healthbR: Unified Access to Brazilian Public Health Data

[SidneyBissoli]

Submitting Author Name: Sidney da Silva Pereira Bissoli
Submitting Author Github Handle: @SidneyBissoli
Other Package Authors Github handles:
Repository: https://github.com/SidneyBissoli/healthbR
Submission type: Pre-submission
Language: en

---

Paste the full DESCRIPTION file inside a code block below:

Package: healthbR
Title: Access Brazilian Public Health Data
Version: 0.2.0
Authors@R:
    person("Sidney", "Bissoli", , "sbissoli76@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0001-0442-3700"))
Description: Provides easy access to Brazilian public health data from multiple
    sources including VIGITEL (Surveillance of Risk Factors for Chronic Diseases
    by Telephone Survey), PNS (National Health Survey), 'PNAD' Continua (Continuous
    National Household Sample Survey), 'POF' (Household Budget Survey with food
    security and consumption data), 'Censo Demografico' (population denominators
    via 'SIDRA' API), SIM (Mortality Information System), SINASC (Live Birth
    Information System), 'SIH' (Hospital Information System),
    'SIA' (Outpatient Information System), 'SINAN' (Notifiable Diseases Surveillance),
    'CNES' (National Health Facility Registry),
    'SI-PNI' (National Immunization Program - aggregated 1994-2019 via FTP,
    individual-level 'microdata' 2020+ via 'OpenDataSUS' API),
    'SISAB' (Primary Care Health Information System - coverage indicators via
    REST API), ANS ('Agencia Nacional de Saude Suplementar' - supplementary
    health beneficiaries, consumer complaints, and financial statements),
    'ANVISA' ('Agencia Nacional de Vigilancia Sanitaria' - product registrations,
    'pharmacovigilance', 'hemovigilance', 'technovigilance', and controlled
    substance sales via 'SNGPC'),
    and other health information systems. Data is downloaded
    from the Brazilian Ministry of Health and 'IBGE' repositories. Data is returned
    in tidy format following tidyverse conventions.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends:
    R (>= 4.2.0)
Imports:
    tibble,
    dplyr,
    curl,
    cli,
    rlang,
    stringr,
    purrr,
    readr,
    jsonlite,
    foreign
Suggests:
    testthat (>= 3.1.5),
    knitr,
    rmarkdown,
    readxl,
    haven,
    furrr,
    future,
    arrow,
    dbplyr,
    duckdb,
    piggyback,
    survey,
    srvyr
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://github.com/SidneyBissoli/healthbR, https://sidneybissoli.github.io/healthbR/
BugReports: https://github.com/SidneyBissoli/healthbR/issues

Scope

I believe my package falls under the following categories:

• data retrieval
• data extraction

healthbR provides unified programmatic access to over 15 Brazilian public health data sources directly from R, including:

DATASUS microdata: SIM (mortality), SINASC (live births), SIH (hospital admissions), SIA (outpatient procedures), SINAN (notifiable diseases), CNES (health facilities) — all using internal .dbc file decompression via vendored C code with no external dependencies.

Population surveys: VIGITEL (telephone surveillance), PNS (National Health Survey), PNAD Contínua (Continuous National Household Sample Survey), POF (Household Budget Survey), Demographic Census — with dual access via microdata and IBGE's SIDRA API.

Other sources: SI-PNI (vaccination), SISAB/e-SUS (primary care), ANS (private health insurance regulator), ANVISA (health products regulator).

The package addresses a well-documented problem: Brazilian public health data is fragmented across dozens of systems with different formats, unstable government portals, and proprietary file formats (.dbc). Researchers and epidemiologists spend significant time just accessing and preparing these data before any analysis can begin. healthbR automates this entire pipeline through a consistent API (*_data(), *_variables(), *_dictionary(), *_info()) and returns tidy tibbles ready for analysis.

Target audience and scientific applications

The primary target audience is epidemiologists and public health researchers who use R to analyze data from Brazil's Unified Health System (SUS). The package also serves data scientists working with Brazilian public data and graduate students in public health and epidemiology.

Scientific applications include: mortality and morbidity analysis, epidemiological surveillance, vaccination coverage assessment, health service utilization studies, population survey analysis, health economics research, and public policy planning.

