788 search results for "KnitR"

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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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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Goodreads API

December 22, 2016
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Goodreads API

It’s December 23rd and I’ve only read 49 books. Whoops. There’s still time, but it’s definitely getting dicey. I’m about halfway through three books right now so I think I’ll be able to pull it off. Fingers crossed. Of course, last year I ...

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suRprise! – Classifying Kinder Eggs by Boosting

December 22, 2016
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suRprise! – Classifying Kinder Eggs by Boosting

Abstract Carrying the Danish tradition of Juleforsøg to the realm of statistics, we use R to classify the figure content of Kinder Eggs using boosted regression trees for the egg's weight and possible rattling noises. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. The markdown+Rknitr source code...

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Animating Plots of Beer Ingredients and Sin Taxes over Time

December 21, 2016
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Animating Plots of Beer Ingredients and Sin Taxes over Time

With the upcoming holidays, I thought it fitting to finally explore the ttbbeer package. It contains data on beer ingredients used in US breweries from 2006 to 2015 and on the (sin) tax rates for beer, champagne, distilled spirits, wine and various tob...

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Baseline Characteristics Tables with qwraps2

December 18, 2016
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Almost every biomedical research paper requires a “Table 1: baseline patient characteristics.” Many developers have published tools to help streamline the construction of such tables. The qwraps2::summary_table function is my contribution to the ...

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How to build a Shiny app for disease- & trait-associated locations of the human genome

December 17, 2016
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This app is based on the gwascat R package and its ebicat38 database and shows trait-associated SNP locations of the human genome. You can visualize and compare the genomic locations of up to 8 traits simultaneously. The National Human Genome Research...

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Learning how to extend #RStudio by reading books

December 17, 2016
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Learning how to extend #RStudio by reading books

This post is part of a series of "learning everything with R: An R book list". You can clink on this link to see other relevant posts. RStudio probably is the most popular interface to use R. But it definitely does not just serve as a code editor (than...

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Gene homology Part 2 – creating directed networks with igraph

December 13, 2016
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Gene homology Part 2 – creating directed networks with igraph

In my last post I created a gene homology network for human genes. In this post I want to extend the network to include edges for other species. First, I am loading biomaRt and extract a list of all available datasets. library(biomaRt) ensembl = useM...

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The Statistician’s Apprentice: An Introduction to the SWP Operator

December 12, 2016
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The Statistician’s Apprentice: An Introduction to the SWP Operator

The sweep operator as defined in (Dempster, 1969), commonly referred to as the SWP operator, is a useful tool for a computational statistician working with covariance matrices. In particular, the SWP operator allows a statistician to quickly regress all variables against one specified variable, obtaining OLS estimates for regression coefficients and variances in a single application. Subsequent...

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