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data-analysis-europe

Data Analysis of Influenzanet at european level

Repository organization

This repository follows the workspace organization described in ifnBase package

This repository is organized with a set of projects, each in one subdirectory. A project is just a way to group scripts with a common purpose/topic. They share a common init script ("conf.R") and can share project specific scripts in a subfolder lib/ and a output directory.

A project must be independent from others and the only scripts known outside it must be "system.R" in its upper level.

The share directory contains common libraries & data shared accross projects. These libraries must be loaded with share.lib function & data using share.data.path() function.

Naming conventions

File names must be in lower case, using underscore as separator

Configuration

Configuration is expected to be in a location.R file in the root of this repository. It contains local configuration specific to this project. It can overrides system-wide or user profile config (.Rprofile file). We use this location.R because several repositories with differents projects can be hosted in the same user space.

Installation

Dependencies:

  • ifnBase
  • swMisc
  • dplyr
  • reshape2
  • ggplot2

Launch R (this repository root dir as working directory) and run

source("share/install.R")

Run scripts

To run a script, the working directory MUST be it's own project directory (not the repository root directory but the subfolder) because all include path are relative to the main running scripts.