BIUMmisc

A collection of R functions and scripts commonly used by the BIUM-MZ Core Facility and the Bioinformatics group at the IMBEI.

You can browse the package contents at https://imbeimainz.github.io/BIUMmisc/.

Installation

You can install the development version of BIUMmisc from GitHub with:

library("remotes")
remotes::install_github("imbeimainz/BIUMmisc")

# this one installs also all the Suggested dependencies and builds the vignette
remotes::install_github("imbeimainz/BIUMmisc",  
                        dependencies = TRUE, 
                        build_vignettes = TRUE)

Contributing guidelines

• Place your function(s) in an R script named in a way that makes it easy to guess what's inside.
• Use Roxygen to document your function(s). Some useful tags: @title, @description, @details, @param, @return, @author, @examples, @export, @import/@importFrom.
• If possible, add an example in the Roxygen preamble to show how to run each function.
• If possible, add one or more unit tests to check that the function(s) work as intended (using testthat).
• If your function uses functions defined in other packages, import the latter by adding @importFrom package function in the Roxygen preamble. Then document the package (e.g. using devtools::document()) to regenerate the NAMESPACE file. It's also considered good practice to refer to these external functions with package::function in the code, to avoid namespace clashes.
• As far as possible, avoid hardcoding options (e.g., point sizes in plots, or other things that someone might want to change). Instead provide them as arguments to your function.
• Generally, it's good to keep functions small (and doing a single thing), for easier testing and increased modularity. As an example, if a function does both some calculations and plotting, it can often be better to split it up into two functions, each with a clearly defined scope.