Hi! I'm Zhian

I'm a computational biologist focused on population genetics of clonal plant pathogens. In fact, I've written an R package for that called poppr

This site serves as my personal site where I can blog about various subjects including R programming, reproducible science, and population genetics.

My Blog

Most of the posts will have something to do with R, population genetics, reproducibility, or academia

I C Bugs

By Zhian N. Kamvar on 2018-01-14

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.

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Poppr 2.6.0: Better Network Plotting

By Zhian N. Kamvar on 2018-01-11

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.

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Using a custom library in R

By Zhian N. Kamvar on 2017-11-18

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-3.4.2/library or

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Installing the ABySS

By Zhian N. Kamvar on 2017-10-05

A couple of weeks ago, I wanted to explore assembling 55 genomes of Sclerotinia sclerotiorum to check for structural rearrangements that could be caused by sub-lethal fungicide exposure. I figured the best way to do this was to assemble these genomes de novo as opposed to aligning them to a reference. This brought me to installing the ABySS de novo assembler on the HCC Tusker Cluster… and I can happily report, that after half a day of command line bullshittery1, I had ABySS up and running 👍.

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