Blog Archives

Working with sparse matrices in C++

January 15, 2018
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Working with sparse matrices is a big part of my day. Social networks are inherently sparse, so sparse matrices are the best buds you can get when representing large networks as adjacency matrices.1 As so, I usually find myself trying to take advantage of their structure as, contrasting dense matrices, we don’t need to write nested for(i...) for (j...)...

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Visualizing Phylogenetic Trees with R and jsPhyloSVG

December 7, 2017
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During the last year I’ve been working on a daily basis with phylogenetic trees, objects that in graph jargon are called Directed Acyclic Graphs. While R does have some cool packages out there to visualize these–including phylocanvas which looks great!–I wanted to tryout jsPhyloSVG, and moreover, to learn how to use htmlwidgets. So, after a week-long process of playing with...

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Read viz attributes from GEXF files

November 26, 2017
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Read viz attributes from GEXF files

So one of the new features that I’ve working on is processing viz attributes. In the CRAN version of rgexf, the function read.gexf only reads in non-visual attributes and the graph structure itself, which is no longer true as of today (at least for the static viz attributes, all the other dynamic features supported by GEXF will come in...

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Some notes on my first shiny app

November 15, 2017
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Since there are plenty of examples out there telling you how to get started with shiny (like Rstudio’s, or Google), I will focus on telling some of the stuff that I did learned and may not be obvious at first, including some of the mistakes I made. Before start, I just want to stress that I’m writing this after my...

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Reboot of rgexf

November 7, 2017
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The rgexf R package has been around a couple of years now, but without much going on on CRAN (my bad!). In this post I’ll show how to use the new version (on development and soon the be shipped to CRAN) together with the netdiffuseR R package to visualize a random diffusion process. First, we load all the packages that...

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New versions of ABCoptim and googlePublicData on CRAN

November 7, 2017
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Finally, after a long wait, the R packages googlePublicData (more than 2 years since the last update!) and ABCoptim (roughly a year since the last update) have new versions on CRAN. The first just got an update that fixed some nasty bugs that were evid...

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Environments in R Rock

October 1, 2017
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Last week I found myself working on netdiffuseR trying to establish nice defaults for some plotting functions with the following goals: Make the code easy to maintain: So if I need to change defaults I just change a few lines and that works for all plot functions, Make the code easy to see in the manual (help) file: So is easier...

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Yet another plot of R’s colors()

September 14, 2017
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Yet another plot of R’s colors()

I know there are plenty of these online, but I just thought about having my own for quick reference… ncols

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Setting up optional OpenMP support with RcppArmadillo

August 28, 2017
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Setting up an R package that supports OpenMP can be a bit awkward. While systems like Ubuntu with g++ have straight forward support for -fopenmp flags, the same may not be true un MacOS’s clang, since the latter is not shipped with it. In order to solve this, it is necesary to have different src/Makevars file depending on whether the...

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