The UCR guide is a little sparse with regard to getting basic information from readAligned.I'd like to add to the general cookbook. If some bioc people out there can contribute some alignment recipes can fill me in on some more basics please comment:alignedReads #how many reads did I ... [Read more...]

Keeping with the theme of the post below, I used a clustering algorithm to group the different countries according to what they eat. I simply played around with the number of clusters until I got something I thought resembled reality, so don't interpre... [Read more...]

This article by REvolution Computing CEO Norman Nie is crossposted from the Future of Open Source Forum. The R Project: despite there being over 2 million users of this open-source language for statistical data analysis, you might not have heard of it ... yet. You might have seen this feature in the ... [Read more...]

Last week, I got news from Springer Verlag about possibly two new editions of my books, one in Chinese and one in Japanese. These were bad news and good news: the bad news was that the Chinese edition was actually a reprint of our original book,  Monte Carlo Statistical Method, ... [Read more...]

Edward Tufte, a pioneer of effective data visualization (and a personal hero) has just been appointed by the White House to the Recovery Independent Advisory Panel. This panel advises The Recovery Accountability and Transparency Board, whose job is to track and explain $787 billion in recovery stimulus funds. Tufte explains: I'm ... [Read more...]

Using this database of food consumption data the blog Canibais e Reis kindly put together, I calculated all values for which the US was at least 2 standard deviations from the world average. Here are the outliers in standard deviations from the w... [Read more...]

The National Oceanic and Atmospheric Administration (NOAA) has a page with some interesting information about last week's earthquake in Chile, but what really stood out for me was this chart of the predicted wave heights around the globe resulting from the associated tsunami: Click to enlarge: it's a fascinating chart. ... [Read more...]

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I needed a fast way of eliminating observed values with zero variance from large data sets using the R statistical computing and analysis platform. In other words, I want to find the columns in a data frame that has zero variance. And as fast as possible, because my data sets ... [Read more...]

This looks interesting: http://infochimps.org/search?query=soil [Read more...]

A few months back I gave a presentation to the NYC R Meetup. (R is a statistical programming language. If this means nothing to you, feel free to stop reading now.) The presentation was on ggplot2, a popular package for generating graphs of data and statistics. In the talk (which ... [Read more...]

Patrick Burns just posted to the mailing list the following massage: There is now a document called “Some hints for the R beginner” whose purpose is to get people up and running with R as quickly as possible. Direct access to it is: http://www.burns-stat.com/pages/Tutor/hints_... [Read more...]

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Here i present some Books and Articles about Ecological Modelling and “R”. Since “R” is integrated in Bio7 all the presented methods in the Books and Articles can also be useful together with Bio7. Books: Ellner, Stephen P. & Guckenheimer, John (2006). Dynamic Models in Biology. Princeton University Press Bolker B (2008) Ecological ... [Read more...]

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In connection with the Le Monde puzzle of last week, I was looking for an R function that would give me the prime factor decomposition of any integer. Such a function exists within the package schoolmath, developped by Joerg Schlarmann and Josef Wienand. It is called prime.factor and it ... [Read more...]

The impacts of drought depend on time-scale. On short time-scales, drought means dry soil. On long time-scales, it means dry rivers and empty reservoirs. A region may simultaneously experience dry conditions on one time-scale and wet conditions on another e.g. wet soil but low streamflow or visa versa. Standardized ... [Read more...]

A contingency table is used in statistics to provide a tabular summary of categorical data and the cells in the table are the number of occassions that a particular combination of variables occur together in a set of data. The relationship between variables in a contingency table are often investigated ... [Read more...]

At the Edinburgh mixture estimation workshop, Murray Aitkin presented his proposal to compare models via the posterior distribution of the likelihood ratio. As already commented in a post last July, the positive aspect of looking at this quantity rather than at the Bayes factor is that the priors are then ... [Read more...]

The R package oro.nifti has been released.  Medical imaging data, in NIfTI or Analyze formats, may be input, created from scratch, converted from DICOM (using oro.dicom) and output to a file.  [Read more...]