rafaelgarrafiel / datasus

An Interface for the Brazilian Public Healthcare Data Repository (DATASUS) for the R Language

datasus - An interface for the Brazilian Public Healthcare datasets in the R language

Author: Daniela Petruzalek
e-mail: [email protected]
License: GPLv3

Introduction

This project is an R package that provides an interface to the Public Healthcare Data repositories made available by the Brazil's Ministry of Health. The government agency responsible for publishing this data is called DATASUS, hence the name of the collection. Also, often the name 'datasus' is used by the community as an alias to refer the datasets.

My motivation for this project is pretty much summarized by this article: http://simplystatistics.org/2016/04/20/data-repositories/

This project's current status is Work in Progress (WIP). If you have any questions, suggestions and improvement requests, please feel free to contact me and I'll do my best to reply.

Code Book

Since most of the original documentation is written in Portuguese, I'm providing a CodeBook with the details of the most relevant fields of the dataset. I encourage the community to contribute to this work by documenting other parts of the dataset or any missing columns in my original work.

See CodeBook.md

Installation

The best way to install this package is using devtools. See below an example of how to install this package directly from GitHub using devtools::install_github:

> devtools::install_github("danicat/datasus")
Downloading GitHub repo danicat/datasus@master
from URL https://api.github.com/repos/danicat/datasus/zipball/master
Installing datasus
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpKjIBxj/devtools713e2faa8a65/danicat-datasus-c0ef52c'  \
  --library='/home/dani/R/x86_64-pc-linux-gnu-library/3.3' --install-tests 

* installing *source* package ‘datasus’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (datasus)

Usage Notes

Before calling any function of the package, please call datasus.init. This will ensure the right environment variables are loaded and force the user (you) to specify a working directory.

The working directory is a local folder on your machine that will store all downloaded files. It's highly recommended that you store locally all the data you are going to use for your analysis to not over-stress the DATASUS' FTP server. Using a local working directory will ensure the downloaded data will be available between sessions without re-downloading everything, assuming you always use the same workdir.

If you call datasus.init without specifying a working directory it will use a tempdir(). While this behaviour is ok for simple tests it is not advisable for anything other than that by the reasons stated above.

Available Functions

Mortality Information System (SIM)

1. sim.load: general loading function for the SIM subsystem
2. sim.do: loads Declaration of Death data
3. sim.dofet: loads Declaration of Death (fetal) data
4. sim.doinf: loads Declaration of Death (infant/children) data
5. sim.domat: loads Declaration of Death (maternal) data
6. sim.doext: loads Declaration of Death (external causes) data

Examples

# Always initialize the package with the local working directory before calling any other function
> datasus.init('~/datasus/data')
DATASUS environment loaded successfuly

# Loading a file for the first time (DO data for the state of PR, 2014)
> df <- sim.load("DO", 2014, "PR")
trying URL 'ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/DOPR2014.dbc'
Content type 'unknown' length 7034278 bytes (6.7 MB)
==================================================
downloaded 6.7 MB

# Loading the same file again (no download) using the DO wrapper function
> df2 <- sim.do(2014, "PR")
> 

# Loading several files at once (DO type, states of PR and SC, years 2011 and 2012)
# Note: only needed files are downloaded
> df3 <- sim.do(c(2011,2012), c("PR","SC"))
trying URL 'ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/DOSC2011.dbc'
Content type 'unknown' length 2040642 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/DOPR2012.dbc'
Content type 'unknown' length 4353850 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DORES/DOSC2012.dbc'
Content type 'unknown' length 2182142 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

# Loading data from several types at once
> df4 <- sim.load(c("DOMAT","DOFET"), c(2009,2010))
trying URL 'ftp://ftp.datasus.gov.br/dissemin/publicos/SIM/CID10/DOFET/DOMAT09.dbc'
Content type 'unknown' length 137755 bytes (134 KB)
==================================================
downloaded 134 KB

Use the package help to see additional usage tips for each individual function, i.e.:

> ?sim.dofet

Dependencies

This code depends on the read.dbc package (also available on CRAN).

Contact Info

If you have any questions, please contact me at [email protected]. You may also follow me on Twitter.