read.dbc

Author: Daniela Petruzalek
e-mail: [email protected]
License: AGPLv3

Introduction

read.dbc is a R package to enable importing data from DBC (compressed DBF) files into data frames. Please note that this is the file format used by DATASUS and it is not related to Microsoft FoxPro or CANdb DBC file formats.

DATASUS is the name of the Department of Informatics of Brazil's Healthcare System (Sistema Unico de Saúde - SUS). They are responsible for publishing Brazilian public healthcare data. Besides DATASUS, the Brazilian National Agency for Supplementary Health (ANS) also uses this file format for its public data.

This code was tested using files from both DATASUS and ANS to ensure compliance with the format, and hence ensure its usability by researchers.

This project is based on the work of Mark Adler (blast) and Pablo Fonseca (blast-dbf).

Neither this project, nor its author, is related in any way to the Brazilian government.

Changelog

For a complete description of the changes, please check CHANGELOG.md.

Repository Contents

• README.md: this file.
• CHANGELOG.md: change history.
• src/blast.c: decompression tools for PKWare Data Compression Library (DCL).
• src/blast.h: blast.c header and usage notes.
• src/dbc2dbf.c: the main program to decompress the dbc files to dbf.
• R/read.dbc.R: the code for reading .dbc files within R.
• R/dbc2dbf.R: a helper function to decompress the .dbc files, it works as a wrapper to the "blast" code.
• man/*: package manuals
• inst/*: test and misc files

Installation

As of June, 7 of 2016, this package officialy became part of CRAN (The Comprehensive R Archive Network). Therefore, it's current stable version can be installed by running install.packages:

    install.packages("read.dbc")

In case you want to install the development version of this package, you still can do it using the devtools library:

    devtools::install_github("danicat/read.dbc")

Usage

Reading a DBC file to a data frame:

    # The 'sids.dbc' file is the compressed version of 'sids.dbf' from the "foreign" package.
    sids <- read.dbc(system.file("files/sids.dbc", package="read.dbc"))
    str(sids)
    summary(sids)

    # The following code will download data from the "Declarations of Death" database for
    # the Brazilian state of Parana, year 2013. Source: DATASUS / Brazilian Ministry of Health
    url <- "ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/DOPR2013.dbc"
    download.file(url, destfile = "DOPR2013.dbc", mode = "wb")
    dopr <- read.dbc("DOPR2013.dbc")
    head(dopr)
    str(dopr)

Decompressing a DBC file to a DBF:

    # Input file name
    in.f  <- system.file("files/sids.dbc", package = "read.dbc")
    
    # Output file name
    out.f <- tempfile(fileext = ".dbc")

    # The call return logi = TRUE on success
    if( dbc2dbf(input.file = in.f, output.file = out.f) ) {
         print("File decompressed!")
         file.remove(out.f)
    }

Contact Info

If you have any questions, please contact me at [email protected].

Developer Information

Mac OS X

Setup:

• Install Xcode
• Install R: https://cran.r-project.org/bin/macosx/
• Install Rstudio: https://posit.co/download/rstudio-desktop/
• Run make setup to install R dependencies
• Run make check to verify the package

You can also run make help to see a list of available commands.

Submitting to CRAN

First make sure all the checks are passing by running make cran.

Once ready, use devtools::submit_cran(). This needs to run from RStudio or the R interpreter itself as the tool doesn't allow non-interactive runs.