Geographic Sampling for Epidemiology
Overview
GeoSampler is a browser-based application that was created to facilitate and standardise procedures for manage sample of geographical information. The application was created and is maintained by Epicentre to support the field activities of Médecins Sans Frontières.
The tool is developed using Shiny, a web application framework for R, a language for statistical computing and graphics.
Sampling and demographic techniques are continually being updated and improved. GeoSampler is flexible to implement new and update old methods.
GeoSampler is currently still in active development phase. Expect breaking changes in the near future.
Installation for developer
options(
repos = c(
'http://cran.msf.net',
'http://cloud.r-project.org'
)
)
install.packages(epi.geosampler)Development version
To get a bug fix or to use a feature from the development version, you can install the development version of dplyr from GitHub.
# install.packages("devtools")
devtools::install_github('epicentre-field-epidemiology-training/epi.geosampler')
# Alternatively, install.packages("pak")
pak::pak('epicentre-field-epidemiology-training/epi.geosampler')Usage
Once all packages are installed, use the commands below to launch the application:
library('epi.geosampler')
app <- Application$new()
app$launch()Getting help
Want some help to use GeoSampler? Go to the Get started page.
Documentation and tutorials are available at Learn page.
If you have any problems with GeoSampler, please use the GitHub issue tracker at https://github.com/epicentre-field-epidemiology-training/epi.geosampler/issues.
Firewall/Antivirus Issues
GeoSampler uses R Shiny for its Graphical Unit Interface (GUI). This latter relies on SockJS based on the HTTP WebSocket protocol to facilitate communication between the browser and the server. Unfortunateley, unencrypted WebSocket traffic is often filtered or blocked. First, you can test if WebSockets work for you.
So, if you get a shaded screen, it’s probably due to either your antivirus, your firewall or if you work within a VPN. To solve this problem, add the URL of the application as an exception (ie an exclusion for the application of the security rules), or as a trusted site, according to your software tools available on your workstation.
The antiviruses known to enforce strict rules for the WebSocket protocol are for example: Kaspersky, Avast
Do not hesitate to ask to your IT administrator for explaination how to proceed.
Credits
GeoSampler would not be possible without R and Shiny. We would like to thank Joe Cheng, Winston Chang, and Yihui Xie for answering questions, providing suggestions, and creating amazing tools for the R community. Other key components used in GeoSampler are ggplot2, dplyr, tidyr, magrittr, broom, shinyAce, rmarkdown, and DT.
Code of conduct
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.