Monthly Archives: July 2007

Adaptive tau-leaping in SSA

July 26, 2007
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Adaptive tau-leaping in SSA

Just a brief update on my activities 11 days before the R package GillespieSSA is to be released. I have been hacking away on the code, debugging, and running test simulations like there is no tomorrow. The last SSA implementation … Continue reading →

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Further Bioclipse QSAR functionality development

July 26, 2007
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Further Bioclipse QSAR functionality development

I had some time to work some more on the QSAR functionality in Bioclipse. There is still much to do, but it is getting there. The calculation of a QSAR descriptor data matrixThis screenshot shows that multi-resource selection is now working, and that t...

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Variance-Covariance Matrix in glm

July 20, 2007
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This is a small function Venables and Ripley provide in their MASS book. You don't need it anymore because vcov() has a method for the glm class. However, it is useful to see how to extract bits from a fitted model object.vcov.glm #return the variance-covariance matrix of a glm object #from p. 188 in Venables and Ripley....

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Variance-Covariance Matrix in glm

July 20, 2007
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This is a small function Venables and Ripley provide in their MASS book. You don't need it anymore because vcov() has a method for the glm class. However, it is useful to see how to extract bits from a fitted model object.vcov.glm #return the variance-covariance matrix of a glm object #from p. 188 in Venables and Ripley....

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Visualizing Data

July 18, 2007
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Sometimes it is helpful to see the plots created from the example files within R libraries. Of course you can paste them directly into R, but this web page allows you to view the images within the context of the help files:R Graphical ManualsAlso, chec...

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Visualizing Data

July 18, 2007
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Sometimes it is helpful to see the plots created from the example files within R libraries. Of course you can paste them directly into R, but this web page allows you to view the images within the context of the help files:R Graphical ManualsAlso, chec...

Read more »

Abstract for useR! 2007 poster

July 15, 2007
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Abstract for useR! 2007 poster

Here’s my submitted abstract for the poster I will be presenting at the useR! 2007 meeting in August. GillespieSSA: A stochastic simulation package for R Mario Pineda-Krch Center for Animal Disease Modeling and Surveillance University of California, Davis Abstract Stochastic … Continue reading →

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Testing for missing values of numeric (double) vectors in R

July 13, 2007
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I just came across this bit of R trickiness when trying to improve the error messages for one of our packages. I tried adding a check at the C level for NA_REAL, but to no avail. The test failed even when I was certain that I was passing down a vector containing missing

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Testing for missing values of numeric (double) vectors in R

July 13, 2007
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I just came across this bit of R trickiness when trying to improve the error messages for one of our packages. I tried adding a check at the C level for NA_REAL, but to no avail. The test failed even when I was certain that I was passing down a vecto...

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ESA 2007 – San Jose here I come!

July 12, 2007
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ESA 2007 – San Jose here I come!

Finally took the leap and decided to go the ESA (Ecological Society of America) meeting despite it clashing with the useR! meeting. After checking out their smörgåsbord of a program there were simply too many yummy temptations, e.g. Alan Hastings … Continue reading →

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