Monthly Archives: March 2011

How to Bootstrap in R: The Case of R-squared

March 29, 2011
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How to Bootstrap in R: The Case of R-squared

I recorded a new video tutorial whose original intent was to demonstrate how to write a for loop. As I wanted to make the for loop count for something, I decided that my application would be to write some code that computes the bootstrap approximation ...

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The Leverage Space Trading Model

March 29, 2011
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The Leverage Space Trading Model

I finally got around to reading Ralph Vince’s latest The Leverage Space Trading Model (for a brief summary see this magazine article in Futures), and I’m happy to say that the book was very helpful in approach and example.  I especially enjoye...

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Prune GWAS data in R

March 29, 2011
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Prune GWAS data in R

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do t...

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Prune GWAS data in R

March 29, 2011
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Prune GWAS data in R

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do t...

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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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