Hoo-boy! It has been a long time since last wrote in this blog and… well… a lot has happened1 since then. I promise that from now on, I will update this blog at least once a week with thoughts or insights I have about R package development, research software engineering, and updates to R packages. In the meantime, have a picture of my precious baby boy, whom I had to leave in California:
Positive Contact This version of poppr is a direct result of feedback that was prompted by my own feedback. I’m always grateful for eagle-eyed users of poppr who report when things are going awry. Recently, I had noticed that poppr was cited in a recent review on the analysis of polyploid genetic data (Meirmans, Liu, and Tienderen 2018) that highlighted some limitations with established methods, including Bruvo’s distance (Bruvo et al.
A Brown marmorated stink bug female from a laboratory colony on a common bean leaf, photographed in the laboratory of Fondazione Edmund Mach, Italy. URL: https://commons.wikimedia.org/wiki/File:Halyomorpha_halys_lab.jpg Occasionally, I hear people complain about the strict policies of CRAN, but I for one quite apprecieate them, especially when dealing with hidden errors in compiled code. Not twenty-four hours after I had submitted poppr version 2.6.0 to CRAN did I receive an email from none other than Brian D.
Poppr version 2.6.0 has officially been released on CRAN and should be built for all operating systems within the next few days 🎉. You can check out the NEWS for full details. This release features a new function called boot.ia() to assess how the Index of Association responds to repeat observations (clones). Perhaps the biggest feature is the change in how minimum spanning networks are plotted. Minimum spanning networks were originally implemented in poppr by Javier Tabima and I, and since then they’ve gone through some tweaking, eventually including features like reticulation of equivalent paths and a GUI to help construct these networks.
I’ve been using a custom library for R since 2012 and I’ve never looked back. I’ve not seen many tutorials for people do do this through R, so I figured I’d write a quick one. Where does your R package library live? You can usually find this out by typing .libPaths() in your R console. If you have an out-of-the-box installation, it will generally be somewhere like: C:/Program Files/R/R-3.
