## Two new rOpenSci R packages are on CRAN

October 27, 2011
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Carl Boettiger, a graduate student at UC Davis, just got two packages on CRAN.  One is treebase, which which handshakes with the Treebase API.  The other is rfishbase, which connects with the Fishbase, although I believe just scrapes XML cont...

## Computing on the Language

October 27, 2011
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And now for something a bit more esoteric…. I recently wrote a function to deal with a strange problem. Writing the function ended up being a fun challenge related to computing on the R language itself. Here’s the problem: Write a function that tak...

## Introduction to “Numerical Methods and Optimization in Finance”

October 27, 2011
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The book is by Manfred Gilli, Dietmar Maringer and Enrico Schumann.  I haven’t actually seen the book, so my judgement of it is mainly by the cover (and knowing the first two authors). The parts of the book closest to my heart are optimization, particularly portfolio optimization, and particularly particularly portfolio optimization via heuristic algorithms.  … Continue reading...

## R Cookbook with examples

October 27, 2011
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An R Cookbook can be found at http://code.ca-net.org/R%20Cookbook. It is a short web document presenting dozens of examples on - Accessing Database with packages RSQLite, RMySQL, RdbiPgSQL and RODBC; - Reading and Writing Data; - Date/Time variable; - Graphics; - … Continue reading →

## Copy all the files in a directory to a new directory using R

October 27, 2011
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Someone asked me how to move a directory full of files from one place to another using R.  The easiest way I've found is as follows (where "oldpath" is the existing directory and "newpath" is the new directory):   file.copy(list.files(oldpath),newpath)   Tags:  R

## Shoe Consumption in the U.S. – GGPlot2 #1

October 26, 2011
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This is the first in a series of blog posts in which I use the R package GGPlot2 to examine real world data. In this post, I construct a line graph of U.S. shoe consumption from 1995 to 2007. A recent survey conducted by Shop Smart magazine found that the average woman in the

## Netflix Post-mortem – How to detect Bubbles

October 26, 2011
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Bubbles. I’m no expert in behavioral economics, but bubbles seem to be well understood (after they occur) although they seem hard to detect (at least in the eyes of outsiders and late bubble participants). This post won’t tell you how to avoid bubbles, but might give you some insight. I came across Minsky’s explanation of

## Mixed-Effects Models in R with Quantum Forest

October 26, 2011
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For anyone who wants to estimate linear or nonlinear mixed-effects models (aka random-effects models, hierarchical models or multilevel models) using the R language, the Quantum Forest blog has several recent posts that will be of interest. Written by Luis Apiolaza from the School of Forestry at the University of Canterbury in New Zealand, the blog includes a number of...

## What do your rules look like? editrules 1.8-x answers with the help of igraph

October 26, 2011
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We (Edwin de Jonge and me) have recently updated our editrules package. The most important new features include (beta) support for categorical data. However, in this post I'm going to show some visualizations we included, made possible by Gabor Csardi's … Continue reading →

## How to display R code on a web page

October 26, 2011
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Starting to write a blog I need a way how to publish my R codes. One possibility would be to just add some formatting with Pretty R. Nice, but I miss a repository with all codes ever submitted and possibility to make corrections.The final solution was ...

## Covariance structures

October 26, 2011
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$Covariance structures$

In most mixed linear model packages (e.g. asreml, lme4, nlme, etc) one needs to specify only the model equation (the bit that looks like y ~ factors...) when fitting simple models. We explicitly say nothing about the covariances that complete … Continue reading →

## Two-sex demographic models in R

October 26, 2011
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Tom Miller (a prof here at Rice) and Brian Inouye have a paper out in Ecology (paper, appendices) that confronts two-sex models of dispersal with empirical data.They conducted the first confrontation of two-sex demographic models with empirical data on...

## Controlling multiple risk measures during construction of efficient frontier

October 26, 2011
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In the last few posts I introduced Maximum Loss, Mean-Absolute Deviation, and Expected shortfall (CVaR) and Conditional Drawdown at Risk (CDaR) risk measures. These risk measures can be formulated as linear constraints and thus can be combined with each other to control multiple risk measures during construction of efficient frontier. Let’s examine efficient frontiers computed

## PAWL package on CRAN

October 26, 2011
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The PAWL package (which I talked about there, and which implements the parallel adaptive Wang-Landau algorithm and adaptive Metropolis-Hastings for comparison) is now on CRAN! http://cran.r-project.org/web/packages/PAWL/index.html which means that within R you can easily install it by typing install.packages("PAWL") Isn’t that amazing? It’s just amazing. Kudos to the CRAN team for their quickness and their

## New features in R-bloggers.com

October 26, 2011
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Hello dear R community, In the past few months I have rolled out a bunch of new features to R-bloggers, and I wanted to raise awareness to them.  Please consider giving some of these a try and leave me any feedback that you have (by leaving a comment on this post): Comments – it is now possible to leave comments in...

