convert graphic object to tree object using treeio

January 1, 2017
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convert graphic object to tree object using treeio

I have splitted ggtree to 2 packages, treeio and ggtree. Now ggtree is mainly focus on visualization and annotation, while treeio focus on parsing and exporting tree files. Here is a welcome message from treeio that you can convert ggtree output to tree object which can be exported as newick or nexus file if you want. Thanks to ggplot2, output...

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A Theory of Nested Cross Simulation

January 1, 2017
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A Theory of Nested Cross Simulation

[Reader’s Note. Some of our articles are applied and some of our articles are more theoretical. The following article is more theoretical, and requires fairly formal notation to even work through. However, it should be of interest as it touches on some of the fine points of cross-validation that are quite hard to perceive or … Continue...

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tidyquant: Bringing Quantitative Financial Analysis to the tidyverse

December 31, 2016
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tidyquant: Bringing Quantitative Financial Analysis to the tidyverse

My new package, tidyquant, is now available on CRAN. tidyquant integrates the best quantitative resources for collecting and analyzing quantitative data, xts, quantmod and TTR, with the tidy data infrastructure of the tidyverse allowing for seamless in...

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Our R package roundup

December 31, 2016
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Our R package roundup

A year in review And yet again, it’s that time of the year when one eats too much and gets in a reflective mood! 2016 is nearly over, and us bloggers here at opiateforthemass.es thought it would be nice to argue endlessly which R package was th...

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Turning KML into tidy data frames

Turning KML into tidy data frames

This note briefly introduces the tidykml package, which turns basic KML geometries into tidy data frames that can be visualized with ggplot2. Summary The tidykml package provides a quick way to import data from Google My Maps into R, in a format that makes it easy to manipulate the data and visualize it with ggplot2. Below is...

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Power BI custom visuals, based on R

December 30, 2016
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Power BI custom visuals, based on R

You've been able to include user-defined charts using R in Power BI dashboards for a while now, but a recent update to Power BI includes seven new custom charts based on R in the customs visuals gallery. You can see the new chart types by visiting the Power BI Custom Visuals Gallery and clicking on the "R-powered visuals" tab....

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Fireworks (in R)

December 30, 2016
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Fireworks (in R)

New Year – a new chapter, new verse, or just the same old story ? Ultimately we write it. The choice is ours. ― Alex Morritt The Analytics Lab and Cmotions wish everybody a happy year. A year full of challenges, new experiences and new knowledge. Github library(ggplot2) rm(list = ls()) # First rocket t1

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Outlier App: An Interactive Visualization of Outlier Algorithms

December 30, 2016
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Outlier App: An Interactive Visualization of Outlier Algorithms

I was recently trying various outlier detection algorithms. For me, the best way to understand an algorithm is to tinker with it. I built a shiny app that allows you to play around with various outlier algorithms and wanted to share it with everyone. The shiny app is available on my site, but even better, Related Post

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Sparse matrices, k-means clustering, topic modelling with posts on the 2004 US Presidential election

December 30, 2016
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Sparse matrices, k-means clustering, topic modelling with posts on the 2004 US Presidential election

Daily Kos bags of words from the time of the 2004 Presidential election This is a bit of a rambly blog entry today. My original motivation was to just explore moving data around from R into the H2O machine learning software. While successful on this,...

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dotplot for GSEA result

December 29, 2016
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dotplot for GSEA result

For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result. In DOSE (and related tools including clusterP...

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How to map your Google location history with R

December 29, 2016
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How to map your Google location history with R

It’s no secret that Google Big Brothers most of us. But at least they allow us to access quite a lot of the data they have collected on us. Among this is the Google location history. If you want to see a few ways how to quickly and easily visualize ...

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Pokemon and TrelliscopeJS!

December 29, 2016
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I’m always looking for ways to spark my kid’s interest in computers, data, etc. This has proven to be more difficult than I thought it would be (kids these days…). I suspect this may have something to do with the ubiquity of electronic devices that “just work”, making them less novel and less interesting to tinker with, but speculation...

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a Galton-Watson riddle

December 29, 2016
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a Galton-Watson riddle

The Riddler of this week has an extinction riddle which summarises as follows: One observes a population of N individuals, each with a probability of 10⁻⁴ to kill the observer each day. From one day to the next, the population decreases by one individual with probability K√N 10⁻⁴ What is the value of K that

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Sampling from shifted Gompertz distribution

December 29, 2016
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Sampling from shifted Gompertz distribution

using Accept-Reject method - Shifted Gompertz distribution Shifted Gompertz distribution is useful distribution which can be used to describe time needed for adopting new innovation within the market. Recent studies showed that it outperforms Bass model of diffusion in some cases1. Its pdf is given by Below we...

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7 Visualizations You Should Learn in R

December 29, 2016
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7 Visualizations You Should Learn in R

7 Visualizations You Should Learn in R With ever increasing volume of data, it is impossible to tell stories without visualizations. Data visualization is an art of how to turn numbers into useful knowledge. R Programming lets you learn this art by offering a set of inbuilt functions and libraries to build visualizations and present... Read MoreThe...

