tl;dr I don’t get paid to maintain poppr anymore and do so on my own time, so if you use it and value the work that I put into it, please donate to RAICES Texas (https://www.raicestexas.org/donate) to help provide legal services to underserved immigrant and refugee families in the United States.
Last Tuesday, I released poppr version 2.8.3, which fixed a corner case in read.genalex() and enhanced minimum spanning network rendering by drawing single-population nodes as circles instead of pies (with contribution by Frédéric Chevalier).
R package for population genetic analysis of clonal/sexual organisms
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.
As I was preparing to push a new version of poppr to CRAN , this tweet (appropriately) came across my feed: Mistakes happen in science. What matters is what you do next. Anyone want to share a story of a mistake & how they handled it? — Adrienne Porter Felt (@__apf__) September 10, 2017 The reason I was updating poppr was to fix a mistake I had made a few
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).
Motivation In February of 2016, I got an email asking if I could provide the code to recreate figure three from my article in Phytopathology on the outbreak of Phytophthora ramorum in Curry County OR from 2001 to 2014 (paywalled, but you can find a copy here).
While I have the code used for the analysis on github, it’s a lot of stuff to sort through, considering that it was my first foray in attempting a reproducible analysis, so for this post, I’m going to recreate it using current tools.