In ghiggi/ProjectTemplate: What the Package Does

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Research Project

Published in: Ghiggi G.,

DOI : http://dx.doi.org/xxxxxxx

Overview of contents

This repository contains materials to reproduce .... to use ............ The repository contains all data, code, and text associated with the publication.

The Rmd files in the docs/vignettes/ directory contain

details of how all the analyses reported in the paper were conducted
instructions on how to rerun the analysis to reproduce the same results.
R code to recreate the figures included in the manuscript

The data/ directory contains all the raw data, clean & tidy data and the final data

The script/ directory contains:

the manuscript as submitted (in MS Word format) and it's Rmd source file
all the data files (in CSV format, in the data/ directory)
supplementary information source files (in R markdown format) and executed versions
all the figures that are included in the paper (in the figures/ directory)

Reproducibility

This repository is organized similarly to an R package. The R package structure is used to help manage dependencies and to to take advantage of continuous integration for automated code testing.

Package dependencies

RStudio has been used on Ubuntu 16.04 and Windows 7. The package has a number of dependencies on other R packages.

These packages are listed at

packrat
checkpoint
docker

The packrat directory contains the source code for all the packages the project we depend on. If all works well, these will be installed on your computer when you open PROJECTNAME.Rproj in RStudio.

The checkpoint (TODO)

The Docker image includes all the necessary software, code and data to run our analysis. The Docker image may give a quicker entry point to the project, and is more self-contained, so might save some fiddling with installing things.