Package {datazoom.saude}

datazoom.saude: Download Brazilian Health Data from DATASUS

Description

Functions to download and treat data regarding the Brazilian Amazon region from a variety of official sources.

Author(s)

Maintainer: Laura Tavares Regadas lauratregadas@gmail.com

Authors:

• Laura Tavares Regadas lauratregadas@gmail.com

• Luana Laport Santos luanalaportsantos@icloud.com

• João Paulo dos Santos P. Barbosa joao.3158129@gmail.com

• Vanndher Amós B. A. de Souza vanndheramos@gmail.com

Other contributors:

• DataZoom (PUC-Rio) datazoom@econ.puc-rio.br [funder]

• Daniela Petruzalek daniela.petruzalek@gmail.com [contributor]

• Mark Adler [contributor]

See Also

Useful links:

• https://datazoom.com.br/en/dz_saude/

• Report bugs at https://github.com/datazoompuc/datazoom.saude/issues

Decompress a DBC (compressed DBF) file

Description

This function allows you decompress a DBC file into its DBF counterpart. Please note that this is the file format used by the Brazilian Ministry of Health (DATASUS), and it is not related to the FoxPro or CANdb DBC file formats.

Usage

dbc2dbf_wrapper(input.file, output.file)

Arguments

Details

DBC is the extension for compressed DBF files (from the 'XBASE' family of databases). This is a proprietary file format used by the brazilian government to make available public healthcare datasets (by it's agency called DATASUS).

It uses internally the PKWare's Data Compression Library (DCL) "implode" compression algorithm. When decompressed, it becomes a regular DBF file.

Value

Return TRUE if succeeded, FALSE otherwise.

Author(s)

Daniela Petruzalek, daniela.petruzalek@gmail.com

Source

The internal C code for dbc2dbf is based on blast decompressor and blast-dbf (see References).

References

The PKWare ZIP file format documentation (contains the "implode" algorithm specification) available at https://pkware.my.site.com/s/, current version https://pkware.cachefly.net/webdocs/casestudies/APPNOTE.TXT.

blast source code in C: https://github.com/madler/zlib/tree/master/contrib/blast

blast-dbf, DBC to DBF command-line decompression tool: https://github.com/eaglebh/blast-dbf

See Also

read.dbc

Examples

in.f <- system.file("files/sids.dbc", package = "datazoom.saude")
out.f <- tempfile(fileext = ".dbf")
if (file.exists(in.f)) {
  dbc2dbf_wrapper(input.file = in.f, output.file = out.f)
}

Loads birth data of newborns from Brazil provided by DATASUS

Description

This function downloads and organizes data from SINASC (Live Birth Information System), part of DATASUS, used in public health analyses.

Usage

load_births(time_period, states = "all", raw_data = FALSE, language = "eng")

Arguments

Value

A data frame containing birth records from SINASC for the specified period and states.

Examples

load_births(time_period = 2023,
            states = "RJ",
            raw_data = FALSE)

Loads hospital admission data from Brazil provided by DATASUS (SIHSUS)

Description

This function downloads and organizes data from SIHSUS (Hospital Information System), part of DATASUS, used in public health and hospital care analyses.

Usage

load_hospital_admissions(
  dataset,
  time_period,
  states = "all",
  raw_data = FALSE,
  language = "eng"
)

Arguments

Details

SIHSUS provides several datasets related to hospital admissions in Brazil:

reduced_aih (RD) - Reduced AIH (Hospital Admission Authorization)

A simplified database with the main information from approved and processed AIHs. It is the most commonly used dataset for statistical and epidemiological analyses, including data on the main procedure, diagnoses, and total values of each admission.

professional_services (SP) - Professional Services

A stratified dataset containing details about services provided during the hospital stay, such as medical procedures, professional identification (CBO/CNS), and values related to professional and hospital services.

rejected_aih (RJ) - Rejected AIHs

Contains rejected AIHs and summarizes the reasons for rejection. It is useful for analyzing the volume and impact of rejected records but does not include detailed information on each rejection.

rejected_aih_error (ER) - Rejected AIHs with Error Code

Includes AIHs rejected due to inconsistencies identified during processing. These records contain specific error codes indicating why the rejection occurred (e.g., patient data inconsistency, procedure incompatibility).

Value

A data frame containing hospital admission records from SIHSUS for the specified period and states.

Examples

load_hospital_admissions(dataset = "professional_services",
                         time_period = 2020,
                         states = "AC")

Load monthly data on hospital beds from Brazil's National Health Facilities Registry

Description

Retrieves and processes structured microdata on hospital beds from the 'CNES' (Cadastro Nacional de Estabelecimentos de Saude), which is part of the 'DATASUS' system, maintained by the Brazilian Ministry of Health. This dataset includes information on the availability and distribution of hospital beds in Brazil.

Usage

load_hospital_beds(
  time_period,
  states = "all",
  raw_data = FALSE,
  language = "eng"
)

Arguments

Details

The data is sourced from the 'CNES-LT' subsystem (Leitos - Beds), which provides monthly information on beds by establishment and type, and can be filtered by state and time period.

