folder and deleted after the reading process.
#'
#' @examples \dontrun{
#' fetch_datasus(year_start = 2010, year_end = 2011,
#' information_system = "SIM-DO")
#'
#' fetch_datasus(year_start = 2014, year_end = 2014,
#' information_system = "SIM-DO",
#' vars = c("CODMUNRES", "DTOBITO", "CAUSABAS"))
#'
#' fetch_datasus(year_start = 2014, month_start = 1,
#' year_end = 2014, month_end = 2,
#' uf = c("RJ", "MG", "SP", "ES"),
#' information_system = "SIH-RD")
#' }
#' @export
fetch_datasus <- function(year_start, month_start = NULL, year_end, month_end = NULL, uf = "all", information_system, vars = NULL, stop_on_error = FALSE, timeout = 240, track_source = FALSE){
# Resets original timeout option on function exit
original_time_option <- getOption("timeout")
on.exit(options(timeout = original_time_option))
# Set new timeout
options(timeout = timeout)
# Assert arguments
# Health information system
sisSIH <- c("SIH-RD","SIH-RJ","SIH-SP","SIH-ER")
sisSIM <- c("SIM-DO", "SIM-DOFET","SIM-DOEXT","SIM-DOINF","SIM-DOMAT")
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", "SINAN-CHIKUNGUNYA", "SINAN-ZIKA", "SINAN-MALARIA")
available_information_system <- c(sisSIH, sisSIM, sisSINASC, sisCNES, sisSIA, sisSINAN)
checkmate::assert_choice(x = information_system, choices = available_information_system)
# Year and month
checkmate::assert_numeric(x = year_start, lower = 1996, null.ok = FALSE)
checkmate::assert_numeric(x = year_end, lower = 1996, null.ok = FALSE)
checkmate::assert_numeric(x = month_start, lower = 1, upper = 12, null.ok = TRUE)
checkmate::assert_numeric(x = month_end, lower = 1, upper = 12, null.ok = TRUE)
# 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" | information_system == "SINAN-CHIKUNGUNYA" | information_system == "SINAN-ZIKA" | information_system == "SINAN-MALARIA"){
date_start <- as.Date(paste0(year_start,"-01-01"))
date_end <- as.Date(paste0(year_end,"-01-01"))
}
# Check dates
if(date_start > date_end){
cli::cli_abort(message = "Start date must be greather than end date.")
}
# Check UF
ufs <- c("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")
checkmate::assert_choice(x = uf, choices = c("all",ufs))
# Check UF for SINAN files
if(information_system %in% sisSINAN & uf[1] != "all"){
cli::cli_alert_info("SINAN files are not available per UF. Ignoring argument 'uf' and downloading data.")
}
# Check local Internet connection
local_internet <- curl::has_internet()
if(local_internet == TRUE){
cli::cli_alert_info("Your local Internet connection seems to be ok.")
} else {
cli::cli_alert_warning("It appears that your local Internet connection is not working. Can you check?")
return(NULL)
}
# Check DataSUS FTP server
datasus_ftp_connection <- RCurl::url.exists("ftp.datasus.gov.br", timeout.ms = 5000)
if(datasus_ftp_connection == TRUE){
cli::cli_alert_info("DataSUS FTP server seems to be up and reachable.")
cli::cli_alert_info("Starting download...")
} else {
cli::cli_alert_warning("It appears that DataSUS FTP is down or not reachable.")
