A lightweight object browser for R

January 15, 2011
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Get access to a simple object browser in R so that you can see what variables, data frames, model objects and other junk you have in memory currently. If you don't want to install a full-fledged integrated development environment, this option may be fo...

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Easiest way to start imagining four-dimensional things is by…

January 15, 2011
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Easiest way to start imagining four-dimensional things is by…

Easiest way to start imagining four-dimensional things is by numbering the corners of a 4-cube. First realize that the eight corners of a cube can be numbered “in binary” 000—001–010–100—110–101–011—111. Just like the four corners of ...

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Easiest way to start imagining four-dimensional things is by…

January 15, 2011
By
Easiest way to start imagining four-dimensional things is by…

Easiest way to start imagining four-dimensional things is by numbering the corners of a 4-cube. First realize that the eight corners of a cube can be numbered “in binary” 000—001–010–100—110–101–011—111. Just like the four corners of ...

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Adding lines or points to an existing barplot

January 15, 2011
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Adding lines or points to an existing barplot

Sometimes you will need  to add some points to an existing barplot. You might try but you will get a funky looking line/points. It’s a bit squeezed. This happens because bars are not drawn at intervals 1:10, but rather on something else. This “else” can be seen if you save your barplot object. You will

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R Code Documentation Template

January 15, 2011
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R Code Documentation Template

# *------------------------------------------------------------------# | PROGRAM NAME: # | DATE: # | CREATED BY: # | PROJECT FILE: # *----------------------------------------------------------------# | PURPOSE: # |# *-------...

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Quickly adapt starting values in MCMC using paste()

January 15, 2011
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Quickly adapt starting values in MCMC using paste()

Waiting for convergence of MCMC models can take some time, therefore it may be a good idea to use better starting values. Using paste, one can quickly convert any (parameter) vector in the workspace into a R-style vector (with c()). Here's a function t...

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Parsing and plotting time series data

January 15, 2011
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Parsing and plotting time series data

This morning I came across a post which discusses the differences between scala, ruby and python when trying to analyse time series data. Essentially, there is a text file consisting of times in the format HH:MM and we want to get an idea of its distribution. Tom discusses how this would be a bit clunky

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sab-R-metrics: Beginning with Boxplots, Scatterplots, and Histograms

January 15, 2011
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sab-R-metrics: Beginning with Boxplots, Scatterplots, and Histograms

Today I decided to begin more with visualizations and less with basic statistical analysis for sabermetrics using R. I'm not really here to teach the ins and outs of regressions and statistical tests, so once I get there, I'm hoping that those who have read this already have a decent understanding of those subjects before implementing them. ...

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sab-R-metrics: Beginning with Boxplots, Scatterplots, and Histograms

January 15, 2011
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sab-R-metrics: Beginning with Boxplots, Scatterplots, and Histograms

Today I decided to begin more with visualizations and less with basic statistical analysis for sabermetrics using R. I'm not really here to teach the ins and outs of regressions and statistical tests, so once I get there, I'm hoping that those who have read this already have a decent understanding of those subjects before implementing them. ...

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Book Review: Mixed Effects Models and Extensions in Ecology with R

January 14, 2011
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A brief review of Zuur et al.'s book "Mixed Effects Models and Extensions in Ecology with R".

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Webinar on Portfolio Design, Optimization and Stability Analysis, Jan 26

January 14, 2011
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We're very excited to host a new webinar from some of the leading researchers in portfolio design: Diethelm Würtz and Mahendra Mehta for the Rmetrics Association. This webinar will give an overview on current and recent developments and tools for portfolio design, optimization and stability analysis with the R/Rmetrics software environment. This webinar will review content available in the...

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Warming in Paris: minimas versus maximas ?

January 14, 2011
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Warming in Paris: minimas versus maximas ?

Recently, I received comments (here and on Twitter) about my previous graphs on the temperature in Paris. I mentioned in a comment (there) that studying extremas (and more generally quantiles or interquantile evolution) is not the same as studying ...

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Bipartite networks and R

January 14, 2011
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Bipartite networks and R

Earlier, I posted about generating networks from abundance distributions that you specify. If this post was interesting, check out Jeff Kilpatrick's website, where he provides code he produced in R and Octave to compare real bipartite networks to ones ...

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Statistical podcast: Random and Pseudorandom

January 14, 2011
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Statistical podcast: Random and Pseudorandom

This morning when I downloaded the latest version of In our time, I was pleased to see that this weeks topic was “Random and Peudorandom.” If you’re not familiar with “In our time”, then I can I definitely recommend the series. Each week three academics and Melvyn Bragg discuss a particular topic from history, science,

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Changing phylogeny tip labels in R

January 14, 2011
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Changing phylogeny tip labels in R

During the process of molecular systematic research, specimens are given code names and numbers to keep track of data through the pipeline. These can contain a lot of information of relevance to the researcher, but unfortunately are meaningless to others who aren't as involved with the data. On publication, it is necessary to change the names from the code...

