ProbaPerception: Introduction

September 21, 2012
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ProbaPerception: Introduction

Plotting Watts-Strogatz model

September 21, 2012
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Plotting Watts-Strogatz model

Recently I wanted to reproduce Figure 2 from Watts and Strogatz (1998). The task using igraph is simple but an interesting task was annotation of the resulting plot.Watts-Strogatz model generates graphs that have so called small-world ne...

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Compactly display the structure of an arbitrary R object

September 21, 2012
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As you advance in your R use past “canned” functions and packages made by others, you may want to take information from one R object for use in another. For example, you may want to estimate a linear model, then use the results of that esti...

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Simple plot with text boxes

September 21, 2012
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Simple plot with text boxes

Was doing a little presentation to our research group and had to explain the difficulties of ‘collapsing’ longitudinal data into a single measure when the Y var is quite variable. For the particular Y var of interest, it represents burden … Continue reading →

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BARUG Meetup at the Googleplex

September 21, 2012
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BARUG Meetup at the Googleplex

What is R?  R is an open-source, statistical programming language that is increasingly becoming the lingua franca of modern data analysis. R developers have created over 4,000 packages to run in the R environment, including several dozen developed by Googlers. We continue to work with the R community through conferences, meetups like this one, Faculty Research...

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Interactive 3d plot, in R

September 20, 2012
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Interactive 3d plot, in R

Following the course of this afternoon, I will just upload some codes to make interactive 3d plots, in R. > library(rgl) > library(evd); > data(lossalae) > U=rank(lossalae+rnorm(nrow(lossalae), + mean=0,sd=.001))/(nrow(lossalae)+1) ...

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Obviousness of REITs?

September 20, 2012
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Obviousness of REITs?

I very much enjoy papers such as Antonacci, Gary, Risk Premia Harvesting Through Momentum (September 5, 2012). Available at SSRN: http://ssrn.com/abstract=2042750 or http://dx.doi.org/10.2139/ssrn.2042750 Faber, Mebane T., A Quantitative Approach to T...

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Descriptive Statistics of Groups in R

September 20, 2012
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The sleep data set—provided by the datasets package—shows the effects of two different drugs on ten patients. Extra is the increase in hours of sleep; group is the drug given, 1 or 2; and ID is the patient ID, 1 to 10.I'll be using this data set to show how to perform descriptive statistics of groups within...

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How to use your favorite fonts in R charts

September 20, 2012
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How to use your favorite fonts in R charts

Today's guest post comes from Winston Chang, a software developer at RStudio — ed. When it comes to making figures in R, you can use any font you like, as long as it's Helvetica, Times, or Courier. Using other fonts that are installed on your computer can seem an impossible task, especially if you want to save the output...

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Converting an R object to text, with dput()

September 20, 2012
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We’ve already briefly covered making a reproducible example, but I thought I’d go a little more in-depth on the very helpful function dput(). Whenever I am having trouble applying an operation to some R object, and need help, but want to av...

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garch estimation on impossibly long series

September 20, 2012
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garch estimation on impossibly long series

The variability of garch estimates when the series has 100,000 returns. Experiment The post “Variability of garch estimates” showed estimates of 1000 series that were each 2000 observations long.  Here we do the same thing except that the series each have 100,000 observations. That would be four centuries of daily data.  It’s not presently feasible … Continue reading...

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(nonparametric) Copula density estimation

September 20, 2012
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(nonparametric) Copula density estimation

Today, we will go further on the inference of copula functions. Some codes (and references) can be found on a previous post, on nonparametric estimators of copula densities (among other related things).  Consider (as before) the loss-ALAE data...

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Long-term precipitation data for your location from the US Historical Climatology Network using R

September 19, 2012
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Long-term precipitation data for your location from the US Historical Climatology Network using R

Abstract Long-term daily precipitation records from the US Historical Climatology Network (USHCN) are processed and summarized using R. Below is R code which examines the data from Livermore, CA, the closest available USHCN station to my present home ...

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ISBA towards higher computing goals [yet another new section!!!]

September 19, 2012
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ISBA towards higher computing goals [yet another new section!!!]

Surrounding the great and exciting gathering of Bayesian statisticians in Kyoto last June, several ISBA sections have appeared in the past weeks, as already mentioned on the ‘Og. Along with Anto Mira and Nicolas Chopin (who did most of the organisational work while I was wandering down under!), we discussed about a Bayesian computation section

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(nonparametric) copula density estimation

September 19, 2012
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(nonparametric) copula density estimation

Today, we will go further on the inference of copula functions. Some codes (and references) can be found on a previous post, on nonparametric estimators of copula densities (among other related things).  Consider (as before) the loss-ALAE dataset (since we’ve been working a lot on that dataset) > library(MASS) > library(evd) > X=lossalae > U=cbind(rank(X)/(nrow(X)+1),rank(X)/(nrow(X)+1)) The standard tool to plot...

