Comparison of functions for comparative phylogenetics

May 11, 2011
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Comparison of functions for comparative phylogenetics

With all the packages (and beta stage groups of functions) for comparative phylogenetics in R (tested here: picante, geiger, ape, motmot, Liam Revell's functions), I was simply interested in which functions to use in cases where multiple functions exis...

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Defining Custom Model Priors in BMS

Bayesian Model Averaging (BMA) allows for any kind of model prior distributions. While the R package BMS has built-in support for several types of commonly used priors, there may be the need for constructing a custom model prior in a particular exerci...

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A clock utility, via console hackery

May 11, 2011
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A clock utility, via console hackery

A discussion on StackOverflow today shows an interesting use of special characters inside the cat function. The most common special characters that you may have come across are the tab and newline characters, represented by \t and \n respectively. Try them for yourself. cat("Red\tlorry\nYellow\tlorry\n") cat also respects the backspace character, \b, and the carriage return

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High Low Clustering on intraday high frequency sampled data

May 10, 2011
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High Low Clustering on intraday high frequency sampled data

Nothing unusually exciting on this post, but I happened to be engaged in some particle based methods recently and made some simple visual observations as I was setting up some of the sampling environment in R.  I am also using Rkward and Ubuntu to...

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Publishing in Veterinary Academic Journals

May 10, 2011
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Publishing in Veterinary Academic Journals

Following the post by Arthur Charpentier (Freakonometrics), I wondered what would be the outcome considering my current engagement (veterinary medicine, epidemiology, bovine mastitis). Briefly, Arthur Charpentier’s post looked at clusters of journals publishing the same kind of papers. So I looked at 25 journals (Journal of Dairy Science, Canadian Journal of Veterinary Medicine, Preventive Veterinary

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ABC model choice by DIC

May 10, 2011
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ABC model choice by DIC

Yet another paper on ABC model choice was posted on arXiv a few days ago, just prior to the ABC in London meeting that ended in the pub above (most conveniently located next to my B&B!). It is written by Olivier Francois and Guillaume Laval and the approach relies on DIC for running model selection.

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Late to the party for R in Finance blogging

May 10, 2011
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Late to the party for R in Finance blogging

I meant to blog about the R/Finance conference during a lull, but I didn’t find too many. Unlike many conferences I’ve been to the structure of R/Finance was simple: one room and one speaker at a time. Relying on each … Continue reading →

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Data Science Toolset discussion at Data Scientist Summit

May 10, 2011
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Heads-up to anyone attending the sold-out Data Science Summit in Las Vegas this week: I'll be there tomorrow and Thursday for the conference and to discuss R on the panel discussion "Data Science Toolset - Recipes That Win" (more details about the panel discussion below.) I'm looking forward to meeting with the other R users there -- tweet or...

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Day #38-39 Data-manipulation Part 1

May 10, 2011
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Last week i created some plots, always for 1 feature. Today I started working on the full script that creates all these plots, 1 per feature. This means, using for loops in R. Let’s see how this is going to work out. Today I mostly worked on data...

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Retail Commodity Investors – A Bleeding Indicator?

May 10, 2011
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Retail Commodity Investors – A Bleeding Indicator?

Problems with plyr — the memory/complexity trade-off

May 10, 2011
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Two types of R users My overwhelming impression from UseR 2010 is that, generally speaking, there are 2 types of regular R users -- those who have heard and are made uncomfortable by the idea of the *apply() functions, and those who really get it. In ...

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Extending mtable() to ivreg, gls and robust standard errors

May 9, 2011
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Extending mtable() to ivreg, gls and robust standard errors

I have written several extensions of the mtable() command in the memisc library that may come in handy. The methods are available in a package I have written called tonymisc (now, available on CRAN). A zipped folder with my package files is available...

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Extending mtable() to ivreg, gls and robust standard errors

May 9, 2011
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Extending mtable() to ivreg, gls and robust standard errors

I have written several extensions of the mtable() command in the memisc library that may come in handy. The methods are available in a package I have written called tonymisc (now, available on CRAN). A zipped folder with my package files is available...

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First-Cut Approach to Synchronizing Field Notes with GPS Data

May 9, 2011
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After a week's worth of work in the field, I typically have several pages of hand-written field notes that are associated with GPS waypoints-- badly in need of some kind of transcription/organization. I have yet to find a simple approach for bringing t...

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Importing Weather Data from Wunderground

May 9, 2011
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Importing Weather Data from Wunderground

Wunderground Example The Wunderground.com website offers several creative interfaces to current and historic weather information. One of the more interesting features is the URL-based interface to personal weather stations. As far as I can tell, the Wu...