Similar packages

Several R packages access subsets of these data individually:

• microdatasus: accesses DATASUS microdata, but depends on the external read.dbc package (currently archived on CRAN) and covers fewer sources.
• datasus: accesses TabNet/DATASUS data with limited scope.
• censobr: focused exclusively on Census data.
• PNADcIBGE and POFIBGE: focused on specific IBGE surveys.
• read.dbc: .dbc file reading only — currently archived on CRAN.

healthbR differentiates itself by:

1. Broad coverage: unifies 15+ data sources in a single package with a consistent API
2. Self-contained: vendors the .dbc decompression C code internally (no dependency on the archived read.dbc package)
3. Smart caching: automatic Parquet conversion via arrow for efficient filtered reads
4. Dual access: microdata + aggregated data via SIDRA API for survey modules
5. Integrated dictionaries: *_dictionary() and *_variables() functions for every module

Other information

• The package is already published on CRAN (current version at https://CRAN.R-project.org/package=healthbR)
• pkgdown site: https://sidneybissoli.github.io/healthbR/
• The package includes individual vignettes for each module
• I intend to actively maintain the package for at least 2 years
• I am available to respond to reviews in a timely manner

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Checks for healthbR (v0.2.0)

git hash: 05254064

• ✔️ Package is already on CRAN.
• ✖️ does not have a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage is 54% (should be at least 75%).
• ✖️ Default GitHub branch of 'master' is not acceptable.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	1604
internal	utils	109
internal	healthbR	99
internal	stats	38
internal	tools	2
imports	cli	142
imports	readr	65
imports	tibble	55
imports	stringr	40
imports	curl	25
imports	dplyr	22
imports	purrr	21
imports	rlang	5
imports	jsonlite	4
imports	foreign	4
suggests	arrow	16
suggests	readxl	6
suggests	haven	1
suggests	survey	1
suggests	srvyr	1
suggests	testthat	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	furrr	NA
suggests	future	NA
suggests	dbplyr	NA
suggests	duckdb	NA
suggests	piggyback	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

c (479), list (174), url (60), file.path (56), if (56), is.null (56), as.integer (52), names (43), paste0 (39), nrow (36), seq_len (34), unique (32), for (29), length (28), character (23), labels (23), grepl (21), vapply (20), tempfile (19), list.files (18), file (16), logical (16), paste (15), toupper (14), sprintf (13), as.character (12), source (12), expand.grid (11), range (11), tolower (11), invisible (10), months (10), table (10), tryCatch (10), intersect (8), setdiff (7), as.POSIXct (6), col (6), drop (6), numeric (6), search (6), tempdir (6), basename (5), file.info (4), format (4), integer (4), is.na (4), missing (4), any (3), min (3), rawToChar (3), return (3), seq_along (3), substr (3), switch (3), charToRaw (2), data.frame (2), dirname (2), force (2), lapply (2), max (2), raw (2), readRDS (2), Reduce (2), sum (2), dir.exists (1), exists (1), file.exists (1), file.remove (1), file.size (1), ifelse (1), list.dirs (1), match.arg (1), options (1), readBin (1), readLines (1), requireNamespace (1), sort (1), sub (1), Sys.Date (1), system (1), which (1), while (1)

cli

cli_abort (70), cli_inform (38), cli_warn (22), cli_bullets (11), col_green (1)

utils

data (72), unzip (19), de (14), citation (3), vi (1)

healthbR

clean_sidra_response (5), has_partitioned_cache (3), pnadc_base_url (3), pnadc_find_data_url (3), pnadc_list_ftp_files (3), pnadc_parse_input_file (3), vigitel_base_url (3), ans_data (2), censo_years (2), pnadc_dictionaries (2), pnadc_modules (2), pnadc_read_fwf (2), pnadc_read_zip (2), pnadc_required_vars (2), pns_dictionary (2), pns_download_data (2), pof_dictionary (2), validate_pnadc_year (2), vigitel_years (2), ans_cache_status (1), ans_clear_cache (1), ans_info (1), ans_operators (1), ans_variables (1), ans_years (1), anvisa_cache_status (1), anvisa_clear_cache (1), anvisa_data (1), anvisa_info (1), anvisa_types (1), anvisa_variables (1), censo_estimativa (1), censo_info (1), censo_populacao (1), censo_sidra_data (1), censo_sidra_search (1), censo_sidra_tables (1), cnes_cache_status (1), cnes_clear_cache (1), cnes_data (1), cnes_dictionary (1), cnes_info (1), cnes_variables (1), cnes_years (1), create_partitioned_cache (1), get_arrow_column_names (1), get_dir_size_mb (1), get_size_mb (1), list_sources (1), pnadc_apply_survey_design (1), pnadc_cache_dir (1), pnadc_cache_status (1), pnadc_clear_cache (1), pnadc_data (1), pnadc_download_file (1), pnadc_has_srvyr (1), pnadc_info (1), pnadc_variables (1), pnadc_years (1), pns_cache_dir (1), pns_cache_status (1), pns_clear_cache (1), pns_data (1), pns_info (1), pns_modules (1), pns_read_microdata (1), pns_years (1), pof_years (1), vigitel_dictionary (1), vigitel_identify_year_column (1), vigitel_identify_year_column_from_schema (1)

