Running an R-based ABM in parallel on a Multicore Desktop

May 6, 2011
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I've been running for the last couple of months a lot of simulations written in R on legion cluster  here at UCL. But I still do many things on our quad-core server here at the institute, and parallelising the simulations is extremely handy.S...

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Extracting reflectance data from SpectraSuite JCAMP files in R

May 6, 2011
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Extracting reflectance data from SpectraSuite JCAMP files in R

I've been using an OceanOptics USB4000 spectrometer in research on biomass accumulation and climate in South Africa. This post presents a R function that will read in JCAMP files from the SpectraSuite software and output a vector of reflectance values.  SpectraSuite can convert binary output files to JCAMP files if they weren't saved as JCAMP. You...

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Extracting reflectance data from SpectraSuite JCAMP files in R

May 6, 2011
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Extracting reflectance data from SpectraSuite JCAMP files in R

I've been using an OceanOptics USB4000 spectrometer in research on biomass accumulation and climate in South Africa.This post presents a R function that will read in JCAMP files from the SpectraSuite software and output a vector of reflectance values.&...

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Is R an ideal language to teach the fundamentals of programming to beginners?

May 6, 2011
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Is R an ideal language to teach the fundamentals of programming to beginners?

I’m helping out some colleagues learn programming from having zero experience with it in any shape or form. It’s quite a daunting task in some senses, because, well, it may not be easy! They are researchers, so they’ll need it for processing data and generating output, and perhaps processing BIG DATA at some point too.

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EC2 Micro instance of RStudio

May 5, 2011
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EC2 Micro instance of RStudio

I wanted to see see if I could setup RStudio on a micro instance on Amazon EC2.  I thought it would be nice to have my own instance running in the cloud and why not use AWS free usage tier … Continue reading →

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BMS 0.3.0 Released

Version of 0.3.0 of the Bayesian Model Averaging package BMS has been released. Apart from numerous bugfixes, BMS 0.3.0 includes two main additions: The ability in bms to keep certain fixed regressors to be included in all sampled models The option t...

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Accessing MySQL through R

May 5, 2011
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Connecting to MySQL is made very easy with the RMySQL package. To connect to a MySQL database simply install the package and load the library.install.packages("RMySQL")library(RMySQL)Connecting to MySQL:Once the RMySQL library is installed create a dat...

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Day #34 Detailing graphs

Today mostly existed in adding details or changing certain aspects of my graphs. For example, I had to turn around the y-axis on my levelplot, circleplot, … which wasn’t so easy at first. But after a bit of googling I found out I had to rev...

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Day #35 replacing characters

Today I had a meeting with Emmanuel. He is a guy from inside Janssen who is very good with R-scripts. He made a lot of great plots which I had to use for our reports. During the meeting we came to a conclusion that all the difficult R-scripting he did,...

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How to access databases from R

May 5, 2011
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From his presentation at the Greater Boston useR Group, R user Jeffrey Breen has shared some useful slides detailing how to bring data from relational databases like MySQL and Oracle. In fact, data from just about any relational database is accessible from R by sending an SQL query to the standard ODBC or JDBC interfaces. R packages also offer...

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sab-R-metrics: Logistic Regression

May 5, 2011
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sab-R-metrics: Logistic Regression

It's been a while since my last sab-R-metrics post, and I have not gotten to the real fun stuff yet. I apologize for the long layoff, and it's likely that these will be sparse for the next couple weeks. I have had some consulting opportunities come u...

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sab-R-metrics: Logistic Regression

May 5, 2011
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sab-R-metrics: Logistic Regression

It's been a while since my last sab-R-metrics post, and I have not gotten to the real fun stuff yet. I apologize for the long layoff, and it's likely that these will be sparse for the next couple weeks. I have had some consulting opportunities come u...

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Mapping airline flight networks with R

May 5, 2011
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Mapping airline flight networks with R

Inspired by the Facebook Social Network chart, FlowingData's Nathan Yau also turns to R to create a beautiful chart of the network of all flight connections between major airlines in the US: Like the Facebook chart, the chart reflects the intensity of the connections (here, the number of flights) between pairs of cities. Nathan explains: Brighter lines represent more...

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Who will be the next President of the US ?

May 5, 2011
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Who will be the next President of the US ?

