dendextend version 1.0.1 + useR!2015 presentation

When using the dendextend package in your work, please cite it using:

Tal Galili (2015). dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering. Bioinformatics. doi:10.1093/bioinformatics/btv428

My R package dendextend (version 1.0.1) is now on CRAN!

The dendextend package Offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. With it you can (1) Adjust a tree’s graphical parameters – the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different dendrograms to one another.

The previous release of dendextend (0.18.3) was half a year ago, and this version includes many new features and functions.

To help you discover how dendextend can solve your dendrogram/hierarchical-clustering issues, you may consult one of the following vignettes:

Here is an example figure from the first vignette (analyzing the Iris dataset)



This week, at useR!2015, I will give a talk on the package. This will offer a quick example, and a step-by-step example of some of the most basic/useful functions of the package. Here are the slides:


Lastly, I would like to mention the new d3heatmap package for interactive heat maps. This package is by Joe Cheng from Rstudio, and integrates well with dendrograms in general and dendextend in particular (thanks to some lovely github-commit-discussion between Joe and I). You are invited to see lively examples of the package in the post at the RStudio blog. Here is just one quick example:

d3heatmap(nba_players, colors = “Blues”, scale = “col”, dendrogram = “row”, k_row = 3)


The dendextend package for visualizing and comparing trees of hierarchical clusterings (slides from useR!2014)

When using the dendextend package in your work, please cite it using:

Tal Galili (2015). dendextend: an R package for visualizing, adjusting, and comparing trees of hierarchical clustering. Bioinformatics. doi:10.1093/bioinformatics/btv428

This week I presented in the useR!2014 my package dendextend (also on github), for easily manipulating, visualizing, and comparing dendrograms. Put simply, it is a package designed to easily create figures like these:

2015-06-28 20_58_26-Clipboard

Here is my presentation from useR:

Download (PDF, 8.42MB)

You are also invited to give a look to the current version of the package vignettes:

I highly welcome features suggestions and bug reports (or just “wow, this is awesome”) sent to my e-mail (tal.galili AT, you can also leave a comment or use the github issue page.

A sidenote on useR!2014: this year’s useR conference was wonderful! I enjoyed the many talks, sessions, posters, and especially the so many wonderful R users I got to meet (and I will not try to list all of you – but you know who you are, and how much I enjoyed seeing you!). As corny as it may sound – we, the people who use R, are truly a community. There is a lot to be said about getting to meet so many people who share my own passion for statistical programming, open source, collaboration, open science, and a better future in general. Gladly, you can get a sense of what happened there by having a look at the twitter hashtag #useR2014. Several great R bloggers already started writing about it, you can see their posts here: 1, 2, 3, 4, 5. And I hope more posts will follow. I hope to see you in next year’s useR!2015!

UseR! 2011 slides and videos – on one page

Links to slides and talks from useR 2011 – all organized in one page.

I was recently reminded that the wonderful team at warwick University made sure to put online many of the slides (and some videos) of talks from the recent useR 2011 conference.  You can browse through the talks by going between the timetables (where it will be the most updated, if more slides will be added later), but I thought it might be more convenient for some of you to have the links to all the talks (with slides/videos) in one place.

I am grateful for all of the wonderful people who put their time in making such an amazing event (organizers, speakers, attendees), and also for the many speakers who made sure to share their talk/slides online for all of us to reference.  I hope to see this open-slides trend will continue in the upcoming useR conferences…

Bellow are all the links:

Tuesday 16th August

09:50 – 10:50

Kaleidoscope Ia, MS.03, Chair: Dieter Menne
Claudia BeleitesSpectroscopic Data in R and Validation of Soft Classifiers: Classifying Cells and Tissues by Raman Spectroscopy[Slides]
Jonathan RosenblattRevisiting Multi-Subject Random Effects in fMRI[Slides]
Zoe HoarePutting the R into Randomisation[Slides]
Kaleidoscope Ib, MS.01, Chair: Simon Urbanek
Markus GesmannUsing the Google Visualisation API with R[Slides]
Kaleidoscope Ic, MS.02, Chair: Achim Zeileis
David SmithThe R Ecosystem[Slides]
E. James HarnerRc2: R collaboration in the cloud[Slides]

11:15 – 12:35

Portfolio Management, B3.02, Chair: Patrick Burns
Jagrata MinardiR in the Practice of Risk Management Today[Slides]
Bioinformatics and High-Throughput Data, B3.03, Chair: Hervé Pagès
Thierry OnkelinxAFLP: generating objective and repeatable genetic data[Slides]
High Performance Computing, MS.03, Chair: Stefan Theussl
Willem LigtenbergGPU computing and R[Slides]
Manuel QuesadaOBANSoft: integrated software for Bayesian statistics and high performance computing with R[Slides]
Reporting Technologies and Workflows, MS.01, Chair: Martin Mächler
Andreas LehaThe Emacs Org-mode: Reproducible Research and Beyond[Slides]
Teaching, MS.02, Chair: Jay G. Kerns
Ian HollidayTeaching Statistics to Psychology Students using Reproducible Computing package RC and supporting Peer Review Framework[Slides]
Achim ZeileisAutomatic generation of exams in R[Slides]

