Day #13 more plots, colors and loess smoothing

March 29, 2011
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Yesterday I tried to insert some more R code into knime. scatterplot smoothed density library("geneplotter")  ## from BioConductor require("RColorBrewer") ## from CRAN x1  <- matrix(rnorm(1e4), ncol=2) x2  <- matrix(rnorm(1e4, mean=3, sd=1.5...

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Day #14 another R-course

March 29, 2011
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So today I’m going to follow another R-course which is supposed to tell me more about Flowcytometry in R. I’ll keep you up to date

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merge with solaR

merge with solaR

The version 0.22 of solaR includes a new method, mergesolaR. It is designed to merge daily time series of several solaR objects. For example, we can obtain the daily irradiation of the whole set of meteorological stations of Madrid (Spain) and use this information to calculate the productivity of a grid connected PV system. It

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Example 8.32: The HistData package, sunflower plots, and getting data from R into SAS

March 29, 2011
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Example 8.32: The HistData package, sunflower plots, and getting data from R into SAS

This entry is mainly a promotion of the fascinating HistData R package. The package, compiled by the psychologist, statistician, and graphics innovator Michael Friendly, contains a number of small data sets of historical interest. These include data ...

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Machine Learning Ex3 – Multivariate Linear Regression

March 29, 2011
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Machine Learning Ex3 – Multivariate Linear Regression

Part 1. Finding alpha. The first question to resolve in Exercise 3 is to pick a good learning rate alpha. This require making an initial selection, running gradient descent and observing the cost function. Read More: 221 Words Totally

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Two R functions for working with DNA alignments

March 28, 2011
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Recently I wrote a couple of small functions as a result of work done by myself and others in my lab group. The first is a function that determines what sites in a sequence alignment are ambiguous (i.e. not A, G, C or T). require(ape)data(woodmouse)is.ambig    x    bases    ambig    ambig > 0}is.ambig(woodmouse)This function utilises the bit-level coding scheme that...

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Two R functions for working with DNA alignments

March 28, 2011
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Recently I wrote a couple of small functions as a result of work done by myself and others in my lab group. The first is a function that determines what sites in a sequence alignment are ambiguous (i.e. not A, G, C or T). require(ape)data(woodmouse)is.ambig    x    bases    ambig    ambig > 0}is.ambig(woodmouse)This function utilises the bit-level coding scheme that...

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Reminder: useR! 2011 abstracts, earlybird registration deadline April 1

March 28, 2011
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If you're planning to attend the worldwide R user conference useR! 2011, don't forget that April 1 (this Friday) is the deadline for submitting abstracts for contributed talks and posters. Early-bird discounts for attendee registrations expire on Friday as well. (Revolution Analytics is a proud sponsor of useR! 2011, and chief scientist Lee Edlefsen is one of the keynote...

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Time series

March 28, 2011
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Time series

(This post got published on The Statistics Forum yesterday.) The short book review section of the International Statistical Review sent me Raquel Prado’s and Mike West’s book, Time Series (Modeling, Computation, and Inference) to review. The current post is not about this specific book, but rather on why I am unsatisfied with the textbooks in

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Using R and snow on Ohio Supercomputer Center’s Glenn cluster

March 28, 2011
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Over the last several days, I have had the “pleasure” of getting parallel processing with R running on the the Ohio Supercomputer Center’s (OSC) Glenn cluster. I am working on a project that uses GenMatch from Sekhon’s Matching, which uses … Continue reading →

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Day #12 5 ways to visualize plots in knime

March 28, 2011
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Today I’m checking which plot function works fastest, I did this via this blogpost. http://www.r-bloggers.com/five-ways-to-visualize-your-pairwise-comparisons/ But I’m not doing this in an Rgui, but in Knime. I read in an example ACS file, ...

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Volatility Violins

March 28, 2011
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Volatility Violins

Unlike many humans, markets love change. In fact, they look forward to it with great anticipation. Regular people like stability, for the most part. Unless you're a career gypsy, you like to stay in one place for some time. Making a home. Settling in, ...

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GUIs for R

March 28, 2011
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A recent post listed at R Bloggers (http://www.r-bloggers.com/r-guis-which-one-fits-you/) made some erroneous statements about R Commander. Here is a revised description of R Commander with some issues addressed from the earlier blog:R Commander works ...

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GUIs for R

March 28, 2011
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A recent post listed at R Bloggers (http://www.r-bloggers.com/r-guis-which-one-fits-you/) made some erroneous statements about R Commander. Here is a revised description of R Commander with some issues addressed from the earlier blog:R Commander works ...