return(NULL)
}
# Prepare sequence of dates
if(substr(information_system,1,3) == "SIH" | substr(information_system,1,4) == "CNES" | substr(information_system,1,3) == "SIA"){
dates <- seq(date_start, date_end, by = "month")
dates <- paste0(substr(lubridate::year(dates),3,4),formatC(lubridate::month(dates), width = 2, format = "d", flag = "0"))
} else if(substr(information_system,1,3) == "SIM" | information_system == "SINASC" | information_system == "SINAN-DENGUE" | information_system == "SINAN-CHIKUNGUNYA" | information_system == "SINAN-ZIKA" | information_system == "SINAN-MALARIA"){
dates <- seq(date_start, date_end, by = "year")
dates <- lubridate::year(dates)
}
# Prepare ufs
lista_uf <- vector()
if(uf[1] == "all"){
lista_uf <- ufs
} else {
lista_uf = uf
}
# Create files list for download
if(information_system == "SIM-DO") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DORES/"
avail_geral <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
avail_prelim <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_geral],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_prelim],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOFET") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOFET", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOFET", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOFET data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOFET", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOFET", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOEXT") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOEXT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOEXT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOEXT data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOEXT", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOEXT", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOINF") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOINF", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOINF", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOINF data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOINF", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOINF", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if (information_system == "SIM-DOMAT") {
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/PRELIM/DOFET/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOMAT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DOMAT", tmp)]
tmp <- unique(substr(x = tmp, start = 6, stop = 7))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DOMAT data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DOMAT", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DOMAT", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-RD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RD", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RD", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"RD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"RD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-RJ") {
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RJ", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("RJ", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about preliminary data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"RJ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"RJ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-SP") {
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("SP", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("SP", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about preliminary data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"SP", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"SP", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIH-ER") {
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIHSUS/199201_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ER", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ER", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about preliminary data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ER", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ER", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINASC") {
# Available dates
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINASC/1994_1995/Dados/DNRES/"
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINASC/1996_/Dados/DNRES/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINASC/PRELIM/DNRES/"
avail_antigo <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 6, stop = 9))
avail_atual <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
avail_prelim <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_antigo, avail_atual, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_antigo, avail_atual, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_antigo, avail_atual, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates are from old folders and and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"DNR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"DN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list_3 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_prelim],".dbc")))
}
files_list <- c(files_list_1, files_list_2, files_list_3)
} else if(information_system == "CNES-LT"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/LT/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"LT", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-ST"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/ST/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"ST", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-DC"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/DC/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"DC", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EQ"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EQ/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EQ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-SR"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/SR/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"SR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-HB"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/HB/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"HB", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-PF"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/PF/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"PF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EP"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EP/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EP", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-RC"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/RC/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"RC", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-IN"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/IN/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"IN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EE"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EE/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EE", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-EF"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/EF/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"EF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "CNES-GM"){
url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/CNES/200508_/Dados/GM/"
avail <- unique(substr(x = unlist(strsplit(x = RCurl::getURL(url = url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n")), start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% avail)){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% avail], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% avail]
# File list
files_list <- paste0(url,"GM", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail],".dbc")))
} else if(information_system == "SIA-AB"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AB", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AB", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AB", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AB", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-ABO"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ABO", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ABO", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ABO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ABO", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-ACF"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ACF", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ACF", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ACF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ACF", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AD", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AD", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AN"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AN", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AN", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AN", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AM"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AM", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AM", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AM", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AM", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AQ"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AQ", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AQ", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AQ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AQ", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-AR"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AR", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("AR", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"AR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"AR", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-ATD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ATD", tmp)]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 8))
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ATD", tmp)]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 8))
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"ATD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"ATD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-PA"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PA", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 9))
avail_atual <- gsub(pattern = "\\.", replacement = "", x = avail_atual)
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PA", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 9))
avail_antigo <- gsub(pattern = "\\.", replacement = "", x = avail_antigo)
# Check if required dates are available
if(!all(dates %in% c(substr(x = avail_atual, start = 0, stop = 4), substr(x = avail_antigo, start = 0, stop = 4)))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(substr(x = avail_atual, start = 0, stop = 4), substr(x = avail_antigo, start = 0, stop = 4))], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- c(avail_atual, avail_antigo)[substr(x = c(avail_atual, avail_antigo), start = 0, stop = 4) %in% dates]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"PA", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"PA", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-PS"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PS", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 9))
avail_atual <- gsub(pattern = "\\.", replacement = "", x = avail_atual)
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^PS", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 9))
avail_antigo <- gsub(pattern = "\\.", replacement = "", x = avail_antigo)
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"PS", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"PS", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SIA-SAD"){
# Available dates
atual_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/200801_/Dados/"
antigo_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIASUS/199407_200712/Dados/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = atual_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^SAD", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_atual <- unique(substr(x = tmp, start = 5, stop = 9))
avail_atual <- gsub(pattern = "\\.", replacement = "", x = avail_atual)
tmp <- unlist(strsplit(x = RCurl::getURL(url = antigo_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("^SAD", tmp)]
tmp <- tmp[substr(x = tmp, start = 3, stop = 4) %in% lista_uf]
avail_antigo <- unique(substr(x = tmp, start = 5, stop = 9))
avail_antigo <- gsub(pattern = "\\.", replacement = "", x = avail_antigo)
# Check if required dates are available
if(!all(dates %in% c(avail_atual, avail_antigo))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS (yymm): ", paste0(dates[!dates %in% c(avail_atual, avail_antigo)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_atual, avail_antigo)]
# Message about old data
if(any(valid_dates %in% avail_antigo)){
cli::cli_alert(paste0("The following dates (yymm) are from old folders and may contain incompatible codes (including old ICD codes): ", paste0(valid_dates[valid_dates %in% avail_antigo], collapse = ", "), "."))