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Changing phylogeny tip labels in R

January 14, 2011
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Changing phylogeny tip labels in R

During the process of molecular systematic research, specimens are given code names and numbers to keep track of data through the pipeline. These can contain a lot of information of relevance to the researcher, but unfortunately are meaningless to others who aren't as involved with the data. On publication, it is necessary to change the names from the code...

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Remove all rows of an R dataframe

January 13, 2011
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Remove all rows of an R dataframe

I should have probably figured this out a long time ago, but as I get deeper into programming with R, I am finding the need to remove all rows from a dataframe.  I was making this alot harder than it had to be. your.df<- your.df Replace your.df with, your dataframe and you are good

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Visualizing the Haiti earthquake with R

January 13, 2011
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Yesterday was the one-year anniversary of the Haiti earthquake, and to put the scale of the event in context San Francisco bureau chief for New Scientist magazine and data journalist Peter Aldhous created a time-lapse animation of all large earthquakes in the last year, beginning with the 7.0-magnitude Haiti event. Peter used USGS data, R and Flash to generate...

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EPL Fantasy Football: Best overall, home and away teams

January 13, 2011
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EPL Fantasy Football: Best overall, home and away teams

I've refined the R code to pick the best fantasy soccer team by using more granular player performance data (available publicly). Here are the best overall, home and away teams. The constraints used are: 1) Number of goalkeepers = 12) Nu...

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EPL Fantasy Football: Best overall, home and away teams

January 13, 2011
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EPL Fantasy Football: Best overall, home and away teams

I've refined the R code to pick the best fantasy soccer team by using more granular player performance data (available publicly). Here are the best overall, home and away teams. The constraints used are: 1) Number of goalkeepers = 12) Nu...

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Survival paper (update)

January 13, 2011
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Survival paper (update)

In a recent post, I discussed some  statistical consultancy I was involved with. I was quite proud of the nice ggplot2 graphics I had created. The graphs nicely summarised the main points of the paper: I’ve just had the proofs from the journal, and next to the graphs there is the following note: It is

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gnmplot

January 13, 2011
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gnmplot

I'm writing a new package that will create nice publication quality graphics of genome information. It's really an adaptor sitting between the biomaRt and ggplot2 packages. Here is the code so far: ## this function integrates 3 steps to creating a g...

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prettyR

January 13, 2011
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I have just remembered a package called 'prettyR' that pretty much does what it says. It makes R code more readable.. so an example from my forthcoming genomeplot package (see forthcoming blog entry):   ## this function integrates 3 steps to creat...

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R: An introduction for psychologists

January 13, 2011
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Here are the slides from the Introduction to R session Danny Kaye and I ran at the BPS Mathematics, Statistics & Computing section CPS Workshop (13 December 2010, Nottingham Trent University).

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More climate extremes, or simply global warming ?

January 12, 2011
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More climate extremes, or simply global warming ?

In the paper on the heat wave in Paris (mentioned here) I discussed changes in the distribution of temperature (and autocorrelation of the time series). During the workshop on Statistical Methods for Meteorology and Climate Change today (here) I o...

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R Code for googleVis Demo

January 12, 2011
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R Code for googleVis Demo

# ------------------------------------------------------------------# | PROGRAM NAME: googleVis_R# | DATE: 1/12/11 # | CREATED BY: Matt Bogard# | PROJECT FILE: # |----------------------------------------------------------------# | PURPOSE: ...

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R: Attack of the hair-trigger bees?

January 12, 2011
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R: Attack of the hair-trigger bees?

In their book “Complex Adaptive Systems”, authors Miller and Page create a theoretic model for bee attacks, based on the real, flying, honey-making, photogenic stingers. Suppose the hive is threatened by some external creature. Some initial group of guard bees sense the danger and fly off to attack. As they go, they lay down a

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CosmoPMC released

January 12, 2011
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CosmoPMC released

Martin Kilbinger, an astronomer (cosmologist) with whom we had worked on population Monte Carlo for cosmological inference , has made the PMC C codes available on the CosmoPMC webpage. He has also written a CosmoPMC manual that is now available from arXiv. And he very kindly associated me to

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Initial Work on a Post Not Yet Completed

January 12, 2011
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Initial Work on a Post Not Yet Completed

It’s no secret I have been learning R for some time now, and one of the best resources out there is the hashtag rstats on twitter (#rstats).  There is a tremendous community of active users who are always willing to help, but not to mention, you can get a first hand view of some of

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