Installing RStudio Server on Scientific Linux 6: My bash notebook

August 18, 2011
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Installing RStudio Server on Scientific Linux 6: My bash notebook

Granted, not a brilliant sysadmin mind at work here, but this might help someone someday.Scientific Linux (SL) is built from Red Hat Enterprise LinuxSee installation instructions here:http://rstudio.org/download/server$ sudo rpm -Uvhhttp://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm password for leipzig: Retrievinghttp://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpmwarning: /var/tmp/rpm-tmp.S2RQAH: Header V3 RSA/SHA256 Signature, key ID0608b895: NOKEYPreparing... ...

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Kaleidoscope IIIb (useR! 2011)

August 18, 2011
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Kaleidoscope IIIb (useR! 2011)

O. Mersmann - The microbenchmark package Slides and code (link). SURGEON GENERAL’s WARNING: Microbenchmarks can lead to a distorted view of reality and massive loss of productivity For a higher-order benchmarking package check out the rbenchmark package on R (suggestion from the speaker). Why do we need micro-benchmarking? A simple example showed that it is currently very

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Big data (useR! 2011)

August 18, 2011
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Big data (useR! 2011)

Unfortunatley, I missed the first and last talks. My notes from a session on Thursday morning J. Demmler – Challenges of working with a large database of routinely collected health data The SAIL data bank holds over 1.9 billion (anonymous) entries. To use the data for research, they need to ensure that proper data security is

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We keep breaking records ? so what ?… Get statistical perspective….

August 17, 2011
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We keep breaking records ? so what ?… Get statistical perspective….

This summer, we have been told that some financial series broke some records (here, in French) For instance, the French CAC40 had negative return for 11 consecutive days (which has never been seen, so far). > library(tseries)> x<-get....

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The stupidest R code ever

August 17, 2011
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The stupidest R code ever

Let’s start this blog off right, with the stupidest R mistake I’ve ever made (I think). In the R package that I write, R/qtl, one of the main file formats is a comma-delimited file, where the blank cells in the second row are important, as they distinguish the initial phenotype columns from the genetic marker

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Real Squeeze

August 17, 2011
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Real Squeeze

Real yields even out to 10 years have now been competely squeezed. Either bond investors need to accept even worse negative real yields or deflation needs to get ugly for additional price returns from here. If deflation is the outcome, then shorts in s...

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One R Tip A Day: How to draw a plot with two Y axises and one X axis

August 17, 2011
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One R Tip A Day: How to draw a plot with two Y axises and one X axis

One R Tip A Day: How to draw a plot with two Y axises and one X axisplot(1:10)par("usr")# 0.64 10.36 0.64 10.36# Now resetting y axis' usr coordinates:par(usr=c(par("usr"), 101, 105))points(1:5, 105:101, col="red")axis(4)par(mar=c(4, 5, 4, 5) ...

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Lies, Damned Lies, and Politicians

August 17, 2011
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Lies, Damned Lies, and Politicians

I like politics; I don’t like all of the lying involved.  If you ask me, I think that there should be “Ethics Committee” investigations into all of the lying.  Sure, tweeting a picture of your junk is probably not the … Continue reading →

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-1% Guaranteed Real Real Return! Yummy??

August 17, 2011
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-1% Guaranteed Real Real Return! Yummy??

If we’re cooking up a bond return, we have access to 3 ingredients: inflation, credit, and real. Historically, the recipe looks like this (as described in Historical Sources of Bond Returns).0-5 parts inflation + 1-2 parts credit + 1-3 parts realand ...

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Introduction

August 17, 2011
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Introduction

I’m at the useR! Conference in Coventry, UK, this week. It’s been every bit as inspiring, interesting and useful as I’d hoped. Particularly interesting were the Lightning talks: a series of 5 minute presentations with one minute in between, with each presentation having 15 slides of 20 sec each, moved forward automatically.  It worked extremely

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useR2011 Easy interactive ggplots talk

August 17, 2011
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useR2011 Easy interactive ggplots talk

I’m talking tomorrow at useR! on making ggplots interactive with the gWidgets GUI framework. For those of you at useR, here is the code and data, so you can play along on your laptops. For everyone else, I’ll make the slides available in the next few days so you can see what you missed. Note

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The R-Files: Martyn Plummer

August 17, 2011
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The R-Files: Martyn Plummer

"The R-Files" is an occasional series from Revolution Analytics, where we profile prominent members of the R Community. Name: Martyn Plummer Occupation: Statistician at International Agency for Research on Cancer Nationality: British Years Using R: 16 Known for: Member of R core group; member of R Journal editorial board Martyn Plummer is a longtime contributor to the R community...

