Johns Hopkins Coursera Statistics Courses

July 18, 2012
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Computing for Data Analysis Data Analysis Mathematical Biostatistics Bootcamp

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Monitor with R: Moisture in Sunflower Seeds Intact

July 18, 2012
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Monitor with R: Moisture in Sunflower Seeds Intact

I had the opportunity today to check the performance of a calibration (moisture in intact sunflower seed in reflectance).This is always a exciting moment:  Does the performance of the calibration for the new validation set is as expected duri...

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Project Euler — problem 15

July 18, 2012
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Project Euler — problem 15

The 15th problem in Project Euler. Starting in the top left corner of a 22 grid, there are 6 routes (without backtracking) to the bottom right corner. How many routes are there through a 2020 grid? Mmm… walk in the … Continue reading →

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50 Shades of Grey Wordcloud

July 17, 2012
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50 Shades of Grey Wordcloud

Sometimes you just want to see what all the fuss is about. File this under the 'because I can' category: I proudly (?) present - a wordcloud produced from the text of E. L. James' "50 Shades of Grey".For a book which is getting all this press about bei...

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Trends in run scoring, NL edition (more R)

July 17, 2012
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Last time around I used R to plot the average runs per game for the American League, starting in 1901. Now I’ll do the same for the National League.  I'll save a comparison of the two leagues for my next post.A fundamental principal of programming is that code can be repurposed for different sets of datas. So...

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Create an R package in under 6 minutes

July 17, 2012
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Create an R package in under 6 minutes

Storing your favorite R functions is best done by creating your own R package. This is a quick way to get started with two example functions.Enjoy!

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R for Ecologists: Creating a Site x Species Matrix

July 17, 2012
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R for Ecologists: Creating a Site x Species Matrix

Today I’m going to adress a fairly common problem in ecology that has been coming up frequently as of late. The issue is how to create a site x species matrix for community composition analysis (i.e. ordination). Moreover, ecologists have to do … Continue reading →

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Plotting the Frequency of Twitter Hashtag Usage Over Time with R and ggplot2

July 17, 2012
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Plotting the Frequency of Twitter Hashtag Usage Over Time with R and ggplot2

The 20th annual ISMB meeting was held over the last week in Long Beach, CA. It was an incredible meeting with lots of interesting and relevant talks, and lots of folks were tweeting the conference, usually with at least a few people in each concurrent ...

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The R packages in a data scientist’s toolbox

July 17, 2012
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John Myles White, self-described "statistics hacker" and co-author of "Machine Learning for Hackers" was interviewed recently by The Setup. In the interview, he describes his some of his go-to R packages for data science: Most of my work involves programming, so programming languages and their libraries are the bulk of the software I use. I primarily program in R,...

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Hierarchical Cluster Analysis (ChemoSpec) – 01

July 17, 2012
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Hierarchical Cluster Analysis (ChemoSpec) – 01

I have been in previous post using the ChemoSpec package for some oil data (olive and sunflower). My spectra has now a range from 1100nm to 2200nm and is raw (not treated mathematically) . I want to start using the ChemoSpec package to start using the ...

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“Computing for Data Analysis” with R on coursera

July 17, 2012
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“Computing for Data Analysis” with R on coursera

Just stumbled on across a course on coursera titled “Computing for Data Analysis” taught by Roger D. Peng the Johns Hopkins Bloomberg School of Public Health. Here is the description of the course. In this course you will learn how to program in R and how to use R for effective data analysis. You will learn … Continue reading...

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Criticism 5 of NHST: p-Values Measure Effort, Not Truth

July 17, 2012
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Criticism 5 of NHST: p-Values Measure Effort, Not Truth

Introduction In the third installment of my series of criticisms of NHST, I focused on the notion that a p-value is nothing more than a one-dimensional representation of a two-dimensional space in which (1) the measured size of an effect and (2) the precision of this measurement have been combined in such a way that

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Optical Art with R

July 16, 2012
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Optical Art with R

Last week, in a post entitled Bridget Riley exhibition in London, the author Markus Gesmann wrote an R script reproducing one of Riley's famous art pieces: Movement in Squares.This reminded me of my own first "brush" with Op art. It was in art class ye...

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Factor Attribution to improve performance of the 1-Month Reversal Strategy

July 16, 2012
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Factor Attribution to improve performance of the 1-Month Reversal Strategy

Today I want to show how to use Factor Attribution to boost performance of the 1-Month Reversal Strategy. The Short-Term Residual Reversal by D. Blitz, J. Huij, S. Lansdorp, M. Verbeek (2011) paper presents the idea and discusses the results as applied to US stock market since 1929. To improve 1-Month Reversal Strategy performance authors

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Data mining for network security and intrusion detection

July 16, 2012
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Data mining for network security and intrusion detection

In preparation for “Haxogreen” hackers summer camp which takes place in Luxembourg, I was exploring network security world. My motivation was to find out how data mining is applicable to network security and intrusion detection. Flame virus, Stuxnet, Duqu proved that static, signature based security systems are not able to detect very advanced, government sponsored

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Convenient access to Gapminder’s datasets from R

July 16, 2012
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Convenient access to Gapminder’s datasets from R

In April, Hans Rosling examined the influence of religion on fertility. I used R to replicate a graphic of his talk:> library(datamart) > gm <- gapminder() > #queries(gm) > # > # babies per woman > tmp <- query(gm, "TotalFertilityRate") > babies <- as.vector(tmp) > names(babies) <- names(tmp) > babies <- babies > countries <- names(babies) > # > # income per capita, PPP adjusted > tmp <- query(gm, "IncomePerCapita") >...

