knitcitations

May 30, 2012
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Included file 'themes/noamblog/rsscss.html' not found in _includes directory Markdown is becoming an increasingly popular platform for lightweight and online publishing. While traditional publishing tools like LaTeX and word processors have long had i...

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Review: “Forest Analytics with R: an introduction”

May 29, 2012
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Review: “Forest Analytics with R: an introduction”

Forestry is the province of variability. From a spatial point of view this variability ranges from within-tree variation (e.g. modeling wood properties) to billions of trees growing in millions of hectares (e.g. forest inventory). From a temporal point of view … Continue reading →

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Google Earth and ocean depth contours

May 29, 2012
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Google Earth and ocean depth contours

Been playing around in R for a while and then a bit in the GIS environment - within R of course. Do not know very much about GIS, but know what I want: Looking at GIS fisheries data across various scales (macro to global). Now we have myriads of websit...

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Better decision tree graphics for rpart via party and partykit

May 29, 2012
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I’ve been using Graphviz to create better decision tree graphics “by hand” for rpart objects created in R (final tree). I stumbled on this post that shows how one could convert an rpart object to a party project via the as.party function in partykit to utilize the plot functions in party. It looks quite nice.... Read more »

Exporting from Win ISI / Importing into R

May 29, 2012
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Exporting from Win ISI / Importing into R

Chemometric software´s  have the option to export a matrix to a TXT file (in this case a constituents matrix), in a way we can import it easily into R, to work with. It is the first step to go into the R world.I use in this case Win ISI Soft...

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Mahalanobis distance with "R" (Exercice)

May 29, 2012
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Mahalanobis distance with "R" (Exercice)

I have developed this exercise with Excel in another post for the same calculations , I am going to develop  it this time with  "R".    edad  long.  peso    mg.kg1    28 &n...

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Project Euler — problem 4

May 29, 2012
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Project Euler — problem 4

It’s midnight already. I’m going to bed after I type this. Now the fourth Euler problem: A palindromic number reads the same both ways. The largest palindrome made from the product of two 2-digit numbers is 9009 = 91 99. Find … Continue reading →

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How to Stay Current in Bioinformatics/Genomics

May 29, 2012
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A few folks have asked me how I get my news and stay on top of what's going on in my field, so I thought I'd share my strategy. With so many sources of information begging for your attention, the difficulty is not necessarily finding what's interesting...

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Choosing colour palettes. Part I: Introduction

May 29, 2012
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Choosing colour palettes. Part I: Introduction

In this series of three posts, we’ll look at colours in R graphics produced with ggplot2: what are the available choices of colour schemes, and how to choose a colour palette most suitable for a particular graphic? In kindergarten, choosing a co...

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Example 9.33: Multiple imputation, rounding, and bias

May 29, 2012
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Example 9.33: Multiple imputation, rounding, and bias

Nick has a paper in the American Statistician warning about bias in multiple imputation arising from rounding data imputed under a normal assumption. One example where you might run afoul of this is if the data are truly dichotomous or count variables, but you model it as normal (either because your software is unable to model dichotomous...

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knitr, Slideshows, and Dropbox

May 29, 2012
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knitr, Slideshows, and Dropbox

I just noticed that Markus Gesmann has a nice post on using RStudio, knitr, Pandoc, and Slidy to create slideshows. After my recent attempt to use deck.rb to turn a Markdown/knitr file into a deck.js presentation I caved in and also decided to go with ...

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Interactive HTML presentation with R, googleVis, knitr, pandoc and slidy

May 29, 2012
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Interactive HTML presentation with R, googleVis, knitr, pandoc and slidy

Tonight I will give a talk at the Cambridge R user group about googleVis. Following my good experience with knitr and RStudio to create interactive reports, I thought that I should try to create the slides in the same way as well. Christopher Gandrud's...

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Backtesting Classical Technical Patterns

May 28, 2012
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Backtesting Classical Technical Patterns

In the last post, Classical Technical Patterns, I discussed the algorithm and pattern definitions presented in the Foundations of Technical Analysis by A. Lo, H. Mamaysky, J. Wang (2000) paper. Today, I want to check how different patterns performed historically using SPY. I will follow the rolling window procedure discussed on pages 14-15 of the

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End of May flotsam

May 28, 2012
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End of May flotsam

The end is near! At least the semester is coming to an end, so students have crazy expectations like getting marks back for assignments, and administrators want to see exam scripts. Sigh! What has been happening meanwhile in Quantum Forest? … Continue reading →

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The R-Podcast Episode 7: Best Practices for Workflow Management

May 28, 2012
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Hello everybody, I am finally back with a new episode! In this episode: Hardware issues, major update to RStudio, new forums, and discussion on managing your workflow for projects. I discuss useful functions for executing R scripts and saving/loading R objects for future sessions, and summarize different solutions for organizing R code based on task

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Optim, you’re doing it wrong?