14:00 – 14:45

Invited Talk, MS.01/MS.02, Chair: David Firth
Ulrike GrömpingDesign of Experiments in R[Slides] [Video]

14:45 – 15:30

Invited Talk, MS.01/MS.02, Chair: David Firth
Jonathan RougierNomograms for visualising relationships between three variables[Slides] [Video]

16:00 – 17:00

Modelling Systems and Networks, B3.02, Chair: Jonathan Rougier
Rachel OxladeAn S4 Object structure for emulation – the approximation of complex functions[Slides]
Christophe DutangComputation of generalized Nash equilibria[Slides]
Visualisation, MS.04, Chair: Antony Unwin
Andrej BlejecanimatoR: dynamic graphics in R[Slides]
Richard M. HeibergerGraphical Syntax for Structables and their Mosaic Plots[Slides]
Dimensionality Reduction and Variable Selection, MS.01, Chair: Matthias Schmid
Marie ChaventClustOfVar: an R package for the clustering of variables[Slides]
Jürg SchelldorferVariable Screening and Parameter Estimation for High-Dimensional Generalized Linear Mixed Models Using l1-Penalization[Slides]
Benjamin HofnergamboostLSS: boosting generalized additive models for location, scale and shape[Slides]
Business Management, MS.02, Chair: Enrico Branca
Marlene S. MarchenaSCperf: An inventory management package for R[Slides]
Pairach PiboonrungrojUsing R to test transaction cost measurement for supply chain relationship: A structural equation model[Slides]
Fabrizio OrtolaniIntegrating R and Excel for automatic business forecasting

17:05 – 18:05

Lightning Talks(see bellow)

Lightning Talks

  • Community and Communication, MS.02, Chair: Ashley Ford
    • George Zhang: China R user conference [Slides]
    • Tal Galili: Blogging and R – present and future [Link]
    • Markus Schmidberger: Get your R application onto a powerful and fully-configured Cloud Computing environment in less than 5 minutes. [Slides]
    • Eirini Koutoumanou: Teaching R to Non Package Literate Users [Slides]
    • Randall Pruim: Teaching Statistics using the mosaic Package [Slides]
  • Statistics and Programming, MS.01, Chair: Elke Thönnes
    • Toby Dylan Hocking: Fast, named capture regular expressions in R2.14 [Slides]
    • John C. Nash: Developments in optimization tools for R [Slides]
    • Christophe Dutang: A Unified Approach to fit probability distributions [Slides]
  • Package Showcase, MS.03, Chair: Jennifer Rogers
    • James Foadi: cRy: statistical applications in macromolecular crystallography [Slides]
    • Emilio López: Six Sigma is possible with R [Slides]
    • Jonathan Clayden: Medical image processing with TractoR [Slides]
    • Richard A. Bilonick: Using merror 2.0 to Analyze Measurement Error and Determine Calibration Curves [Slides]

Wednesday 17th August

09:00 – 09:50

Invited Talk, MS.01/MS.02, Chair: Ioannis Kosmidis
Lee E. EdlefsenScalable Data Analysis in R[Slides] [Video]

11:15 – 12:35

Spatio-Temporal Statistics, B3.02, Chair: Julian Stander
Nikolaus UmlaufStructured Additive Regression Models: An R Interface to BayesX[Slides]
Molecular and Cell Biology, B3.03, Chair: Andrea Foulkes
Matthew NunesSummary statistics selection for ABC inference in R[Slides]
Maarten van ItersonPower and minimal sample size for multivariate analysis of microarrays[Slides]
Mixed Effect Models, MS.03, Chair: Douglas Bates
Ulrich HalekohKenward-Roger modification of the F-statistic for some linear mixed models fitted with lmer[Slides]
Marco Geracilqmm: Estimating Quantile Regression Models for Independent and Hierarchical Data with R[Slides]
Kenneth KnoblauchMixed-effects Maximum Likelihood Difference Scaling[Slides]
Programming, MS.01, Chair: Uwe Ligges
Ray BrownriggTricks and Traps for Young Players[Slides]
Friedrich SchusterSoftware design patterns in R[Slides]
Patrick BurnsRandom input testing with R[Slides]
Data Mining Applications, MS.02, Chair: Przemysaw Biecek
Stephan StahlschmidtPredicting the offender’s age
Daniel ChapskyLeveraging Online Social Network Data and External Data Sources to Predict Personality[Slides]

