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Download SINAN Notifiable Disease Microdata

Source: R/sinan.R
sinan_data.Rd

Downloads and returns notifiable disease microdata from DATASUS FTP. Each row represents one notification record (Ficha de Notificacao). Data is downloaded as national .dbc files (one file per disease per year), decompressed internally, and returned as a tibble.

Usage

sinan_data(
  year,
  disease = "DENG",
  vars = NULL,
  parse = TRUE,
  col_types = NULL,
  cache = TRUE,
  cache_dir = NULL,
  lazy = FALSE,
  backend = c("arrow", "duckdb")
)

Arguments

year

Integer. Year(s) of the data. Required.

disease

Character. Disease code to download. Default: "DENG" (Dengue). Use sinan_diseases() to see all available codes.

vars

Character vector. Variables to keep. If NULL (default), returns all available variables. Use sinan_variables() to see available variables.

parse

Logical. If TRUE (default), converts columns to appropriate types (integer, double, Date) based on the variable metadata. Use sinan_variables() to see the target type for each variable. Set to FALSE for backward-compatible all-character output.

col_types

Named list. Override the default type for specific columns. Names are column names, values are type strings: "character", "integer", "double", "date_dmy", "date_ymd", "date_ym", "date". Example: list(DT_NOTIFIC = "character") to keep DT_NOTIFIC as character.

cache

Logical. If TRUE (default), caches downloaded data for faster future access.

cache_dir

Character. Directory for caching. Default: tools::R_user_dir("healthbR", "cache").

lazy

Logical. If TRUE, returns a lazy query object instead of a tibble. Requires the arrow package. The lazy object supports dplyr verbs (filter, select, mutate, etc.) which are pushed down to the query engine before collecting into memory. Call dplyr::collect() to materialize the result. Default: FALSE.

backend

Character. Backend for lazy evaluation: "arrow" (default) or "duckdb". Only used when lazy = TRUE. DuckDB backend requires the duckdb package.

Value

A tibble with notifiable disease microdata. Includes columns year and disease to identify the source when multiple years are combined.

Details

SINAN files are national (not per-state). Each file contains all notifications for a given disease in a given year across all of Brazil. To filter by state, use the SG_UF_NOT (UF of notification) or ID_MUNICIP (municipality code) columns after download.

Data is downloaded from DATASUS FTP as .dbc files. The .dbc format is decompressed internally using vendored C code from the blast library. No external dependencies are required.

See also

Other sinan: sinan_cache_status(), sinan_clear_cache(), sinan_dictionary(), sinan_diseases(), sinan_info(), sinan_variables(), sinan_years()

Examples

if (FALSE) { # interactive()
# dengue notifications, 2022
dengue_2022 <- sinan_data(year = 2022)

# tuberculosis, 2020-2022
tb <- sinan_data(year = 2020:2022, disease = "TUBE")

# only key variables
sinan_data(year = 2022, disease = "DENG",
           vars = c("DT_NOTIFIC", "CS_SEXO", "NU_IDADE_N",
                    "CS_RACA", "ID_MUNICIP", "CLASSI_FIN"))
}