mages' blog

Reminder: Next Kölner R User Meeting 6 July 2012

This post is a quick reminder that the next Cologne R user group meeting is only one week away. We will meet on 6 July 2012. The meeting will kick off at 18:00 with three short talks at the Institute of Sociology and will continue, even more informal, from 20:00 in a pub (LUX) nearby.

All details are available on the KölnRUG Meetup site. Please sign up if you would like to come along. Notes from the first Cologne R user group meeting are available here.

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 shortly after Andrew Huxley died, 30th May 2012, aged 94.

In 1952 Hodgkin and Huxley published a series of papers, describing the basic processes underlying the nervous mechanisms of control and the communication between nerve cells, for which they received the Nobel prize in physiology and medicine, together with John Eccles in 1963.

Their research was based on electrophysiological experiments carried out in the late 1940s and early 1950 on a giant squid axon to understand how action potentials in neurons are initiated and propagated.

Dynamical systems in R with simecol

This evening I will talk about Dynamical systems in R with simecol at the LondonR meeting.

Thanks to the work by Thomas Petzoldt, Karsten Rinke, Karline Soetaert and R. Woodrow Setzer it is really straight forward to model and analyse dynamical systems in R with their deSolve and simecol packages.

I will give a brief overview of the functionality using a predator-prey model as an example.

This is of course a repeat of my presentation given at the Köln R user group meeting in March.

For a further example of a dynamical system with simecol see my post about the Hodgkin-Huxley model, which describes the action potential of a giant squid axon.

I shouldn't forget to mention the other talks tonight as well:

• Writing R for Dummies - Andrie De Vries
• News from data.table 1.6, 1.7 and 1.8 - Matthew Dowle
• Converting S Plus Applications into R - Andy Nicholls (postponed to 18 September 2012)
  

For more information about venue and timing see the LondonR web site.

Transforming subsets of data in R with by, ddply and data.table

Transforming data sets with R is usually the starting point of my data analysis work. Here is a scenario which comes up from time to time: transform subsets of a data frame, based on context given in one or a combination of columns.

As an example I use a data set which shows sales figures by product for a number of years:

df <- data.frame(Product=gl(3,10,labels=c("A","B", "C")), 
                 Year=factor(rep(2002:2011,3)), 
                 Sales=1:30)
head(df)
##   Product Year Sales
## 1       A 2002     1
## 2       A 2003     2
## 3       A 2004     3
## 4       A 2005     4
## 5       A 2006     5
## 6       A 2007     6

I am interested in absolute and relative sales developments by product over time. Hence, I would like to add a column to my data frame that shows the sales figures divided by the total sum of sales in each year, so I can create a chart which looks like this:
There are lots of ways of doing this transformation in R. Here are three approaches using:

• base R with by,
• ddply of the plyr package,
• data.table of the package with the same name.

by

The idea here is to use by to split the data for each year and to apply the transform function to each subset to calculate the share of sales for each product with the following function: fn <- function(x) x/sum(x). Having defined the function fn I can apply it in a by statement, and as its output will be a list, I wrap it into a do.call command to row-bind (rbind) the list elements:

R1 <- do.call("rbind", as.list(
  by(df, df["Year"], transform, Share=fn(Sales))
))

head(R1)
##         Product Year Sales      Share
## 2002.1        A 2002     1 0.03030303
## 2002.11       B 2002    11 0.33333333
## 2002.21       C 2002    21 0.63636364
## 2003.2        A 2003     2 0.05555556
## 2003.12       B 2003    12 0.33333333
## 2003.22       C 2003    22 0.61111111

ddply

Hadely's plyr package provides an elegant wrapper for this job with the ddply function. Again I use the transform function with my self defined fn function:

library(plyr)
R2 <- ddply(df, "Year", transform, Share=fn(Sales))

head(R2)
##   Product Year Sales      Share
## 1       A 2002     1 0.03030303
## 2       B 2002    11 0.33333333
## 3       C 2002    21 0.63636364
## 4       A 2003     2 0.05555556
## 5       B 2003    12 0.33333333
## 6       C 2003    22 0.61111111

data.table

With data.table I have to do a little bit more legwork, in particular I have to think about the indices I need to use. Yet, it is still straight forward:

