Monthly Archives: June 2012

Olive Oil NIR/VIS Spectra – 001 (ChemSpec)

June 25, 2012
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Olive Oil NIR/VIS Spectra – 001 (ChemSpec)

I continue with the practicing with ChemSpec, and this time I import seven spectra of olive oil. This time I have been more careful and I have the frequency column as numeric form the CSV file. Once I have the spectra (with and offset):Take in account ...

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Avoid Overplotting of Text in Ordination Diagram

June 25, 2012
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Avoid Overplotting of Text in Ordination Diagram

Referring to a recent posting on r-sig-eco mailing list I'll add this example to theBioBucket:library(vegan)library(vegan)data(dune)sol <- metaMDS(dune) # use ordipointlabel -# here is an example where I added cex according to species frequencies:pl...

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Grouped means (or anything else…)

June 25, 2012
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Grouped means (or anything else…)

An easy one today, but something that stumped me for a while* the first time I tried it out. How do you get a group mean (or other summary statistic) from R? Lets say you have a Y variable that represents repetitions for each of however many factors. You could subset the data by each

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Example 9.36: Levene’s test for equal variances

June 25, 2012
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Example 9.36: Levene’s test for equal variances

The assumption of equal variances among the groups in analysis of variance is an expression of the assumption of homoscedasticity for linear models more generally. For ANOVA, this assumption can be tested via Levene's test. The test is a function of the residuals and means within each group, though various modifications are used, including the Brown-Forsythe...

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Euro 2012: Day 18

June 25, 2012
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Euro 2012: Day 18

As promised. Looks like a Spain Germany final.

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How many ecologists were on ECOLOG in 1992?

June 25, 2012
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How many ecologists were on ECOLOG in 1992?

Remember 1992? I had just turned 13 and was still a year away from highschool when my true descent into nerdom and the internet would begin. Back then it was with a local BBS (Bulletin Board System) run by a guy in a trailer park named Charlie and a 1200 baud modem on...

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Making Reproducible Research Enjoyable

June 25, 2012
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Making Reproducible Research Enjoyable

Note: this is a contributed article for the ICSA Bulletin and the basic idea can be summarized in this picture. It is hard to convince people to think about reproducible research (RR). There are two parts of difficulties: (1) tools used to be for ex...

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Grid2Polygons

June 25, 2012
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Grid2Polygons

I’d like to introduce you to the Grid2Polygons function; an R function for converting sp spatial objects from class SpatialGridDataFrame to SpatialPolygonsDataFrame. The significance of this conversion is that spatial polygons can be transformed to a different projection or datum with the spTransform function in package rgdal. Postscript files created with spatial polygons are reduced in size and...

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Hodgkin-Huxley model in R

June 24, 2012
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Hodgkin-Huxley model in R

One of the great research papers of the 20th century celebrates its 60th anniversary in a few weeks time: A quantitative description of membrane current and its application to conduction and excitation in nerve by Alan Hodgkin and Andrew Huxley. Only a...

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Split-plot 1: How does a linear mixed model look like?

June 24, 2012
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Split-plot 1: How does a linear mixed model look like?

I like statistics and I struggle with statistics. Often times I get frustrated when I don’t understand and I really struggled to make sense of Krushke’s Bayesian analysis of a split-plot, particularly because ‘it didn’t look like’ a split-plot to … Continue reading →

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