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.
Using lldb to track down a bug in C
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.
My R package poppr hit over 20,000 downloads on CRAN. I thought this would be a nice opportunity to briefly talk about what initiated the development. Before that, let’s look at the cumulative number of downloads:
CRAN you dig it? Thanks to the fantastic cranlogs package, assessing the download history of a package is quite simple (with the caveat that these are logs from the rstudio mirror, so the value is almost always lower than the true value).