Landscape Metrics with R, SDMTools, ImageJ and Bio7

February 2, 2012
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01.02.2012 Landscape metrics were developed to analyze spatial patterns of landscapes (e.g. composition and spatial arrangement). In R it is possible to calculate these metrics with the “SDMTools” package. Bio7 offers an easy to use interface to R and ImageJ and can use these tools to simplify a workflow to analyze image data (e.g. vegetation

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Two courses in R programming by Ken Rice and Thomas Lumley

February 2, 2012
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Ken Rice and Thomas Lumley will give a course on advanced R programming in two locations this summer. 1. In Edinburgh, June 13-15 (the week before the International Conference in Quantitative Genetics). See http://www.eisg2012.org.uk/ 2. In Seattle, July 23-25, as part of the Summer Institute in Statistical Genetics. See http://www.biostat.washington.edu/suminst/sisg/general The course is about 60% lecture and 40% lab session (BYO R),...

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Analytic applications are built by data scientists

February 1, 2012
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Ventana Research analyst David Menninger was on the judging panel for the Applications of R in Business contest. In a post on the Ventana research blog, he offers his perspectives on the contest, noting that R, as a statistical package, includes many algorithms for predictive analytics, including regression, clustering, classification, text mining and other techniques. The contest submissions supported...

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Cochran Q Test for k related samples in R

February 1, 2012
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Cochran Q Test for k related samples in R

To run the Cochran Q Test in R, we need to download the package of it first, since it is not built-in in R. The name of the package is RVAideMemoire authored by Maxime Hervé. Here's how to do it.Codes:Here we are installing the package named RVAideMem...

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Transformation of Several Variables in a Dataframe

February 1, 2012
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Transformation of Several Variables in a Dataframe

This is how I transform several columns of a dataframe, i.e., with count-data into binary coded data (this would apply also for any other conversion..).count1

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Vectorized R vs Rcpp

February 1, 2012
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Vectorized R vs Rcpp

In my previous post, I tried to show, that Rcpp is 1000 faster than pure R and that generated the fuss in the comments. Being lazy, I didn’t vectorize R code and at the end I was comparing apples vs oranges. To fix that problem, I built a new script, where I’m trying to compare

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Are Recessions Environmentally Beneficial?

February 1, 2012
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Are Recessions Environmentally Beneficial?

Description:Total energy consumption in the United States by sector.  Vertical gray lines represent periodsof recession.Data:http://www.eia.gov/totalenergy/data/annual/index.cfm#consumptionhttp://en.wikipedia.org/wiki/List_of_recessions_in_the_Uni...

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MAT886 mean excess function (and reinsurance)

February 1, 2012
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MAT886 mean excess function (and reinsurance)

Tomorrow, in the course on extreme value, we will focus on applications. We will discuss reinsurance pricing. Consider a random variable , a threshold and define the mean excess function. This function is known in life insurance as the average ...

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"R": Looking at the Data (Gasoline) – 001

February 1, 2012
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"R": Looking at the Data (Gasoline) – 001

As other softwares "R" has nice tools to look to the data before to develop the calibration.Statistics for the "Y" variable (in this case octane number) like Maximun, Minimun,..,standard deviation,...are important:> library(ChemometricsWithR)> data(gasoline)> summary(gasoline$octane)   Min.  1st Qu.  Median    Mean   3rd Qu.    Max.   83.40   85.88    87.75    87.18   88.45    89.60> sd(gasoline$octane) 1.530078And of course the Histogram:> hist(gasoline$octane)

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Confirming SSR, SSE, and SST using matrix in R

February 1, 2012
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Confirming SSR, SSE, and SST using matrix in R

The codes below was done in our regression laboratory class. Here, we run first the data in SPSS, and take the ANOVA output where we can find the computed values of SSR, SSE, and SST.ANOVAb Model Sum of Squares df Mean Square F Sig. 1 Regress...

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R Training Course in the Bay Area

February 1, 2012
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R Training Course in the Bay Area

An introduction to R for sofware developers and data analysts Saturday March 10th, 2012 8:30-5:00pm EBay 2161 North 1st Street San Jose, California I will be presenting a one day professional development workshop on R programming for software developers and … Continue reading →

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the birthday problem [X'idated]

February 1, 2012
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the birthday problem [X'idated]

The birthday problem (i.e. looking at the distribution of the birthdates in a group of n persons, assuming a uniform distribution of the calendar dates of those birthdates) is always a source of puzzlement ! For instance, here is a recent post on Cross Validated: I have 360 friends on facebook, and, as

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RStudio Server: accessing the RStudio R IDE through your browser

February 1, 2012
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I like having all my important documents and scripts in one single place. This saves me from having to synchronize them between the different workplaces I have, and makes backupping much less of a pain. One way of achieving this… See more ›

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R is the easiest language to speak badly

February 1, 2012
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R is the easiest language to speak badly

I am amazed by the number of comments I received on my recent blog entry about "by", "apply" and friends. I had started my post by pointing out that R is a language. Well indeed, I have come to the conclusion, that it is a language with lots of irregul...