readr

locale (20), cols (16), read_delim (13), col_character (4), fwf_positions (3), read_csv (3), read_fwf (2), read_lines (2), SideEffectChunkCallback$new (2)

tibble

tibble (53), add_column (1), as_tibble (1)

stringr

str_c (33), str_detect (2), str_match (2), str_extract_all (1), str_replace (1), str_replace_all (1)

stats

df (18), line (6), start (5), as.formula (3), end (3), weights (2), C (1)

curl

new_handle (10), curl_download (7), curl_fetch_memory (4), curl_fetch_disk (2), handle_setopt (1), multi_download (1)

dplyr

bind_rows (10), mutate (10), collect (1), distinct (1)

purrr

map (6), map_int (6), imap (3), map_chr (3), map_lgl (3)

arrow

open_dataset (16)

readxl

read_excel (5), excel_sheets (1)

rlang

check_installed (5)

foreign

read.dbf (4)

jsonlite

fromJSON (4)

tools

R_user_dir (2)

haven

read_dta (1)

srvyr

as_survey_design (1)

survey

svydesign (1)

---

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in C (4% in 3 files) and R (96% in 36 files)
• 1 authors
• 17 vignettes
• no internal data file
• 10 imported packages
• 121 exported functions (median 12 lines of code)
• 270 non-exported functions in R (median 9 lines of code)
• 9 R functions (median 41 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	36	92.0
files_src	3	86.3
files_inst	1	83.8
files_vignettes	17	99.9
files_tests	25	96.6
loc_R	9097	97.7	TRUE
loc_src	413	45.9
loc_inst	23	17.1
loc_vignettes	2689	98.3	TRUE
loc_tests	6487	98.3	TRUE
num_vignettes	17	99.9	TRUE
n_fns_r	391	98.4	TRUE
n_fns_r_exported	121	95.8	TRUE
n_fns_r_not_exported	270	98.7	TRUE
n_fns_src	9	82.1
n_fns_per_file_r	11	92.3
n_fns_per_file_src	3	83.1
num_params_per_fn	1	3.5	TRUE
loc_per_fn_r	9	29.0
loc_per_fn_r_exp	12	29.8
loc_per_fn_r_not_exp	9	62.8
loc_per_fn_src	41	98.1	TRUE
rel_whitespace_R	20	98.0	TRUE
rel_whitespace_src	13	84.6
rel_whitespace_inst	43	85.9
rel_whitespace_vignettes	42	99.7	TRUE
rel_whitespace_tests	27	99.5	TRUE
doclines_per_fn_exp	18	15.2
doclines_per_fn_not_exp	1	62.4
fn_call_network_size	534	94.7

---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
22043130845	pkgdown.yaml	success	052540	51	2026-02-15
22043130852	R-CMD-check.yaml	success	052540	53	2026-02-15
22043130860	test-coverage.yaml	success	052540	52	2026-02-15

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following check_fail:

1. cyclocomp

Test coverage with covr

Package coverage: 54.04

The following files are not completely covered by tests:

file	coverage
R/censo.R	60.28%
R/dbc_infrastructure.R	12.9%
R/pnadc.R	29.03%
R/pns.R	40.7%
R/pof.R	24.23%
R/sia.R	69.19%
R/sih.R	69.82%
R/sim.R	68.31%
R/sipni.R	39.75%
R/sisab.R	63.68%
R/utils-sidra.R	0%
R/vigitel.R	40.67%
R/zzz.R	33.33%
src/blast.c	0%
src/dbc2dbf.c	0%

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
sipni_data	60
vigitel_data	33
pnadc_data	27
pns_data	23
pof_data	23
sisab_data	23
sim_data	21
pns_dictionary	19
sia_data	17
pns_sidra_data	15
sih_data	15

Static code analyses with lintr

lintr found no issues with this package!

---

Package Versions

package	version
pkgstats	0.2.2.6
pkgcheck	0.1.2.269

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

This package has some noteworthy properties, see 'Package Statistics' details above.