14:45 – 15:30

Invited Talk, MS.01/MS.02, Chair: John Aston
Brandon WhitcherQuantitative Medical Image Analysis[Slides] [Video]

16:00 – 17:00

Development of R, B3.02, Chair: John C. Nash
Andrew R. RunnallsInterpreter Internals: Unearthing Buried Treasure with CXXR[Slides]
Geospatial Techniques, B3.03, Chair: Roger Bivand
Binbin LuConverting a spatial network to a graph in R[Slides]
Rainer M KrugSpatial modelling with the R-GRASS Interface[Slides]
Daniel Nüstsos4R – Accessing SensorWeb Data from R[Slides]
Genomics and Bioinformatics, MS.03, Chair: Ramón Diaz-Uriarte
Sebastian GibbMALDIquant: Quantitative Analysis of MALDI-TOF Proteomics Data[Slides]
Regression Modelling, MS.01, Chair: Cristiano Varin
Bettina GrünBeta Regression: Shaken, Stirred, Mixed, and Partitioned[Slides]
Rune Haubo B. ChristensenRegression Models for Ordinal Data: Introducing R-package ordinal[Slides]
Giuseppe BrunoMultiple choice models: why not the same answer? A comparison among LIMDEP, R, SAS and Stata[Slides]
R in the Business World, MS.02, Chair: David Smith
Derek McCrae NortonOdysseus vs. Ajax: How to build an R presence in a corporate SAS environment[Slides]

17:05 – 18:05

Hydrology and Soil Science, B3.02, Chair: Thomas Petzoldt
Wayne JonesGWSDAT (GroundWater Spatiotemporal Data Analysis Tool)[Slides]
Pierre RoudierVisualisation and modelling of soil data using the aqp package[Slides]
Biostatistical Modelling, B3.03, Chair: Holger Hoefling
Annamaria GuoloHigher-order likelihood inference in meta-analysis using R[Slides]
Cristiano VarinGaussian copula regression using R[Slides]
Psychometrics, MS.03, Chair: Yves Rosseel
Florian WickelmaierMultinomial Processing Tree Models in R[Slides]
Basil Abou El-KombozDetecting Invariance in Psychometric Models with the psychotree Package[Slides]
Multivariate Data, MS.01, Chair: Peter Dalgaard
John FoxTests for Multivariate Linear Models with the car Package[Slides]
Julie JossemissMDA: a package to handle missing values in and with multivariate exploratory data analysis methods[Slides]
António Pedro Duarte SilvaMAINT.DATA: Modeling and Analysing Interval Data in R[Slides]
Interfaces, MS.02, Chair: Matthew Shotwell
Xavier de Pedro PuenteWeb 2.0 for R scripts and workflows: Tiki and PluginR[Slides]
Sheri GilleyA new task-based GUI for R[Slides]

Thursday 18th August

09:00 – 09:45

Invited Talk, MS.01/MS.02, Chair: Julia Brettschneider
Wolfgang HuberGenomes and phenotypes[Slides] [Video]

09:50 – 10:50

Financial Models, B3.02, Chair: Giovanni Petris
Peter Ruckdeschel(Robust) Online Filtering in Regime Switching Models and Application to Investment Strategies for Asset Allocation[Slides]
Ecology and Ecological Modelling, B3.03, Chair: Karline Soetaert
Christian KampichlerUsing R for the Analysis of Bird Demography on a Europe-wide Scale[Slides]
John C. NashAn effort to improve nonlinear modeling practice[Slides]
Generalized Linear Models, MS.03, Chair: Kenneth Knoblauch
Ioannis Kosmidisbrglm: Bias reduction in generalized linear models[Slides]
Merete K. HansenThe binomTools package: Performing model diagnostics on binomial regression models[Slides]
Reporting Data, MS.01, Chair: Martyn Plummer
Sina RüegeruniPlot – A package to uniform and customize R graphics[Slides]
Alexander KowariksparkTable: Generating Graphical Tables for Websites and Documents with R[Slides]
Isaac SubiranacompareGroups package, updated and improved[Slides]
Process Optimization, MS.02, Chair: Tobias Verbeke
Emilio LópezSix Sigma Quality Using R: Tools and Training[Slides]
Thomas RothProcess Performance and Capability Statistics for Non-Normal Distributions in R[Slides]