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Registration open for Rmetrics Workshop on Computational Finance

May 9, 2011
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The Rmetrics Association is once again holding its annual Workshop and Summer School on Computational Finance and Financial Engineering at Meielisalp (on Lake Thune in Switzerland) from June 26-30. Now in its fifth year, the workshop consists of Summer School-like tutorial sessions and a user/developer meeting: Both focus on topics from "Computational Finance and Financial Engineering" and on the...

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Accessing Databases From R

May 9, 2011
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Accessing Databases From R

Jeffrey Breen put together a useful slideshow on accessing databases from R. I use RODBC every single day to access my own local MySQL server from R. I've had trouble with RMySQL, so I've always used RODBC instead after setting up my localhost MySQL se...

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Accessing Databases From R

May 9, 2011
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Jeffrey Breen put together a useful slideshow on accessing databases from R. I use RODBC every single day to access my own local MySQL server from R. I've had trouble with RMySQL, so I've always used RODBC instead after setting up my localhost MySQL se...

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making meat shares more efficient with R and Symphony

May 9, 2011
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making meat shares more efficient with R and Symphony

In my previous post, I motivated a web application that would allow small-scale sustainable meat producers to sell directly to consumers using a meat share approach, using constrained optimization techniques to maximize utility for everyone involved. In this post, I’ll walk through some R code that I wrote to demonstrate the technique on a small

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Comments on an R Connections API

May 9, 2011
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I wrote this post months ago but never hit 'Publish'. But, the subject has changed little since then. So, here's to cleaning out the draft folder... R's connections are the heart of data/code/text input and output. Without connections, R would be crippled. Additional connections make R more ... connected with potential data sources and output

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Multiple Y-axis in a R plot

May 9, 2011
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Multiple Y-axis in  a R plot

I often have to to plot multiple time-series with different scale of values for comparative purposes, and although placing them in different rows are useful, placing on a same graph is still useful sometimes...I searched a bit about this, and found som...

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Multiple Y-axis in a R plot

May 9, 2011
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Multiple Y-axis in  a R plot

I often have to to plot multiple time-series with different scale of values for comparative purposes, and although placing them in different rows are useful, placing on a same graph is still useful sometimes...I searched a bit about this, and found som...

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One minor detail for getting 64-bit R-2.13 running with Eclipse/StatET

May 9, 2011
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Upgrading from R-2.12 to R-2.13 was fairly painless, except for one minor hiccup in trying to get the 64-bit version running on my installation of Eclipse + StatET under Windows 7. The setup instructions are almost entirely the same as I have outlined ...

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Unused function parameters

May 8, 2011
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Unused function parameters

I have started redoing the source code measurements that appear in my C book, this time using a lot more source, upgraded versions of existing tools, plus some new tools such as Coccinelle and R. The intent is to make the code and data available in a form that is easy for others to use

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Charting the Defeat of AV using R (and some ggplot2 and merge operations on top)

May 8, 2011
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Charting the Defeat of AV using R (and some ggplot2 and merge operations on top)

In this post, I’ll be graphing some results from a recent referendum held here in the UK and combining it with the results of a set of local elections that were held at the same time. I’ll give some examples of graphing stuff using ggplot2 and will also show some info regarding merging datasets. At

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quantmod makes it easy to watch silver prices crash in R #rstats

May 7, 2011
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quantmod makes it easy to watch silver prices crash in R #rstats

Jeffrey Ryan's quantmod package makes it simple to download and graph pricing data from a variety of sources. A couple of lines of R is all it takes to see that silver has had a very bad week.

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Slides: “Accessing Databases from R” #rstats

May 7, 2011
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Slides: “Accessing Databases from R” #rstats

For the past few meetings of the Greater Boston useR Group, we have been opened with an introductory “useR Vignette” talk on a topic which may be helpful for new R users. This week, I presented an overview of accessing databases from R. Several people have tweeted and blogged nice things about my talk and

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R you ready for this? Statistics for free!

May 7, 2011
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R you ready for this? Statistics for free!

If you’ve listened to the show for a while or if you’ve been reading the paleocave blog from the beginning (like when we actually used to update it regularly), then you might know that I’m rather fascinated with statistics. Imagine my delight a few years ago when I found out that one of the most

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Pair-Trading in R – Update

May 7, 2011
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I found amazing R package in one of posts on R-bloggers website. It's called RcppAmadillo and you can find more info here. The function I am using from this package is called fastLm. Whereas I am interested in special case of Ax = b problem where A and...

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