Blog Archives

Using ARPACK to compute the largest eigenvalue of a matrix

February 7, 2013
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Thanks to Gábor Csárdi, author of the R interface to ARPACK, for this example of using (the R/Igraph interface to) arpack for finding the largest eigenvalue of a matrix. The key insight is that arpack solves the function passed to … Continue reading →

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finding meaningful clusters in phylogenetic trees or other hierarchical clusterings

November 8, 2012
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finding meaningful clusters in phylogenetic trees or other hierarchical clusterings

Phylogenetic trees are a specialization of hierarchical clustering which elegantly capture relatedness between observations, grouping like with like. Yet hierarchical clusterings have one common complaint, as compared to density/distribution based clustering, the ability to classify the data into different types. … Continue reading →

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Making a hive plot of HIV transmission network — tutorial

October 4, 2012
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Making a hive plot of HIV transmission network — tutorial

Hiveplots are the über-cool graph visualization created by the prolific Martin Krzywinski and ported to R by the equally talented Bryan Hanson. Martin has created a network visualization tool which displays the underlying structure of a network and ends the … Continue reading →

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Ebola in the Congo

August 23, 2012
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Ebola in the Congo

Ebola has also appeared in the Democratic Republic of the Congo. The WHO report from 21 August reports 15 cases and 10 deaths, mostly in the town of Isiro. This outbreak is in no way related to the Ugandan outbreak … Continue reading →

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Did the Kigadi Ebola outbreak threaten to become an (inter)national epidemic?

August 22, 2012
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Did the Kigadi Ebola outbreak threaten to become an (inter)national epidemic?

We want to evaluate the seriousness of the threat posed by the recent ebola outbreak in western Uganda. The outbreak appeared in Kigadi, a small village in the Kibaale district. The disease was first confirmed by the government on 28 … Continue reading →

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