May 28, 2012
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Optim, you’re doing it wrong?

Call me uncouth, but I like my TV loud, my beer cold and my optimization functions as simple as possible. Therefore, what I write in this blog post is very much from a layman’s perspective, and I am happy to be corrected on any fundamental errors. I have recently become interested in writing my own

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Industrial Statistics Seminars

May 28, 2012
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Andrea Spanò, founder and partner at Quantide, held two seminars about Industrial Statistics at the University of Bergamo. Process Capability Analysis and Gage R&R were topics of seminars. Registered Milano R net users can download presentations from this page.

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ICES and NAFO statistical areas viewed in Google Earth

May 28, 2012
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ICES and NAFO statistical areas viewed in Google Earth

On the ICES Spatial Facility webpage one can obtain a view of the ICES statistical areas. Now since the projection used is more than a bit misleading I was wandering how these statistical areas would look like in Google Earth. Thankfully the ...

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Again on polar/star/pie charts

May 28, 2012
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Again on polar/star/pie charts

Haven't had much time to devote to new visualisations, mostly because work and baby have taken the precedence.But I just wanted to take a few minutes to share the latest version of the script I showed last time.It now saves to a pdf file, but that's no...

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Jackknifing portfolio decision returns

May 28, 2012
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Jackknifing portfolio decision returns

A look at return variability for portfolio changes. The problem Suppose we make some change to our portfolio.  At a later date we can see if that change was good or bad for the portfolio return.  Say, for instance, that it helped by 16 basis points.  How do we properly account for variability in that … Continue reading...

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ABC+EL=no D(ata)

May 27, 2012
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ABC+EL=no D(ata)

It took us a loooong while but we finally ended up completing a paper on ABC using empirical likelihood (EL) that was started by me listening to Brunero Liseo’s tutorial in O’Bayes-2011 in Shanghai… Brunero mentioned empirical likelihood as a semi-parametric technique w/o much Bayesian connections and this got me thinking

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The aesthetics of error bars

May 27, 2012
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The aesthetics of error bars

This blog and my other main blog (the companion blog for my book) are now syndicated via R-bloggers (posts tagged R only) and statsblogs.com. The latter is a relatively new blog aggregator but looks to have some interesting content. R-bloggers it quite...

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Ben Schmid took ship’s log data (previously visualized in…

May 27, 2012
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Ben Schmid took ship’s log data (previously visualized in…

Ben Schmid took ship’s log data (previously visualized in static form on the the Spatial Analysis blog), and used ggplot and ffmpeg to animate the paths of individual voyages from 1750-1850. The images above come from the animation that combines all ...

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Project Euler — problem 3

May 27, 2012
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The third problem: The prime factors of 13195 are 5, 7, 13 and 29. What is the largest prime factor of the number 600851475143 ? My solvement is straightforward: firstly to identify all the prime numbers between 2 and sqrt(n); secondly … Continue reading →

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Tweets Analysis about Himpuan Jutaan Belia PutraJaya (Malaysia Youth Day 2012)

May 27, 2012
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Tweets Analysis about Himpuan Jutaan Belia PutraJaya (Malaysia Youth Day 2012)

I’m using the Twitter Listening Robot to know what people is talking Najib Razak, Malaysia Prime Minister. Apparently,  23-27 are the Malaysia Youth Day 2012.  There were many funny retweets (more than 50 times) by the public: RT @Faizrawrr: Be...

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Updating to R 2.15, warnings in R and an updated function list for Serious Stats

May 27, 2012
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Updating to R 2.15, warnings in R and an updated function list for Serious Stats

Whilst writing the book  the latest version of R changed several times. Although I started on an earlier version, the bulk of the book was written with 2.11 and it was finished under R 2.12. The final version of the R scripts were therefore run and checked using R 2.12 and, in the main, the most recent

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PLoS computational biology meets wikipedia

May 26, 2012
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PLoS computational biology meets wikipedia

Robin Ryder pointed out to me this new experiment run by PLoS since March 2012, namely the introduction of a new article type, “called “Topic Pages” and written in the style of a Wikipedia article“. Not only this terrific idea gives more credence to Wikipedia biology pages, at least in their early stage, but also

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Cross-valitation variability example, part I

May 26, 2012
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Cross-valitation variability example, part I

Recently I had a discussion with a student about variability of results obtained from cross-validation procedure. While the subject is well known there are not many examples on the web showing it, so I have written its simple presentation.Results from ...

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Automating repetitive plot elements

May 26, 2012
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Automating repetitive plot elements

The syntax of ggplot2 emphasizes constructing plots by adding components, or layers, using +. Possibly one of the most useful, but least remarked upon, consequences of this syntax is that it allows for an incredible degree of flexibility in saving and...

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