## Batch Processing vs. Interactive Sessions

October 26, 2011
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We introduced batch processing 3 weeks ago. Many people asked about differences and benefits of batch processing or interactive sessions. Lets start with the definitions: Batch Processing / Batch Jobs: Batch processing is the execution of a series of programs or only one task on a computer environment without manual intervention. All data and commands

## Machine Learning Ex 5.2 – Regularized Logistic Regression

October 25, 2011
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Now we move on to the second part of the Exercise 5.2, which requires to implement regularized logistic regression using Newton's Method. Plot the data:

## treebase package on cran

October 25, 2011
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My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition requirements at journals such as Evolution, Am Nat, and Sys Bio, and data management plan

## The Psychology of Music and the ‘tuneR’ Package

October 25, 2011
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Introduction This semester I’m TA’ing a course on the Psychology of Music taught by Phil Johnson-Laird. It’s been a great course to teach because (i) so much of the material is new to me and (ii) because the study of the psychology of music brings together so many of the intellectual tools I enjoy, including

## "Anyone planning to work with Big Data ought to learn Hadoop and R"

October 25, 2011
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Dan Woods at Forbes interviewed LinkedIn's Daniel Tunkelang about the rise of data science and on building data science teams. When asked how students today should prepare themselves to be data scientists, Tunkelang gives some good advice: When we built the data science team at LinkedIn a few years ago, we looked for raw talent, assuming that smart people...

## Catching up faster by switching sooner

October 25, 2011
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Here is our discussion (with Nicolas Chopin) of the Read Paper of last Wednesday by T. van Erven, P. Grünwald and S. de Rooij (Centrum voor Wiskunde en Informatica, Amsterdam), entitled Catching up faster by switching sooner: a predictive approach to adaptive estimation with an application to the Akaike information criterion–Bayesian information criterion dilemma. It

## Mapping Hotspots with R: The GAM

October 25, 2011
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I've been getting a lot of questions about the method used to map the hotspots in the seasonal drunk-driving risk maps.  It uses the GAM (Geographical Analysis Machine), a way of detecting spatial clusters from two data inputs: the data of interes...

## Installing the RMySQL package on Windows 7

October 25, 2011
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So you want to get statistical? Nowadays one of the ways to go is to use R, mostly in combination with ggplot2 for generating the plots. These plots and graphs however need some data, for that we use data sources. There are a lot of data sources availa...

## Example 9.11: Employment plot

October 25, 2011
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A facebook friend posted the picture reproduced above-- it makes the case that President Obama has been a successful creator of jobs, and also paints GW Bush as a president who lost jobs. Another friend pointed out that to be fair, all of Bush's presi...

## Consecutive number and lottery

October 25, 2011
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Recently, I have been reading odd things about strategies to win at the lottery. E.g. or I wrote something a long time ago, but maybe it would be better to write another post. First, it is easy to get data on the French lotteries, including dra...

## Longitudinal analysis: autocorrelation makes a difference

October 25, 2011
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Back to posting after a long weekend and more than enough rugby coverage to last a few years. Anyway, back to linear models, where we usually assume normality, independence and homogeneous variances. In most statistics courses we live in a … Continue reading →

## Expected shortfall (CVaR) and Conditional Drawdown at Risk (CDaR) risk measures

October 25, 2011
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$Expected shortfall (CVaR) and Conditional Drawdown at Risk (CDaR) risk measures$

In the Maximum Loss and Mean-Absolute Deviation risk measures post I started the discussion about alternative risk measures we can use to construct efficient frontier. Another alternative risk measures I want to discuss are Expected shortfall (CVaR) and Conditional Drawdown at Risk (CDaR). I will use methods presented in Comparative Analysis of Linear Portfolio Rebalancing

## Email Netiquette

October 25, 2011
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A short piece of web-scrapping I sent as a reminder to my colleague. If you run it the result should be something like... Datatata!