[ggtree] annotate phylogenetic tree with local images

August 1, 2015
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[ggtree] annotate phylogenetic tree with local images

In ggtree, we provide a function annotation_image for annotating phylogenetic tree with images. To demonstrate the usage, I created a tree view from a random tree as shown below: Read More: 973 Words Totally

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Streamgraphs in R

July 31, 2015
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Streamgraphs in R

It's not easy to visualize a quantity that varies over time and which is composed of more than two subsegments. Take, for example, this stacked bar chart of religious...

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Rendering LaTeX Math Equations in GitHub Markdown

July 31, 2015
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Rendering LaTeX Math Equations in GitHub Markdown

The Problem: GitHub README.md won't render LaTeX I have many times wondered about getting LaTeX math to render in a README file on GitHub. Apparently, many others ( 1,...

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Building a user interface for spatstat

July 30, 2015
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Building a user interface for spatstat

Contents Introduction Get and run it! Roadmap Introduction RStudio developed shiny, an R package that, quoting from their website, “makes it super simple for R users...

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15 Questions All R Users Have About Plots

July 30, 2015
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15 Questions All R Users Have About Plots

R allows you to create different plot types, ranging from the basic graph types like density plots, dot plots, bar charts, line charts, pie charts, boxplots and scatter plots,...

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MRAN’s Packages Spotlight

July 30, 2015
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MRAN’s Packages Spotlight

by Joseph Rickert New R packages just keep coming. The following plot, constructed with information from the monthly files on Dirk Eddelbuettel's CRANberries site, shows a plot of the...

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The little mixed model that could, but shouldn’t be used to score surgical performance

July 30, 2015
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The little mixed model that could, but shouldn’t be used to score surgical performance

The Surgeon Scorecard Two weeks ago, the world of medical journalism was rocked by the public release of ProPublica’s Surgeon Scorecard. In this project ProPublica “calculated death and complication...

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Empirical bias analysis of random effects predictions in linear and logistic mixed model regression

July 30, 2015
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Empirical bias analysis of random effects predictions in linear and logistic mixed model regression

In the first technical post in this series, I conducted a numerical investigation of the biasedness of random effect predictions in generalized linear mixed models (GLMM), such as the ones...

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#rstats Make arrays into vectors before running table

July 29, 2015
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#rstats Make arrays into vectors before running table

Setup of Problem While working with nifti objects from the oro.nifti, I tried to table the values of the image. The table took a long time to compute. I...

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R Oddities: Strings in DataFrames

July 29, 2015
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R Oddities:  Strings in DataFrames

Have you ever read a file into R and then encountered strange problems filtering and sorting because the strings were converted to factors?  For...

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But I Don’t Want to Be a Statistician!

July 29, 2015
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But I Don’t Want to Be a Statistician!

"For a long time I have thought I was a statistician.... But as I have watched mathematical statistics evolve, I have had cause to wonder and to doubt.... All...

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Mapping the past and the future with Leaflet

July 29, 2015
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Mapping the past and the future with Leaflet

I have been working on mapping things for a while and I must say that I really like the Leaflet package from Rstudio. It makes it very easy and...

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Player Value Gap Assessment

July 29, 2015
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Player Value Gap Assessment

Looking at fantasy football projections we have a group of experts providing their views on how a player will do during the football season. We have collected projections from...

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Predict Social Network Influence with R and H2O Ensemble Learning

July 29, 2015
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Predict Social Network Influence with R and H2O Ensemble Learning

What is H2O? H2O is an awesome machine learning framework. It is really great for data scientists and business analysts “who need scalable and fast machine learning”. H2O is...

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Hockey Elbow and Other Response Time Injuries

July 29, 2015
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Hockey Elbow and Other Response Time Injuries

You've heard of tennis elbow. Well, there's a non-sports, performance injury that I like to call hockey elbow. An example of such an "injury" is shown in Figure...

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The most popular programming languages on StackOverflow

July 29, 2015
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The most popular programming languages on StackOverflow

by Andrie de Vries Last week, IEEE Spectrum said R rised to #6 in Top Programming languages. They use a weighted methodology of 12 factors to compute their score....

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Introducing the nominatim geocoding package

July 29, 2015
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Introducing the nominatim geocoding package

In the never-ending battle for truth, justice and publishing more R packages than Oliver, I whipped out an R package for the OpenStreetMap Nominatim API. It actually hits the...

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Computing AIC on a Validation Sample

July 29, 2015
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Computing AIC on a Validation Sample

This afternoon, we’ve seen in the training on data science that it was possible to use AIC criteria for model selection. > library(splines) > AIC(glm(dist ~ speed, data=train_cars, family=poisson(link="log")))...

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Mongolite 0.5: authentication and iterators

July 28, 2015
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Mongolite 0.5: authentication and iterators

A new version of the mongolite package has appeared on CRAN. Mongolite builds on jsonlite to provide a simple, high-performance...

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I loved this %>% crosstable

July 28, 2015
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This is a public tank you for @heatherturner's contribution. Now the SciencesPo's crosstable can work in a chain (%>%) fashion; useful for using along with other packages that have...

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Pluto: To Catch an Icy King

July 28, 2015
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Pluto: To Catch an Icy King

Sly as a fox, it is. Mysterious and diminutive, it has eluded us for decades. Despite what we've learned about Pluto, constant debate continues to rage over its classification....

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Goals for the New R Consortium

July 28, 2015
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Goals for the New R Consortium

by Bob Muenchen The recently-created R Consortium consists of companies that are deeply involved in R such as RStudio, Microsoft/Revolution Analytics, Tibco, and others. The Consortium’s goals include advancing...

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R tutorial on the Apply family of functions

July 28, 2015
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R tutorial on the Apply family of functions

Introduction In our previous tutorial Loops in R: Usage and Alternatives , we discussed one of the most important constructs in programming: the loop.  Eventually we deprecated the usage of loops in...

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Modelling Occurence of Events, with some Exposure

July 28, 2015
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Modelling Occurence of Events, with some Exposure

This afternoon, an interesting point was raised, and I wanted to get back on it (since I did publish a post on that same topic a long time ago)....

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Efficient Accumulation in R

July 28, 2015
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Efficient Accumulation in R

by John MountData Scientist, Win-Vector LLC R has a number of very good packages for manipulating and aggregating data (plyr, sqldf, RevoScaleR, data.table, and more), but when it comes to...

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The complete catalog of argument variations of select() in dplyr

July 28, 2015
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When I read the dplyr vignette, I found a convenient way to select sequential columns such as select(data, year:day). Because I had inputted only column names to select()...

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Visualising Claims Frequency

July 28, 2015
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Visualising Claims Frequency

A few years ago, I did publish a post to visualize and empirical claims frequency in a portfolio. I wanted to update the code. Here is a code to...

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Notes from the 3rd R in Insurance Conference

July 28, 2015
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Notes from the 3rd R in Insurance Conference

Photo: Arthur CharpentierThe R in Insurance conference in Amsterdam was a sold out success! Congratulations to the organising committee at the University of Amsterdam, and many thanks to our...

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upsetplot in ChIPseeker

July 28, 2015
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upsetplot in ChIPseeker

ChIPseeker is an R package for ChIP peak annotation, comparison and visualization. We have implemented several visualization methods, including vennpie that was designed for viewing annotation overlap as shown below:

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