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Quadratic Discriminant Analysis of Two Groups

December 29, 2016
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As mentioned in the post on classification with linear discriminant analysis, LDA assumes the groups in question have equal covariance matrices . Therefore, often when the groups do not have equal covariance matrices, observations are frequently assigned to groups with large variances on the diagonal of its corresponding covariance matrix... The post Quadratic Discriminant Analysis of Two Groups...

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Using R to prevent food poisoning in Chicago

December 29, 2016
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There are more than 15,000 restaurants in Chicago, but fewer than 40 inspectors tasked with making sure they comply with food-safety standards. To help prioritize the facilities targeted for inspection, the City of Chicago used R to create a model that predicts which restaurants are most likely to fail an inspection. Using this model to deploy inspectors, the City...

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Intermediate Tree 1

December 29, 2016
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Intermediate Tree 1

If you followed through the Basic Decision Tree exercise, this should be useful for you. This is like a continuation but we add so much more. We are working with a bigger and badder datasets. We will be also using techniques we learned from model evaluation and work with ROC, accuracy and other metrics. Answers

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An Interview With Jo Hardin, author of Foundations of Inference

December 29, 2016
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Hey R fans! A new episode of DataCamp's DataChats video series is out!  In this episode, we interview Jo Hardin. Jo is a Professor of Mathematics at Pomona College with many years of R experience.  She has a pure passion for education and has been w...

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Reactive acronym list in stratvis, a timevis-based Shiny app

December 29, 2016
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Reactive acronym list in stratvis, a timevis-based Shiny app

Abstract I present a method for reactively updating a table of acronyms from a Shiny interactive timeline using renderDataTable and timevis. The method is used in the new Shiny app, stratvis. The stratvis app The stratvis Shiny app provides a rich a...

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Euler Problem 5: Smallest Multiple

December 29, 2016
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Solution to Euler Problem 5 in the R Language for Statistical Computing: What is the smallest positive number that is evenly divisible by all of the numbers from 1 to 20? Continue reading → The post Euler Problem 5: Smallest Multiple appeared first on The Devil is in the Data.

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The Instant Rise of Machine Intelligence?

December 28, 2016
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The Instant Rise of Machine Intelligence?

Currently the news are filled with articles about the rise of machine intelligence, artificial intelligence and deep learning. For the average reader it seems that there was this single technical breakthrough that made AI possible. While I strongly bel...

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Tip: Optimize your Rcpp loops

December 28, 2016
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Tip: Optimize your Rcpp loops

In this post, I will show you how to optimize your Rcpp loops so that they are 2 to 3 times faster than a standard implementation. Context Real data example For this post, I will use a big.matrix which represents genotypes for 15,283 individuals, corresponding to the number of mutations (0, 1 or 2) at 287,155 different loci. Here, I will use...

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Combine choropleth data with raster maps using R

December 28, 2016
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Combine choropleth data with raster maps using R

Switzerland is a country with lots of mountains, and several large lakes. While the political subdivisions (called municipalities) cover the high mountains and lakes, nothing much of economic interest happens in these places. (Raclette and sailing are wonderful, but don't count for our purposes.) For this reason, the Swiss Federal Statistical Office publishes the boundaries of the "productive" parts...

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Exploratory Data Analysis Using R (Part-I)

December 28, 2016
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Exploratory Data Analysis Using R (Part-I)

The greatest value of a picture is when it forces us to notice what we never expected to see. — John W. Tukey. Exploratory Data Analysis.Why do we use exploratory graphs in data analysis?Understand data propertiesFind patterns in dataSuggest mod...

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Celebrating our 100th R exercise set

December 28, 2016
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Celebrating our 100th R exercise set

Yesterday we published our 100th set of exercises on R-exercises. Kudos and many thanks to Avi, Maria Elisa, Euthymios, Francisco, Imtiaz, John, Karolis, Mary Anne, Matteo, Miodrag, Paritosh, Sammy, Siva, Vasileios, and Walter for contributing so much great material to practice R programming! Even more thanks to Onno, who is working (largely) behind the scenes

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Making Shiny apps awesome

Making Shiny apps awesome

A week before Christmas our CTO, Marek Rogala gave a speech about ways to make Shiny apps do much more than usual during R enthusiasts meeting in Warsaw. In case you have missed this event we have published his presentation online: NOTE! in this pr...

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R code to accompany Real-World Machine Learning (Chapters 2-4 Updates)

December 28, 2016
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R code to accompany Real-World Machine Learning (Chapters 2-4 Updates)

Abstract I updated the R code to accompany Chapter 2-4 of the book “Real-World Machine Learning” by Henrik Brink, Joseph W. Richards, and Mark Fetherolf to be more consistent with the listings and figures as presented in the book. rwml-R Chapters...

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Behind the scenes of CRAN

December 27, 2016
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(Just from my point of view as a package maintainer.)New users of R might not appreciate the full benefit of CRAN and new package maintainers may not appreciate the importance of keeping their packages updated and free of warnings and errors. This is something I only came to realize myself in the last few years

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