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Programming (useR! 2011)

August 17, 2011
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Programming (useR! 2011)

Ray Brownrigg – Tips and Tricks for young R programmers Problem: Calculate the distribution function of a bivariate Kolomogorov Smirnoff statistic. Essentially three loops. Basic exhaustive search is O(N^3). Fortran gives a single order of magnitude speed-up. Restructuring in R using a single loop is an order faster than fortran. Further improvements make the algorithm

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Teaser: Running R as a map/reduce job from Riak

August 17, 2011
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Teaser: Running R as a map/reduce job from Riak

Alliterations aside, here is a preview of something I’ve been tinkering with. My goal is to be able to run …Continue reading »

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Kaleidoscope IIb (useR! 2011)

August 17, 2011
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Kaleidoscope IIb (useR! 2011)

L Collingwood – RTextTools RTextTools. A machine learning library for automated text classification. This package builds on previous packages such as tm and random forests. Use case: undergrad labels congressional bills but then quits. Using the previously labelled data, automatically classify the remaining documents. The speaker gave a nice overview of machine learning techniques, but I

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Lee E. Edlefsen – Scalable Data Analysis in R (useR! 2011)

August 17, 2011
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Lee E. Edlefsen – Scalable Data Analysis in R (useR! 2011)

The RevoScaleR package isn’t open source, but it is free for academic users. Collect and storing data has outpaced our ability to analyze it. Can R cope with this challenge? The RevoScaleR package is part of the revolution R Enterprise. This package provides data management and data analysis. Uses multiple cores and should scale. Scalability

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RTextTools v1.2 Available on CRAN + useR! 2011 Kaleidoscope Session

RTextTools v1.2 was released today and we're pleased to announce that the package is finally available on CRAN. Additionally, this update brings minor changes to the API, improvements to the GLMNET algorithm, and more comprehensive documentation. Get started by following our installatio

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The fun Package: Use R for Fun!

August 16, 2011
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The fun Package: Use R for Fun!

A couple of days ago we released a package named fun to CRAN, but I did not dare to send an announcement to [email protected] as usual. This package is a collection of some classical computer games (e.g. the Mine sweeper and Five in a row) as well as other funny stuff. Some examples: ## install.packages('fun')

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Forecasting in R: Starting From Square One

August 16, 2011
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Forecasting in R: Starting From Square One

Okay in the past few posts I jumped the gun a little bit.  Errors I made include rushing everything, not explaining anything and not giving my blog readers the love and respect they deserve.  What am I talking about? Well before we do anythin...

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ttrTests Experimentation

August 16, 2011
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ttrTests Experimentation

I was intrigued by the CRAN update on a package ttrTests, especially since quantstrat is not built for backtesting system parameters and analyzing system performance as I mentioned in A Quantstrat to Build On Part 6.  ttrTests offers a nice start ...

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R Code Optimization

August 16, 2011
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R Code Optimization

Handling Large Data with R The following experiments are inspired from this excellent presentation by Ryan Rosario: http://statistics.org.il/wp-content/uploads/2010/04/Big_Memory%20V0.pdf. R presents many I/O functions to the users for reading/writing data such as ‘read.table’ , ‘write.table’ -> http://cran.r-project.org/doc/manuals/R-intro.html#Reading-data-from-files. With data growing larger by the day many new methodologies are available in order to achieve faster I/O operations.

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Brian Ripley on The R Development Process

August 16, 2011
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R Core member Professor Brian Ripley from Oxford University gave the first keynote presentation of useR! 2011 today, and gave some insights into what goes on behind the scenes to create two updates to R (plus several patches) every year. He began with some facts about the history of R (noting that if they'd known R would take off...

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The R Ecosystem

August 16, 2011
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I gave my talk to the useR! 2011 conference this morning: The R Ecosystem. The goal of the talk was to show R in context: that the combination of the R project and its leadership, the R userbase, and the companies supporting and using R makes for a thriving ecosystem and is indicative of an extremely successful open source...

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ggplot2 Version of Figures in “25 Recipes for Getting Started with R”

August 16, 2011
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ggplot2 Version of Figures in “25 Recipes for Getting Started with R”

In order to provide an option to compare graphs produced by basic internal plot function and ggplot2, I recreated the figures in the book, 25 Recipes for Getting Started with R, with ggplot2. The code used to create the images is in separate paragraphs, allowing easy comparison. Read...

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Jonathan Rougier – Nomograms for visualising relationships between three variables (useR! 2011)

August 16, 2011
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Jonathan Rougier – Nomograms for visualising relationships between three variables (useR! 2011)

Background: Donkeys in Kenya. Tricky to find the weight of a donkey in the “field” – no pun intended! So using a few measurements,  estimate the weight. Other covariates include age. Standard practice is to fit: for adult donkeys, and other slightly different models for young/old and ill donkeys. What can a statistician add: Add

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Ulrike Gromping – Design of Experiments in R

August 16, 2011
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Ulrike Gromping – Design of Experiments in R

Example: Car seat occupation: Algorithm must decide whether airbag opens: Must open for adult but not for small child or if the seat if empty a few others I missed. Key questions are: What type of design: 32 run regular fractional factorial Response measurement – depends on dummy position, so repeat for 3 different dummy

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High Performance Computing

August 16, 2011
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High Performance Computing

Wilem Ligtenberg – GPU computing and R Why GPU computing – theoretical GFLOPs for a GPU is three times greater than a CPU. Use GPUs for same instruction multiple data problems (SIMD). Initially GPUs were developed for texture problems. For example, a wall smashed into lots of pieces. Each core handled a single piece. CUDA

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Using Deducer to work with R

August 16, 2011
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Using Deducer to work with R

If one checks out the initial question that prompted this series, a common theme in the answers is that one should use the GUI as a tool to help one build code (and not just as a crutch to do the analysis). Being able to view the code produced by the GUI should help beginner R users

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R Code Examples on Graphics

August 16, 2011
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R Code Examples on Graphics

Some useful R code examples on  graphics are: Learn R Toolkit: It contains PowerPoint slideshows, videos, R scripts and data files to help Excel users move up to R. R code examples are provided for panel charts, conditional format, dot … Continue reading →

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