Monthly Archives: March 2013

p-values are (possibly biased) estimates of the probability that the null hypothesis is true

March 31, 2013
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p-values are (possibly biased) estimates of the probability that the null hypothesis is true

Last week, I posted about statisticians’ constant battle against the belief that the p-value associated (for example) with a regression coefficient is equal to the probability that the null hypothesis is true, for a null hypothesis that beta is zero or negative. I argued that (despite our long pedagogical practice) there are, in fact, many

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To plot them is my real test

March 31, 2013
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To plot them is my real test

I almost couldn’t bring myself to post this, but it’s April Fools’ Day, so I’ll never have a better opportunity. This Gist shows how to scrape “stats” and .PNG images from, erm, Bulbapedia, run a simple dimensionality reduction on those “stats,” and plot all 151 original Pokemon. I don’t know much about Pokemon, so I can’t vouch for...

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R and the last comma

March 31, 2013
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In R, every comma matters. When creating a vector, c(1, 2, 5) will do the right thing, but add one unfortunate comma and c(1, 2, 5,) will greet you with a deadly Error in c(1, 2, 5, ) : argument 4 is empty. Other languages like Perl are less strict when defining basic data structures: having a comma after...

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How do Dew and Fog Form? Nature at Work with Temperature, Vapour Pressure, and Partial Pressure

How do Dew and Fog Form?  Nature at Work with Temperature, Vapour Pressure, and Partial Pressure

In the early morning, especially here in Canada, I often see dew – water droplets formed by the condensation of water vapour on outside surfaces, like windows, car roofs, and leaves of trees.  I also sometimes see fog – water droplets or ice crystals that are suspended in air and often blocking visibility at great

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Gary King and Stuart Shieber on Open Access

March 31, 2013
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Harvard Professors Gary King and Stuart Shieber provide advice to graduate students about open access, dissertations, and journal publishing. They explain how freely available publications are essential to the scientific community, but also benefit your own career. King suggests a clever way of dealing with publisher copyright agreements to prevent locking up your work behind ...

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Checking for Normality with Quantile Ranges and the Standard Deviation

Checking for Normality with Quantile Ranges and the Standard Deviation

Introduction I was reading Michael Trosset’s “An Introduction to Statistical Inference and Its Applications with R”, and I learned a basic but interesting fact about the normal distribution’s interquartile range and standard deviation that I had not learned before.  This turns out to be a good way to check for normality in a data set.

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Easter

March 31, 2013
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Easter

This morning, there was an interesting post entitled “why does Easter move around so much?” online on http://economist.com/blogs/economist-explains/… In my time series classes, I keep saying that sometimes, series can exhibit seasonlity, but the seasonal effect can be quite irregular. It is the cas for river levels, where snowmelt can have a huge impact, and it is irregular. Similarly, chocolate sales...

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R function to retrieve pubmed citations from pmid number

March 30, 2013
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This is useful number if you have hundreds of PMIDs and need specific fields from the pubmed/medline citation.  

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Importing Data to R

March 30, 2013
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There are number of ways in importing data into R, and several formats are available,From Excel to R From SPSS to RFrom Stata to R, and more hereIn this post, I'm going to talk about importing common data format that we often encounter, such as Excel, ...

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RSAGA: Getting Started

March 30, 2013
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RSAGA provides access to geocomputation capabilities of SAGA GIS from within R environment. Having SAGA GIS installed is a (quite obvious) pre-requirement to use RSAGA. In Linux x64 sometimes additional preparations are needed. In Linux SAGA as we...

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