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2012-5 Voronoi Treemaps in R

September 19, 2012
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A Voronoi Treemap is a visualisation tool for displaying data with a hierarchical structure.  This article describes an open source implementation of Voronoi Treemaps in the R language and environment for statistical computing and graphics.  The article includes example usage … Continue reading →

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FinancialInstrument Moves to CRAN

September 19, 2012
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FinancialInstrument Moves to CRAN

I thought I would break up the posts about GSOC (no, I’m not done yet – there are a few more to do) with a quick note about FinancialInstrument. The FinancialInstrument package provides a construct for defining and storing meta-data for tradable contracts (referred to as instruments, e.g., stocks, futures, options, etc.). The package can

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Why are pirates called pirates?

September 19, 2012
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Why are pirates called pirates?

In homage to International Talk Like a Pirate Day… I recently stumbled across a series of blog posts from the folks at IDV that visualised the archive of recorded pirate attacks which has been collected by the US National Geospatial-Intelligence Agency. It’s a dataset of 6000+ pirate attacks which have been recorded over the last 30 … Continue reading...

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The PMML Revolution: Predictive analytics at the speed of business

September 19, 2012
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The PMML Revolution: Predictive analytics at the speed of business

This guest post is by Alex Guazzelli, VP of Analytics at Zementis Inc. -- ed. PMML, the Predictive Model Markup Language, is the de facto standard to represent predictive analytics and data mining models. With PMML, it is extremely easy to move a predictive solution from one system to another, since it avoids proprietary issues and incompatibilities. Companies around...

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Stock Market and US elections

September 19, 2012
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Stock Market and US elections

Quantitative Finance, Technical Trading & Analysis. Fotis Papailias, Dimitrios Thomakos Fotis Quantitative Finance & Technical Trading Stock Market and US elections We made a very simple R file that historically gathers the period before and after the US elections. The inexperienced user has the ability to set the tickers of asset she wants to study and the look-back and look-forward...

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SPSS and R day in York

September 19, 2012
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SPSS and R day in York

On 2 November there are some introductory health-focussed training sessions on SPSS and R software going on in York: Two sets of two half-day parallel workshops and two tutorial sessions are provisionally planned to be held at the Alcuin Research … Continue reading →

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(Unsurprisingly) users default to the defaults

September 19, 2012
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(Unsurprisingly) users default to the defaults

Oddities tend to jump out when one uses software in a daily basis. The situation is even clearer when using software for teaching: many more people looking at it with fresh eyes. Let’s say that we are fitting a simple … Continue reading →

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Vertnet – getting vertebrate museum record data and a quick map

September 19, 2012
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Vertnet – getting vertebrate museum record data and a quick map

We (rOpenSci) started a repo to wrap the API for VertNet, an open access online database of vertebrate specimen records across many collection holders. Find the open source code here - please contribute if you are so inclined. We had a great Google Su...

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Divide or Mix. Flexible Approaches to Data Analysis

September 19, 2012
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A very interesting paradigm in data analysis comes from the necessity to model data where it is difficult to think of a single global function to be capable to represent adequately the data. We could see a spectrum of models … Continue reading →

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Technical Analysis of Montana Voter Registration Files

September 18, 2012
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Technical Analysis of Montana Voter Registration Files

By Earl F Glynn | Franklin Center This article shows how to analyze Montana voter registration files using R. The Montana Secretary of State sells two files of voter registration records for a fee of $1000: Statewide Voter File Voter History File The Montana Secretary of State provides information about the two files on this

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Automatic drug utilization reports with R and ggplot2

September 18, 2012
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Automatic drug utilization reports with R and ggplot2

This program takes a data set of drug utilisation of 4 fictional drugs in 10 fictional hospitals and plots each time-series with a locally weighted regression (Lowess) trend line. It also places an time-series trend of the usage for each … Continue reading →

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RcppArmadillo 0.3.4.1

September 18, 2012
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Conrad released the bug-fix release 3.4.1 of Armadillo earlier today, and the corresponding RcppArmadillo package 0.3.4.1 is already on CRAN. No R level or interface changes were, the upstream changes are summarized below. Changes in RcppArmadillo...

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DESeq vs edgeR Comparison

September 18, 2012
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DESeq vs edgeR Comparison

Update (Dec 18, 2012): Please see this related post I wrote about differential isoform expression analysis with Cuffdiff 2.DESeq and edgeR are two methods and R packages for analyzing quantitative readouts (in the form of counts) from high-throughput e...

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Creating Posters using R, Latex, Beamer and Beamerposter

September 18, 2012
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Creating Posters using R, Latex, Beamer and Beamerposter

A while ago I had the need to produce some posters that included lots of data (scientific style).  Having recently got back into R and learning LaTex I googled for a way to do this using R.  Here's what I found and ended up with, using R, LaT...

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