Description
Current version of sivirep provides functions for data wrangling and automated reports based on data from SIVIGILA, which is the official epidemiological surveillance system of Colombia, South America.
Disclaimer
The use of this package, as well as the data, generated reports, and other products derived from it, is the sole responsibility of the user. Neither the authors of the package, nor the Pontificia Universidad Javeriana, nor the source of the information assume any responsibility for the results obtained or the use made of these products.
Motivation
Latin America has progressed in the quality of epidemiological notification and surveillance systems. Particularly, Colombia has improved over the years the quality and openness of its official epidemiological surveillance system, SIVIGILA. This system is regulated by Colombia’s National Institute of Health and operated by thousands of health workers at local secretaries of health, hospitals, and local notification units.
However, some challenges remain particularly at local levels in terms of timeliness and quality of epidemiological analytics and epidemiological reports. These tasks may involve a great effor of manual labor reinforced by limitations in training for data analytics, time, technology and quality of internet access in some locations.
sivirep is aimed at providing a set of customisable
functions for:
- Downloading, pre-processing and preparing SIVIGILA data for further analysis.
- Producing customisable epidemiological automated reports.
- Getting feedback on the surveillance system to the source provider.
Potential users
- Public health professionals and field epidemiologist users of SIVIGILA source at local levels
- Epidemiology and public health students
- National and international researchers and data analysts
Future versions
Future versions of sivirep may include:
- Interaction with other data sources in Colombia
- Other epidemiological surveillance systems in Latin America
Contributions
Contributions are welcome via pull requests.
Contributors to the project include:
Autores: Geraldine Gómez-Millán, Zulma M. Cucunubá, Jennifer A. Mendez-Romero y Claudia Huguett-Aragón
Contribuyentes: Hugo Gruson, Juanita Romero-Garcés, Andrés Moreno, Miguel Gámez, Laura Gómez-Bermeo, Johan Calderón, Lady Flórez-Tapiero, Verónica Tangarife-Arredondo y Gerard Alarcon
Code of conduct
Please note that the linelist project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Installation
You can install the development version of sivirep from
GitHub with:
install.packages("pak")
pak::pak("epiverse-trace/sivirep")Alternatively, you can also use:
install.packages("remotes")
remotes::install_github("epiverse-trace/sivirep")
install.packages("sivirep",
repos = c("https://epiverse-trace.r-universe.dev",
"https://cloud.r-project.org"))Quick start
You can start by importing the package after installation is complete using the following command:
You can check the available diseases and years for free download using the commands:
lista_eventos <- list_events()
knitr::kable(lista_eventos)🦠Listado de enfermedades (haz clic para ver)
Code Disease Year 100 Accidente Ofídico 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 300 Agresiones Por Animales Potencialmente Transmisores De Rabia 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 735 Anomalías Congénitas 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 110 Bajo Peso Al Nacer 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 155 Cáncer De La Mama Y Cuello Uterino 2016, 2017, 2018, 2019, 2020, 2021, 2023 459 Cáncer Infantil 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 205 Chagas 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 217 Chikunguya 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 210 Dengue 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 220 Dengue Grave 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 112 Desnutrición Aguda En Menores De 5 Años 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 230 Difteria 2018, 2019, 2021 345 Esi - Irag (Vigilancia Centinela) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 349 Eta Colectivo 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 298 Evento Adverso Grave Posterior A La Vacunación 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 228 Exposición A Flúor 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 310 Fiebre Amarilla 2007, 2008, 2009 320 Fiebre Tifoidea Y Paratifoidea 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 330 Hepatitis A 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 340 Hepatitis B, C Y Coinfección Hepatitis B Y Delta 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 341 Hepatitis C 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 343 Hipotiroidismo Congénito 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 348 Infección Respiratoria Aguda Grave Irag Inusitada 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 356 Intento De Suicidio 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 412 Intoxicación Por Gases 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 370 Intoxicación Por Medicamentos 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 390 Intoxicación Por Metales Pesados 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 380 Intoxicación Por Metanol 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 410 Intoxicación Por Otras Sustancias Químicas 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 360 Intoxicación Por Plaguicidas 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 400 Intoxicación Por Solventes 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 420 Leishmaniasis Cutánea 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 430 Leishmaniasis Mucosa 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 440 Leishmaniasis Visceral 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 450 Lepra 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 455 Leptospirosis 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 452 Lesiones Por Artefactos Explosivos (Pólvora Y Minas Antipersonal) 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 458 Lesiones Por Pólvora Y Explosivos 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014 456 Leucemia Aguda Pediátrica Linfoide 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 457 Leucemia Aguda Pediátrica Mieloide 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 465 Malaria 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 460 Malaria Asociada (Formas Mixtas) 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 495 Malaria Complicada 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 470 Malaria Falciparum 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 490 Malaria Vivax 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 500 Meningitis Meningocócica 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 510 Meningitis Por Haemophilus Influenzae 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 520 Meningitis Por Neumococo 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 530 Meningitis Tuberculosa 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 549 Morbilidad Materna Extrema 2012, 2013, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 998 Morbilidad Por Eda 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 995 Morbilidad Por Ira 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 550 Mortalidad Materna 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 560 Mortalidad Perinatal Y Neonatal Tardía 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 580 Mortalidad Por Dengue 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 590 Mortalidad Por Eda 0-4 Años 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 600 Mortalidad Por Ira 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 540 Mortalidad Por Malaria 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 620 Parotiditis 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 670 Rabia Humana 2007, 2008, 2009, 2010, 2012, 2015, 2016, 2017, 2020 710 Rubeola 2007, 2008, 2009, 2010, 2011, 2012 730 Sarampión 2011, 2012, 2013, 2015, 2018, 2019, 2020 739 Síndrome Inflamatorio Multisistémico En Niños Asociado A Sars-Cov2 2022, 2023 760 Tétanos Accidental 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 770 Tétanos Neonatal 2007, 2008, 2009, 2010, 2012, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 790 Tifus Endémico Trasmitido Por Pulgas 2013, 2014 780 Tifus Epidémico Transmitido Por Piojos 2014 800 Tos Ferina 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 305 Tracoma 2017, 2018, 2019, 2022 810 Tuberculosis Extra Pulmonar 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 825 Tuberculosis Farmacorresistente 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 820 Tuberculosis Pulmonar 2010, 2011, 2016, 2017, 2018, 2019, 2020, 2021, 2022 831 Varicela Individual 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 875 Vigilancia En Salud Pública De La Violencia De Género E Intrafamiliar 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023 895 Zika 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023
Automated report
Currently, sivirep provides a report template
calledReporte Evento {sivirep}, which takes the following input
parameters:
- Name of the disease
- Year
- Country
- Name of the department (optional)
- Name of the municipality (optional)
- Cache data (checkbox - optional) : choose whether the downloaded data for the event and incidence should be stored in the user’s session cache to avoid re-downloading it when generating the report again with the same inputs.
These parameters are used to download data from the SIVIGILA source.
To use the report template, you can follow these steps:
The report generated using the sivirep template looks
like this:
If you want to generate the report in PDF format, you need to install
LaTeX.
You can install it by following the instructions in the R
Markdown Cookbook.
Custom analysis
sivirep offers a suite of functions that can be used in
different scenarios —
from downloading data to creating custom analyses or building full
pipelines.
To explore the available functions and examples of their suage, please visit the Custom analysispage.