11:15 – 12:35

Inference, B3.02, Chair: Peter Ruckdeschel
Henry DengDensity Estimation Packages in R[Slides]
Population Genetics and Genetics Association Studies, B3.03, Chair: Martin Morgan
Benjamin FrenchSimple haplotype analyses in R[Slides]
Neuroscience, MS.03, Chair: Brandon Whitcher
Karsten TabelowStatistical Parametric Maps for Functional MRI Experiments in R: The Package fmri[Slides]
Data Management, MS.01, Chair: Barry Rowlingson
Susan RanneyIt’s a Boy! An Analysis of Tens of Millions of Birth Records Using R[Slides]
Joanne DemmlerChallenges of working with a large database of routinely collected health data: Combining SQL and R[Slides]
Interactive Graphics in R, MS.02, Chair: Paul Murrell
Richard CottonEasy Interactive ggplots[Slides]

14:00 – 15:00

Kaleidoscope IIIa, MS.03, Chair: Adrian Bowman
Thomas PetzoldtUsing R for systems understanding – a dynamic approach[Slides]
David L. MillerUsing multidimensional scaling with Duchon splines for reliable finite area smoothing[Slides]
Alastair SandersonStudying galaxies in the nearby Universe, using R and ggplot2[Slides]
Kaleidoscope IIIb, MS.02, Chair: Frank Harrell
Paul MurrellVector Image Processing[Slides]


The present and future of the R blogosphere (~7 minute video from useR2011)

This is (roughly) the lightning talk I gave in useR2011. If you are a reader of then this talk is not likely to tell you anything new. However, if you have a friend, college or student who is a new useRs of R, this talk will offer him a decent introduction to what the R […]

This is (roughly) the lightning talk I gave in useR2011. If you are a reader of then this talk is not likely to tell you anything new. However, if you have a friend, college or student who is a new useRs of R, this talk will offer him a decent introduction to what the R blogosphere is all about.

The talk is a call for people of the R community to participate more in reading, writing and interacting with blogs.

I was encouraged to record this talk per the request of Chel Hee Lee, so it may be used in the recent useR conference in Korea (2011)

The talk (briefly) goes through:

  1. The widespread influence of the R blogosphere
  2. What R bloggers write about
  3. How to encourage a blogger you enjoy reading to keep writing
  4. How to start your own R blog (just go to
  5. Basic tips about writing a blog
  6. One advice about marketing your R blog (add it to
  7. And two thoughts about the future of R blogging (more bloggers and readers, and more interactive online visualization)

My apologies for any of the glitches in my English. For more talks about R, you can visit the R user groups blog. I hope more speakers from useR 2011 will consider uploading their talks online.

Blogging about R – presentation and audio

At the useR!2010 conference I had the honor of giving a (~15 minute) talk titled “Blogging about R”. The following is the abstract I submited, followed by the slides of the talk and the audio file of a recording I made of the talk (I am sad it got a bit of “hall echo”, but it’s still listenable…)

P.S: this post does not absolve me from writing up something (with many thanks and links to people) about the useR2010 conference, but I can see it taking a bit longer till I do that.


Abstract of the talk

This talk is a basic introduction to blogs: why to blog, how to blog, and the importance of the R blogosphere to the R community.

Because R is an open-source project, the R community members rely (mostly) on each other’s help for statistical guidance, generating useful code, and general moral support.

Current online tools available for us to help each other include the R mailing lists, the community R-wiki, and the R blogosphere. The emerging R blogosphere is the only source, besides the R journal, that provides our community with articles about R. While these articles are not peer reviewed, they do come in higher volume (and often are of very high quality).

According to the meta-blog, the (English) R blogosphere has produced, in January 2010, about 115 “articles” about R. There are (currently) a bit over 50 bloggers (now about 100) who write about R, with about 1000 (now ~2200) subscribers who read them daily (through e-mails or RSS). These numbers allow me to believe that there is a genuine interest in our community for more people – perhaps you? – to start (and continue) blogging about R.

In this talk I intend to share knowledge about blogging so that more people are able to participate (freely) in the R blogosphere – both as readers and as writers. The talk will have three main parts:

  • What is a blog
  • How to blog – using the (free) blogging service (with specific emphasis on R)
  • How to develop readership – integration with other social media/networks platforms, SEO, and other best practices

* * *
Tal Galili founded and blogs on
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Audio recording of the talk

Continue reading “Blogging about R – presentation and audio”

June 20, online Registration deadline for useR! 2010

useR!2010 is coming. I am going to give two talks there (I will write more of that soon), but in the meantime, please note that the online registration deadline is coming to an end.

This was published on the R-help mailing list today:


The final registration deadline for the R User Conference is June 20,
2010, one week away.  Later registration will not be possible on site!

Conference webpage:
Conference program:


The conference is scheduled for July 21-23, 2010, and will take place at
the campus of the National Institute of Standards and Technology (NIST) in
Gaithersburg, Maryland, USA.

Continue reading “June 20, online Registration deadline for useR! 2010”