ghruR

This package contains useful R functions for analysing GHRU data

See the HTML docs for documentation of the functions

See these vignettes for examples basic principals making microreact data

Installation

Install from the source from within the R console or the Console in RStudio using (R>= 3.2.0)

• First download dependencies install.packages(c("googledrive", "googlesheets4", "dplyr", "tidyr", "readr", "stringr", "purrr", "anytime", "magrittr", "ape", "tibble", "GrpString", "ggplot2", "ggeasy", "ggthemes", "RColorBrewer", "ggpubr", "cowplot", "ggupset", "epiR", "forcats", "memoise"", "collections"))

Choose one of the following options

1. Directly from the latest source code on gitlab (master branch) devtools::install_git("https://gitlab.com/cgps/ghru/ghrur.git")
2. Install a specific version (0.3.2 in this example) install.packages("https://gitlab.com/cgps/ghru/ghrur/raw/master/ghruR_0.3.2.tar.gz",repos=NULL, method="libcurl")

Testing

To run the tests in the tests directory use the following command

devtools::test()

Make the docs html page

pkgdown::build_site()

Make the vignette html page

If you have added new examples to the vignettes, use the following command to make a new html file

rmarkdown::render('vignettes/analysing_ghru_data.Rmd')
rmarkdown::render('vignettes/making_microreact_compatible_data.Rmd')

Update documents

To generate docs for the package run

devtools::document()

Building the source

To build the package use the command

 devtools::build(path='.')

Recommended development cycle

1. Edit code
2. Run tests devtools::test()
3. Build vignettes, docs and source package for (file in list.files('vignettes', pattern = '*.Rmd', full.names = TRUE)) { rmarkdown::render(file) } devtools::document() pkgdown::build_site(lazy = TRUE) devtools::build(path='.')
4. Commit changes to git and push git add . git commit -m 'Message about changes' git push