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MINE: Maximal Information-based NonParametric Exploration

February 1, 2012
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MINE: Maximal Information-based NonParametric Exploration

There was a lot of buzz in the blogosphere as well as the science community about a new family of algorithms that are able to find non-linear relationships over extremely large fields of data. What makes it particularly useful is that the measure(s) it...

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New R User Group in Cambridge, UK

January 31, 2012
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Yet another new local R user group has launched this month, this time in Cambridge, UK. Cambridge RUG was created by data analyst Andrew Caines to promote the use of R in the Cambridge area. The group aims to encourage people try the R language, act as an advice centre to help people get where they want to with...

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Weak Law of Large Numbers

January 31, 2012
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Weak Law of Large Numbers

1 Description The weak law of large numbers is a result in probability theory also known as Bernoulli’s

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quick tips: within function assignment and specific object removal

January 31, 2012
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quick tips: within function assignment and specific object removal

If you’re familiar with the faster iterations on objects such as lapply, sapply, or apply for matrices, you might get surprised that the function call saves new assignments only locally. One of my favorite lines in R comes from the … Continue reading →

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Example: Two Sample t-Test

January 31, 2012
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Example: Two Sample t-Test

The recovery time (in days) is measured for 10 patients taking a new drug and for 10 different patients taking a placebo. We wish to test the hypothesis that the mean recovery time for patients taking the drug is less than for those taking placebo. The...

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Given a room with n people in it, what is the probability any two will have the same birthday?

January 31, 2012
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Given a room with n people in it, what is the probability any two will have the same birthday?

Revisiting a fun puzzle I remember first encountering as an undergraduate. Nice example of creating a plot in R using ggplot2. I also plot the probability of someone in the room having the same birthday as you.

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Example: One Sample t-Test

January 31, 2012
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Example: One Sample t-Test

Using the stack loss dataset, test the hypothesis that the mean of the stackloss is equal to 20 versus a two-sided alternative. Solution:Codes:Output:Interpretation: With the p-value greater than the level of significance alpha at 0.05, then we la...

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Surfaces in ternary plots

January 31, 2012
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Surfaces in ternary plots

In mixture experiments there is a constraint that the variables are the proportions of components that are mixed together with the consequence that these proportions sum to one. When fitting regression models to data from mixture experiments we may be interested in reprenting the fitted model with a surface plot. The constraint on proportions means

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ultimate R recursion

January 31, 2012
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ultimate R recursion

One of my students wrote the following code for his R exam, trying to do accept-reject simulation (of a Rayleigh distribution) and constant approximation at the same time: which I find remarkable if alas doomed to fail! I wonder if there exists a (real as opposed to fantasy) computer language where you could introduce constants

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This graph makes me think Kobe is not that good, he just shoots a lot

January 31, 2012
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This graph makes me think Kobe is not that good, he just shoots a lot

I find it surprising that NBA commentators rarely talk about field goal percentage. Everybody knows that the more you shoot the more you score. But players that score a lot are admired without consideration of their FG%. Of course having a high FG% is ...

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Given a room with n people in it, what is the probability any two will have the same birthday?

January 31, 2012
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Given a room with n people in it, what is the probability any two will have the same birthday?

Revisiting a fun puzzle I remember first encountering as an undergraduate. Nice example of creating a plot in R using ggplot2. I also plot the probability of someone in the room having the same birthday as you. ## See http://en.wikipedia.org/wiki/Bi...

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Given a room with n people in it, what is the probability any two will have the same birthday?

January 31, 2012
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Given a room with n people in it, what is the probability any two will have the same birthday?

Revisiting a fun puzzle I remember first encountering as an undergraduate. Nice example of creating a plot in R using ggplot2. I also plot the probability of someone in the room having the same birthday as you. ## See http://en.wikipedia.org/wiki/Bi...

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Computational Econometrics: Aggregate Demand with Random Parameters

January 31, 2012
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Computational Econometrics: Aggregate Demand with Random Parameters

Computational Econometrics: Aggregate Demand with Random Parameters: From microeconomics we know that individuals and firms have demand curves for goods and services. But what happens when you try to get a picture of the demand for goods and services f...

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Collapse pasting in R

January 30, 2012
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Collapse pasting in R

How do you take a vector in R, and paste the individual elements together?  Easy, a loop.  No, bad! **slap on the wrist**  Here’s an example why not.   So let’s start by concatenating a few character strings and showing some … Continue reading →

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Using LaTeX, R, and Sweave to Create Reports in Windows

January 30, 2012
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Using LaTeX, R, and Sweave to Create Reports in Windows

LaTeX is a typesetting system that can easily be used to create reports and scientific articles, and has excellent formatting options for displaying code and mathematical formulas. Sweave is a package in base R that can execute R code embedded in LaTe...

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