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A Lattice Panel Function for Filled Polygons that Accounts for Missing Data

March 28, 2011
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A Lattice Panel Function for Filled Polygons that Accounts for Missing Data

This is a quick update to some code posted while back, related to plotting filled polygons within a lattice panel function. After attempting to use the originally described function to plot data with NA, I quickly realized that a more robust approach w...

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R Tutorial Series: 2011 ANOVA Article Data

March 28, 2011
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R Tutorial Series: 2011 ANOVA Article Data

Having wrapped up a recent flurry of R ANOVA articles (and exhausted my knowledge of the subject), I decided to take a look at the R Tutorial Series' Google Analytics data from the past few months. Since I posted the Two-Way Omnibus ANOVA article on J...

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R Tutorial Series: 2011 ANOVA Article Data

March 28, 2011
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R Tutorial Series: 2011 ANOVA Article Data

Having wrapped up a recent flurry of R ANOVA articles (and exhausted my knowledge of the subject), I decided to take a look at the R Tutorial Series' Google Analytics data from the past few months. Since I posted the Two-Way Omnibus ANOVA article on J...

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The devil of overfitting

March 27, 2011
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The devil of overfitting

Overfitting is a problem when trying to predict financial returns.  Perhaps you’ve heard that before.  Some simple examples should clarify what overfitting is — and may surprise you. Polynomials Let’s suppose that the true expected return over a period of time is described by a polynomial. We can easily do this in R.  The first … Continue reading...

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R-bloggers: I’m syndicated!

March 27, 2011
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Today Left Censored became a contributor to R-Bloggers. If you’ve never heard of it, R-Bloggers is a blog aggregator that brings together R-related posts from a large number of blogs across the Internet. It’s an excellent resource for those who … Continue reading →

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R [re-]exam

March 27, 2011
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R [re-]exam

In what seems like an endless cuRse, I found this week I had to re-grade a dozen R exams a TA’s did not grade properly! The grades I (X) got are plotted below against those of my TA (Y). There is little connection between both gradings… As if this was not enough trouble, I also

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R GUIs: Which one fits you?

March 27, 2011
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R GUIs: Which one fits you?

The gap of the new “digital divide” between those who only use computers when they are as easy to use as iPads and smartphones and those who like (or at least accept) to type commands to perform jobs, seems to get bigger and bigger. R – the lingua franca of statistical computing – is exactly

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R Matrix Operations

March 27, 2011
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R Matrix Operations

R can be used to perform various matrix calculations. This include functions for creating matrices (matrix), addition (+), multiplication (%*%) and inversion (solve). Fast Tube by Casper Other useful resources are provided on the Supplementary Material...

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More on Ultraedit to R

March 27, 2011
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I think I have found a superior solution to integrating Ultraedit and R. See my post over at IDM Users forum.

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R-ecap [-16]

March 26, 2011
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R-ecap [-16]

This morning, I noticed that none of my R related posts had appeared on R-bloggers for the past fortnight… After investigating, this was caused by…cut-and-paste! Indeed, when advertising about the special issue of TOMACS Arnaud Doucet and I edit about Monte Carlo methods in Statistics, I copied the main parts from the pdf announcement, straight

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clusterProfiler in Bioconductor 2.8

March 26, 2011
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In recently years, high-throughput experimental techniques such as microarray and mass spectrometry can identify many lists of genes and gene products. The most widely used strategy for high-throughput data analysis is to identify different gene clusters based on their expression profiles. Another commonly used approach is to annotate these genes to biological knowledge, such as Gene Ontology (GO) and...

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“An R package” or “A R package”

March 26, 2011
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“An R package” or “A R package”

I’m currently writing some lecture notes on R and I used the phrase “a R package” without thinking. Since the word following the article “a” was a consonant, I automatically went for “a” instead of “an”. The problem is that “R” sounds likes a vowel, so “a R package” grates on the listener. The correct

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solaR 0.22 is at CRAN

solaR 0.22 is at CRAN

The version 0.22 of solaR is now available at CRAN. Besides, solaR is now registered at R-Forge. A new mergesolaR method has been defined for merging solaR objects. The calculation of the sunset time has been improved. The voltage dependency of the efficiency curve of the inverter is now included in fProd and calcGCPV. The

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How to backtest a strategy in R

March 26, 2011
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This is the third post in the Backtesting in Excel and R series and it will show how to backtest a simple strategy in R.  It will follow the 4 steps Damian outlined in his post on how to backtest a simple strategy in Excel.Step 1: Get the dataThe ...

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How to backtest a strategy in R

March 26, 2011
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This is the third post in the Backtesting in Excel and R series and it will show how to backtest a simple strategy in R.  It will follow the 4 steps Damian outlined in his post on how to backtest a simple strategy in Excel.Step 1: Get the dataThe ...

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