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README.md

README.md

NOWAC Lite

This is the light version of NOWAC R Package. Here you'll find only package structure, basic functions, and general information about the package. The version that is populated with data and documentation from the NOWAC study is not publicly available, but the NOWAC team members can access it here: https://ice-git.cs.uit.no/nowac/nowac.

Download, installation and usage

Installing the package using command line tools, e.g. the shell in RStudio.

require(devtools)
install_github('uit-bdps/nowaclite')

Using the package:

  • Load the package library(nowaclite)
  • type ?nowaclite to get more information about the package

Data

We use git submodules to keep track of data (in data/ and data-raw). data-raw contains the raw-est form of a datasets we have managed to find. For the biological datasets we have put the raw output from the machines in the data-raw repository, while analysis-ready .RData files are put in the data repository.

Note that the contents of the data and data-raw is not publicly available, as well as some R scripts closely connected to the data, so data/ and data-raw folders will be empty after cloning down the repository and datasets and documentation is not available in nowaclite.

Though you can obtain test data and get the idea of the data structure we have in NOWAC project. In order to get test data you can follow the steps described in R notebook tools/data-preparation.Rmd

Structure

  • R/ contains the R source code.
  • data-raw raw databasets. This folder is populated on our server, but empty on github.
  • data analysis-ready datasets. This folder is populated on our server, but empty on github.
  • man/ used for nowaclite R package documentation.

Guidelines

  • Source code and documentation must be written in english.
  • We follow Hadley Wickham's R package guide.
  • Datasets generated with our pipeline/r package must be complemented with an R script or R markdown file describing how the dataset was created.

Contributions

The following have contributed to the NOWAC R package: Bjørn Fjukstad, Nikita Shvetsov, Therese H. Nøst, Einar Holsbø, Knut Hansen, Eiliv Lund, Lars Ailo Bongo

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