}
# File list
files_list_1 <- if(any(valid_dates %in% avail_antigo)){
paste0(antigo_url,"SAD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_antigo],".dbc")))
}
files_list_2 <- if(any(valid_dates %in% avail_atual)){
paste0(atual_url,"SAD", as.vector(sapply(lista_uf, paste0, valid_dates[valid_dates %in% avail_atual],".dbc")))
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-DENGUE"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DENGBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("DENGBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("DENGUE data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"DENGBR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"DENGBR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-CHIKUNGUNYA"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("CHIKBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("CHIKBR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("CHIKUNGUNYA data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"CHIKBR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"CHIKBR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-ZIKA"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ZIKABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("ZIKABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("ZIKA data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"ZIKABR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"ZIKABR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
} else if(information_system == "SINAN-MALARIA"){
# Available dates
geral_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/FINAIS/"
prelim_url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SINAN/DADOS/PRELIM/"
tmp <- unlist(strsplit(x = RCurl::getURL(url = geral_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("MALABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_geral <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
tmp <- unlist(strsplit(x = RCurl::getURL(url = prelim_url, ftp.use.epsv = TRUE, dirlistonly = TRUE), split = "\n"))
tmp <- tmp[grep("MALABR", tmp)]
tmp <- unique(substr(x = tmp, start = 7, stop = 8))
avail_prelim <- sort(as.numeric(ifelse(test = substr(tmp, 0, 1) == "9", yes = paste0("19", tmp), no = paste0("20", tmp))))
# Check if required dates are available
if(!all(dates %in% c(avail_geral, avail_prelim))){
cli::cli_alert(paste0("The following dates are not availabe at DataSUS: ", paste0(dates[!dates %in% c(avail_geral, avail_prelim)], collapse = ", "), ". Only the available dates will be downloaded."))
}
valid_dates <- dates[dates %in% c(avail_geral, avail_prelim)]
# Message about preliminary data
if(any(valid_dates %in% avail_prelim)){
cli::cli_alert(paste0("The following dates are preliminar: ", paste0(valid_dates[valid_dates %in% avail_prelim], collapse = ", "), "."))
}
# File list
if(uf != "Any"){
cli::cli_alert(paste0("MALARIA data is not available by UF. Downloading all data available instead. "))
}
files_list_1 <- if(any(valid_dates %in% avail_geral)){
paste0(geral_url,"MALABR", substr(valid_dates[valid_dates %in% avail_geral], 3, 4),".dbc")
}
files_list_2 <- if(any(valid_dates %in% avail_prelim)){
paste0(prelim_url,"MALABR", substr(valid_dates[valid_dates %in% avail_prelim], 3, 4),".dbc")
}
files_list <- c(files_list_1, files_list_2)
}
# Dowload files
data <- NULL
for(file in files_list){
# Temporary file
temp <- tempfile()
# Empty data.frame
partial <- data.frame()
# Try to download file
tryCatch({
utils::download.file(file, temp, mode = "wb", method = "libcurl")
partial <- read.dbc::read.dbc(temp, as.is = TRUE)
file.remove(temp)
},
error=function(cond) {
cli::cli_alert_info(paste("Something went wrong with this URL:", file))
cli::cli_alert("This can be a problem with the Internet or the file does not exist yet.")
cli::cli_alert("If the file is too big, try to increase the timeout argument value.")
if(stop_on_error == TRUE){
cli::cli_abort("Stopping download.")
}
})
# Merge files
if(nrow(partial) > 0){
if(track_source == TRUE){
partial$source <- basename(file)
}
if(!all(vars %in% names(partial))) cli::cli_abort("One or more variables names are unknown. Typo?")
if(is.null(vars)){
data <- dplyr::bind_rows(data, partial)
} else {
data <- dplyr::bind_rows(data, subset(partial, select = vars))
}
}
}
# Return
return(data)
}
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