ncov-outputs-example

This is a stripped down version of the outputs from analysis of 2019-nCoV - it is an orderly project. The directories are:

• src: create new outputs here
• archive: versioned results of running your output
• data: copies of data used in the outputs

Quickstart

Really quick

Clone the repository onto your computer

git clone https://github.com/ncov-ic/ncov-outputs-example

Open the Rstudio project from within ncov-outputs

Orderly documentation

There is some basic documentation here: https://vimc.github.io/orderly/articles/orderly.html but these are still quite VIMC specific. We will improve them! Please post questions/complaints/suggestions for improvements to the slack or to the ncov-outputs issue tracker.

Package installation

You need a few packages to compile outputs:

# install.packages("drat") # (install this if you don't have it already)
drat:::add("ncov-ic")
install.packages(c("orderly", "vaultr", "orderlyweb"))

orderly and vaultr are on CRAN but you will need orderlyweb if you want to pull reports from the server.

Create a new output skeleton

orderly::orderly_new("my_output_name")

The name is important as it cannot be changed after outputs have been run. Consider a good prefix.

Run your output locally

orderly::orderly_run("my_output_name")

if you want your R objects to persist in the session later then add envir = .RGlobalEnv; see ?orderly_run for more details.