Monthly Archives: March 2010

Example 7.25: compare draws with distribution

March 5, 2010
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In example 7.24, we demonstrated a Metropolis-Hastings algorithm for generating observations from awkward distributions. In such settings it is desirable to assess the quality of draws by comparing them with the target distribution.Recall that the dis...

Getting data from an image (introductory post)

March 5, 2010
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Hi there! This blog will be dedicated to data visualization in R. Why? Two reasons. First, when it comes to statistics, I am always starting by some exploratory analyses, mostly with plots. And when I handle large quantities of data, it’s nice to make some graphs to get a grasp about what is going on.

Accessing Climate Change Data and a Custom Panel Function for Filled Polygons

March 4, 2010
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GCS Model Grids

Recently finished some collaborative work with Vishal, related to visualizing climate change data for the SEI. This project was funded in part by the California Energy Commission, with additional technical support from the Google Earth Team. One of the final products was an...

March 4, 2010
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As a coincidence, or not, I received the following email just before starting our mixture estimation workshop (the above is Ben Nevis on Monday, whose skyline really looks like a three component mixture!) and giving a discussion on label switching: I am implementing a Markov-Chain Monte Carlo method for Gibbs sampling from a simple mixture

Yet Another plyr Example

March 4, 2010
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another plyr example quantiles (0.05, 0.25, 0.5, 0.75, 0.95) of DSC by temperature bin

There are plenty of good examples on how to use functions from the plyr package. Here is one more, demonstrating how to use ddply with a custom function. Note that there...

More on the Economist’s special report on big data

March 4, 2010
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I totally missed this the other day, but there's much more to that special report on the data deluge in The Economist. (Thanks to readers SB and DN for pointing this out.) There's an total of nine articles in the report (you can find them all in the Related Items box on this page), including a section on business...

New Le Monde puzzle

March 3, 2010
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$New Le Monde puzzle$

When I first read Le Monde puzzle this weekend, I though it was even less exciting than the previous one: find and , such that is a multiple of . The solution is obtained by brute-force checking through an R program: and then the a next solution is (with several values for N). However, while

Quality trimming in R using ShortRead and Biostrings

March 3, 2010
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I wrote an R function to do soft-trimming, right clipping FastQ reads based on quality.

This function has the option of leaving out sequences trimmed to extinction and will do left-side fixed trimming as well.

`#softTrim#trim first position lower than minQuality and all subsequent positions#omit sequences that after trimming are shorter than minLength#left trim to firstBase, (1 implies no left trim)#input:...Read more »`

Quality trimming in R using ShortRead and Biostrings

March 3, 2010
By

I wrote an R function to do soft-trimming, right clipping FastQ reads based on quality.

This function has the option of leaving out sequences trimmed to extinction and will do left-side fixed trimming as well.

`#softTrim#trim first position lower than minQuality and all subsequent positions#omit sequences that after trimming are shorter than minLength#left trim to firstBase, (1 implies no left trim)#input:...Read more »`

Example of plotting a serial position curve in R

March 3, 2010
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A while ago I wrote a co-wrote chapter for an introductory psychology text book Essential Psychology: A Concise Introduction. This is a book edited and written by members of the department where I work. My contribution was the chapter on huma...