A lot of weird facts (?) can be found on the internet. For instance, about the height of the winner of Presidential elections in the US: the taller always win... "Still, being short does, on average, hurt a person's prospects...The tall guy gets th...

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S&P 500 High Beta and Low Volatility Indexes and Powershares ETFs

May 5, 2011
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S&P 500 High Beta and Low Volatility Indexes and Powershares ETFs

There must be a useful insight, concept, or system provided by the new S&P 500 High Beta and Low Volatility Indexes.  Now with the announcement by Powershares of etfs for these indicies http://www.invescopowershares.com/volatility/, any of the...

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Build instructions for R on Amazon EC2

May 4, 2011
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Build instructions for R on Amazon EC2

In this post, I will show: - How to create an Amazon EC2 micro instance - How to login to the EC2 instance using PuTTY - How to install the R source and build it. - Use R in the … Continue reading →

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Bank of America Merrill Lynch Bond Returns on St. Louis Fed

May 4, 2011
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Bank of America Merrill Lynch Bond Returns on St. Louis Fed

After all my complaining about proprietary data, the St. Louis Federal Reserve announced today the availability of Bank of America Merrill Lynch Bond Indicies on their FRED site.  The data is limited in scope and duration, but accessibility especi...

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Using R for Map-Reduce applications in Hadoop

May 4, 2011
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Data Scientist Antonio Piccolboni recently published this comparison of the various language and interfaces available for programming Big Data analysis tasks in the map-reduce framework. The interfaces he reviewed included: Java Hadoop (mature and efficient, but verbose and difficult to program) Cascading (brings an SQL-like flavor to Java programming with Hadoop) Pipes/C++ (a C++ interface to programming on Hadoop)...

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R Exercise with USDA Data

May 4, 2011
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R Exercise with USDA Data

After the helpful comment by Bradley on my post Commodity Index Estimators, How about the National Agricultural Statistics Service (NASS)? Looks like they have information for prices received back to 1908 for many agricultural goods (http://www.nass.u...

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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f...

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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f...

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Whassup with glm()?

May 4, 2011
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We're having problem with starting values in glm(). A very simple logistic regression with just an intercept with a very simple starting value (beta=5) blows up....

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Again with Ledoit-Wolf and factor models

May 4, 2011
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Again with Ledoit-Wolf and factor models

We come closer to a definitive answer on the relative merit of Ledoit-Wolf shrinkage versus a statistical factor model for variance matrices. Previously This post builds on the post entitled: A test of Ledoit-Wolf versus a factor model That post depended on some posts previous to it. New information Previously we generated random portfolios with … Continue reading...

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Invisible blogs!

May 4, 2011
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Invisible blogs!

Julien just signaled an intermitent disappearance of the posts on the ‘Og, depending on the operating system: Ubuntu 10.10 seems to be working (most of the time!) while Mac and Windows are having problems… This is beyond my abilities, I have contacted WordPress support, maybe they are working on some new feature, maybe I once

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Day #35 replacing characters

May 4, 2011
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Today I had a meeting with Emmanuel. He is a guy from inside Janssen who is very good with R-scripts. He made a lot of great plots which I had to use for our reports. During the meeting we came to a conclusion that all the difficult R-scripting he did,...

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bigkmeans also works well for ordinary matrix objects: The biganalytics package

May 4, 2011
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bigkmeans also works well for ordinary matrix objects: The biganalytics package

The bigmemory is an excellent package for handling big matrix in R. There are several sister packages provided by "The Bigmemory Project": biganalytics for analysis, bigtabulate for tabulation, bigalgebra for linear algebra functionality, synchronicity for synchronization via mutexes and interprocess communication and message passing.biganalytics provides a few functions for analysis: linear regression model, generalized linear regression model, and...

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bigkmeans also works well for ordinary matrix objects: The biganalytics package

May 4, 2011
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bigkmeans also works well for ordinary matrix objects: The biganalytics package

The bigmemory is an excellent package for handling big matrix in R. There are several sister packages provided by "The Bigmemory Project": biganalytics for analysis, bigtabulate for tabulation, bigalgebra for linear algebra functionality, synchronicity...

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Extension to mtable function

May 4, 2011
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Here are some useful extension to the "mtable" function in the memisc package.

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Extension to mtable function

May 4, 2011
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Here are some useful extension to the "mtable" function in the memisc package.

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