library(data.table)
## Convert df into a data.table
dt <- data.table(df) 
## Set Year as a key
setkey(dt, "Year") 
## Calculate the sum of sales per year(=key(dt))
X <- dt[, list(SUM=sum(Sales)), by=key(dt)] 
## Join X and dt, both have the same key and
## add the share of sales as an additional column
R3 <- dt[X, list(Sales, Product, Share=Sales/SUM)]

head(R3)
##      Year Sales Product      Share
## [1,] 2002     1       A 0.03030303
## [2,] 2002    11       B 0.33333333
## [3,] 2002    21       C 0.63636364
## [4,] 2003     2       A 0.05555556
## [5,] 2003    12       B 0.33333333
## [6,] 2003    22       C 0.61111111

Although data.table may look cumbersome compared to ddply and by, I will show below that it is actually a lot faster than the two other approaches.

Plotting the results

With any of the three outputs I can create the chart from above with latticeExtra:

library(latticeExtra)
asTheEconomist(
 xyplot(Sales + Share ~ Year, groups=Product, 
  data=R3, t="b", 
  scales=list(relation="free",x=list(rot=45)), 
  auto.key=list(space="top", column=3),
  main="Product information")
)

Comparing performance of by, ddply and data.table

Let me move on to a more real life example with 100 companies, each with 20 products and a 10 year history:

set.seed(1)
df <- data.frame(Company=rep(paste("Company", 1:100),200),
                 Product=gl(20,100,labels=LETTERS[1:20]), 
                 Year=sort(rep(2002:2011,2000)), 
                 Sales=rnorm(20000, 100,10))

I use the same three approaches to calculate the share of sales by product for each year and company, but this time I will measure the execution time on my old iBook G4, running R-2.15.0:

r1 <- system.time(
 R1 <- do.call("rbind", as.list(
   by(df, df[c("Year", "Company")], 
      transform, Share=fn(Sales))
 ))
)

r2 <- system.time(
 R2 <- ddply(df, c("Company", "Year"), 
             transform, Share=fn(Sales))
)

r3 <- system.time({
 dt <- data.table(df)
 setkey(dt, "Year", "Company")
 X <- dt[, list(SUM=sum(Sales)), by=key(dt)]
 R3 <- dt[X, list(Company, Sales, Product, Share=Sales/SUM)]
})

And here are the results:

r1 # by
##  user  system elapsed 
## 13.690   4.178  42.118 
r2 # ddply 
##  user  system elapsed 
## 18.215   6.873  53.061
r3 # data.table 
##  user  system elapsed 
## 0.171   0.036   0.442

It is quite astonishing to see the speed of data.table in comparison to by and ddply, but maybe it shouldn't be surprise that the elegance of ddply comes with a price as well.

Addition (13 June 2012): See also Matt's comments below. I completely missed ave from base R, which is rather simple and quick as well. Additionally his link to a stackoverflow discussion provides further examples and benchmarks.

Finally my session info:

> sessionInfo() # iBook G4 800 MHZ, 640 MB RAM
R version 2.15.0 Patched (2012-06-03 r59505)
Platform: powerpc-apple-darwin8.11.0 (32-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] latticeExtra_0.6-19 lattice_0.20-6      RColorBrewer_1.0-5 
[4] data.table_1.8.0    plyr_1.7.1         

loaded via a namespace (and not attached):
[1] grid_2.15.0

UK house prices visualised with googleVis-0.2.16

A new version of googleVis has been released on CRAN and the project site. Version 0.2.16 adds the functionality to plot quarterly and monthly data as a motion chart.

To illustrate the new feature I looked for a quarterly data set and stumbled across the quarterly UK house price data published by Nationwide, a building society. The data is available in a spread sheet format and presents the average house prices and indexed to 100 in Q1 1993 by region in the UK from Q4 1973 to Q1 2012. Unfortunately the data is formated for human eyes rather than for computers, see the screen shot below.

Screen shot of Nationwide's UK house price data in Excel

Never-mind, the XLConnect package by Mirai Solutions does a fabulous job in reading Excel files into R. An advantage of XLConnect, compared to other packages, is that it also works on a Mac, although I had to install the package from source (install.packages("XLConnect", type="source")).