File downloads are performed via the official DATASUS FTP server. Users can choose to retrieve raw or pre-processed data, and label variables in English or Portuguese.

This function downloads and processes data from the CNES-LT subsystem, which is part of the Brazilian National Health Facilities Registry. It uses the DATASUS FTP server and handles compressed data in DBF format, using packages such as foreign and RCurl.

The function labels variables using a built-in dictionary and offers harmonized column names depending on the selected language. A filter by state and year is applied to reduce file size and processing time.

Value

A tibble (if raw_data = FALSE) containing harmonized monthly hospital bed data from Brazil, or a list of raw data frames (if raw_data = TRUE).

Note

The foreign and RCurl packages must be installed to use this function. They are listed in Suggests to avoid installing them by default.

Examples

# Load beds data for RO in 2020
beds <- load_hospital_beds(time_period = "2020",
                           states = "RO",
                           raw_data = FALSE,
                           language = "eng")

Load Brazilian mortality data from the SIM system via DATASUS

Description

Retrieves mortality records from Brazil's official Mortality Information System (SIM), made available through DATASUS (Department of Informatics of the Brazilian Unified Health System). This dataset includes detailed information on deaths by cause, location, sex, age, and other demographic characteristics. Data is useful for public health research, epidemiology, and demographic analysis.

Usage

load_mortality(
  dataset,
  time_period,
  states = "all",
  raw_data = FALSE,
  keep_all = FALSE,
  language = "eng"
)

Arguments

Value

A data frame containing the mortality records.

Examples

load_mortality(dataset = "general",
               time_period = 2022,
               states = "RJ")

load_mortality(dataset = "maternal",
               time_period = 2020,
               raw_data = FALSE,
               language = "pt")

Loads oncology case data from Brazil provided by DATASUS

Description

This function downloads and organizes data from the Oncology Panel (Painel de Oncologia), part of DATASUS, used in public health and epidemiological analyses.

Usage

load_oncology_case(time_period, raw_data = FALSE, language = "eng")

Arguments

Value

A data table containing oncology case records from the Oncology Panel of all Brazilian states for the specified period.

Examples

# Download processed oncology data for the year 2023.
# This will return data from the Oncology Panel for all Brazilian states.
oncology_cases_treated <- load_oncology_case(time_period = 2023,
                                             raw_data = FALSE,
                                             language = "eng"
                                             )

Loads outpatient procedure data from Brazil provided by 'SIASUS' (Ambulatory Information System)

Description

This function downloads and organizes public health data from 'SIASUS' – the Ambulatory Information System from Brazil's national health database, 'DATASUS'. It contains records of outpatient medical procedures performed throughout the country.

Usage

load_outpatient_procedures(
  dataset,
  time_period,
  states = "all",
  raw_data = FALSE,
  language = "eng"
)

Arguments

Details

SIASUS provides multiple datasets that cover different aspects of outpatient care in Brazil:

bariatric_surgery_follow_up

General preventive and primary care procedures, such as check-ups and vaccinations.

diverse_reports

Outpatient dental procedures including extractions, restorations, and preventive services.

medicines

Higher complexity procedures including specialized consultations and diagnostic exams.

nephrology

Procedures related to early-life screening tests, including metabolic and sensory testing.

chemotherapy

Outpatient procedures provided through structured home care programs.

radiotherapy

Procedures focused on physical, cognitive, and functional rehabilitation.

ambulatory_production

High-cost procedures that require prior authorization, such as cancer treatment or dialysis.

psychosocial

Aggregated or simplified records of outpatient procedures with limited detail.

post_bariatric_surgery_follow_up

Records from specialized dental centers providing oral health care.

fistula_confection

Data on medication dispensing and pharmaceutical consultations.

dialytic_treatment

Procedures related to therapies such as chemotherapy and radiotherapy.

home_care

Home-based specialized care such as oxygen therapy and related services.

Value

A data frame containing outpatient procedure records from SIASUS for the specified period and states.

Examples

load_outpatient_procedures(dataset = "diverse_reports",
                           time_period = 2016,
                           states = "PI",
                           language = "pt")

Load Brazilian vaccination data from the SI-PNI system via DATASUS

Description

Retrieves vaccination records from Brazil's official National Immunization Program Information System (SI-PNI), made available through DATASUS. This function supports two data ingestion modes. For historical data (1994-2022), it can perform automated web scraping on the legacy SI-PNI Web portal to extract consolidated records of applied doses. For more recent years (2023 to present), the user must provide a locally downloaded file, in which case the function performs only data validation, cleaning, harmonization, and standardization.

Usage

load_vaccines(
  year,
  state,
  strategy = NULL,
  product = NULL,
  dose = NULL,
  data = NULL,
  language = "eng"
)

Arguments

Details

Regardless of the ingestion mode, the returned dataset is fully harmonized and consistent with the historical SI-PNI data structure.

Value

A tibble (data frame) containing state, year, municipality codes, municipality names, strategy, product, month, dose type, and the quantity of doses applied.

Examples

# Example: Loading Yellow Fever vaccine data for Acre in 2020
data <- load_vaccines(year = 2020,
                      state = "AC",
                      strategy = "Rotina",
                      product = "Febre amarela - FA",
                      language = "eng")