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Holt-Winters forecast using ggplot2

July 16, 2012
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Holt-Winters forecast using ggplot2

R has great support for Holt-Winter filtering and forecasting. I sometimes use this functionality, HoltWinter & predict.HoltWinter, to forecast demand figures based on historical data. Using the HoltWinter functions in R is pretty straightforward. Let's say our dataset looks as follows; demand <- ts(BJsales, start = c(2000, 1), frequency =  Read more...

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Using integer programming in R to optimize cargo loads

July 16, 2012
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Using integer programming in R to optimize cargo loads

Linear Programming is a mathematical technique used to find the values of some variables (within the bounds of some defined constraints) to find the maximum value of a quantity. For example, consider this problem from the FishyOperations blog: A trading company is looking for a way to maximize profit per transportation of their goods. The company has a train...

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Example 9.38: dynamite plots, revisited

July 16, 2012
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Example 9.38: dynamite plots, revisited

Dynamite plots are a somewhat pejorative term for a graphical display where the height of a bar indicates the mean, and the vertical line on top of it represents the standard deviation (or standard error). These displays are commonly found in many scientific disciplines, as a way of communicating group differences in means. Many...

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Holt-Winters forecast using ggplot2

July 16, 2012
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Holt-Winters forecast using ggplot2

R has great support for Holt-Winter filtering and forecasting. I sometimes use this functionality, HoltWinter & predict.HoltWinter, to forecast demand figures based on historical data. Using the HoltWinter functions in R is pretty straightforward. Let's say our dataset looks as follows; demand <- ts(BJsales, start = c(2000, 1), frequency = 12) plot(demand) Now I pass the timeseries object to HoltWinter and...

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Best Books for Social Scientists on Bayesian Analysis

July 16, 2012
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I list and discuss the three books on Bayesian analysis that I recommend to social scientists.

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2 dimensions of portfolio diversity

July 16, 2012
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2 dimensions of portfolio diversity

Portfolio diversity is a balancing act. Previously The post “Portfolio diversity” talked about the role of the correlation between assets and the portfolio.  The current post fills a hole in that post. The 2 dimensions asset-portfolio correlation Each asset in the universe has a correlation with the portfolio.  If there are any assets that have … Continue reading...

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Project Euler — problem 14

July 16, 2012
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Project Euler — problem 14

It’s Monday today! It’s work day! And I’ve already worked on computer for two hours. Time for a break, which is the 14th problem of Project Euler. The following iterative sequence is defined for the set of positive integers: n n/2 (n … Continue reading →

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Map biodiversity records with rgbif and dismo packages in R

July 15, 2012
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Map biodiversity records with rgbif and dismo packages in R

In the earlier post we generated maps from GBIF biodiversity records using maps and ggplot2 packages. We used world map with country borders for that. Now we will generate maps with google maps as base layer using dismo package. Like earlier we download data for Danaus chrysippus from GBIF using occurrencelist function into a data

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Map biodiversity records with rgbif and dismo packages in R

July 15, 2012
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Map biodiversity records with rgbif and dismo packages in R

In the earlier post we generated maps from GBIF biodiversity records using maps and ggplot2 packages. We used world map with country borders for that. Now we will generate maps with google maps as base layer using dismo package. Like earlier we download data for Danaus chrysippus from GBIF using occurrencelist function into a data

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A simple Approximate Bayesian Computation MCMC (ABC-MCMC) in R

July 15, 2012
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A simple Approximate Bayesian Computation MCMC (ABC-MCMC) in R

Approximate Bayesian Computing and similar techniques, which are based on calculating approximate likelihood values based on samples from a stochastic simulation model, have attracted a lot of attention in the last years, owing to their promise to provide a general statistical technique for stochastic processes of any complexity, without the limitations that apply to “traditional”…

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Sourcing an R Script from Dropbox

July 14, 2012
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Working on my R bootcamp materials and I thought it would be handy to get the bootcamp computers setup by sourcing an R script that will install all necessary non-core packages in it. The problem? How to deploy this script efficiently. A quick method w...

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Trends in AL run scoring (using R)

July 14, 2012
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I have started to explore the functionality of R, the statistical and graphics programming language. And with what better data to play than that of Major League Baseball?There have already been some good examples of using R to analyze baseball data. The most comprehensive is the on-going series at The Prince of Slides (Brian Mills, aka...

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