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