OUseful.Info, the blog…

Trying to find useful things to do with emerging technologies in open education

Posts Tagged ‘R

Using One Programming Language In the Context of Another – Python and R

Over the last couple of years, I’ve settled into using R an python as my languages of choice for doing stuff:

  • R, because RStudio is a nice environment, I can blend code and text using R markdown and knitr, ggplot2 and Rcharts make generating graphics easy, and reshapers such as plyr make wrangling with data realtvely easy(?!) once you get into the swing of it… (though sometimes OpenRefine can be easier…;-)
  • python, because it’s an all round general purpose thing with lots of handy libraries, good for scraping, and a joy to work with in iPython notebook…

Sometimes, however, you know – or remember – how to do one thing in one language that you’re not sure how to do in another. Or you find a library that is just right for the task hand but it’s in the other language to the one in which you’re working, and routing the data out and back again can be a pain.

How handy it would be if you could make use of one language in the context of another? Well, it seems as if we can (note: I haven’t tried any of these recipes yet…):

Using R inside Python Programs

Whilst python has a range of plotting tools available for it, such as matplotlib, I haven’t found anything quite as a expressive as R’s ggplot2 (there is a python port of ggplot underway but it’s still early days and the syntax, as well as the functionality, is still far from complete as compared to the original [though not a far as it was given the recent update;-)] ). So how handy would it be to be able to throw a pandas data frame, for example, into an R data frame and then use ggplot to render a graphic?

The Rpy and Rpy2 libraries support exactly that, allowing you to run R code within a python programme. For an example, see this Example of using ggplot2 from IPython notebook.

There also seems to be some magic help for running R in iPython notebooks and some experimental integrational work going on in pandas: pandas: rpy2 / R interface.

(See also: ggplot2 in Python: A major barrier broken.)

Using python Inside R

Whilst one of the things I often want to do in python is plot R style ggplots, one of the hurdles I often encounter in R is getting data in in the first place. For example, the data may come from a third party source that needs screenscraping, or via a web API that has a python wrapper but not an R one. Python is my preferred tool for writing scrapers, so is there a quick way I can add a python data grabber into my R context? It seems as if there is: rPython, though the way code is included looks rather clunky and WIndows support appears to be moot. What would be nice would be for RStudio to include some magic, or be able to support python based chunks…

(See also: Calling Python from R with rPython.)

(Note: I’m currently working on the production of an Open University course on data management and use, and I can imagine the upset about overcomplicating matters if I mooted this sort of blended approach in the course materials. But this is exactly the sort of pragmatic use that technologists use code for – as a tool that comes to hand and that can be used quickly and relatively efficiently in concert with other tools, at least when you’re working in a problem solving (rather than production) mode.)

Written by Tony Hirst

January 22, 2014 at 12:11 pm

Posted in Infoskills, Rstats

Tagged with , , ,

Over on F1DataJunkie, 2011 Season Review Doodles…

Things have been a little quiet, post wise here, of late, in part because of the holiday season… but I have been posting notes on a couple of charts in progress over on the F1DataJunkie blog. Here are links to the posts in chronological order – they capture the evolution of the chart design(s) to date:

You can find a copy of the data I used to create the charts here: F1 2011 Year in Review spreadsheet.

I used R to generate the charts (scripts are provided and/or linked to from the posts, or included in the comments – I’ll tidy them and pop them into a proper Github repository if/when I get a chance), loading the data in to RStudio using this sort of call:

require(RCurl)

gsqAPI = function(key,query,gid=0){ return( read.csv( paste( sep="",'http://spreadsheets.google.com/tq?', 'tqx=out:csv','&tq=', curlEscape(query), '&key=', key, '&gid=', curlEscape(gid) ), na.strings = "null" ) ) }

key='0AmbQbL4Lrd61dEd0S1FqN2tDbTlnX0o4STFkNkc0NGc'
sheet=4

qualiResults2011=gsqAPI(key,'select *',sheet)

If any other folk out there are interested in using R to wrangle with F1 data, either from 2011 or looking forward to 2012, let me know and maybe we could get a script collection going on Github:-)

Written by Tony Hirst

December 30, 2011 at 3:59 pm

Posted in Data, digital storytelling, Rstats

Tagged with ,

Power Tools for Aspiring Data Journalists: Funnel Plots in R

Picking up on Paul Bradshaw’s post A quick exercise for aspiring data journalists which hints at how you can use Google Spreadsheets to grab – and explore – a mortality dataset highlighted by Ben Goldacre in DIY statistical analysis: experience the thrill of touching real data, I thought I’d describe a quick way of analysing the data using R, a very powerful statistical programming environment that should probably be part of your toolkit if you ever want to get round to doing some serious stats, and have a go at reproducing the analysis using a bit of judicious websearching and some cut-and-paste action…

R is an open-source, cross-platform environment that allows you to do programming like things with stats, as well as producing a wide range of graphical statistics (stats visualisations) as if by magic. (Which is to say, it can be terrifying to try to get your head round… but once you’ve grasped a few key concepts, it becomes a really powerful tool… At least, that’s what I’m hoping as I struggle to learn how to use it myself!)

I’ve been using R-Studio to work with R, a) because it’s free and works cross-platform, b) it can be run as a service and accessed via the web (though I haven’t tried that yet; the hosted option still hasn’t appeared yet, either…), and c) it offers a structured environment for managing R projects.

So, to get started. Paul describes a dataset posted as an HTML table by Ben Goldacre that is used to generate the dots on this graph:

The lines come from a probabilistic model that helps us see the likely spread of death rates given a particular population size.

If we want to do stats on the data, then we could, as Paul suggests, pull the data into a spreadsheet and then work from there… Or, we could pull it directly into R, at which point all manner of voodoo stats capabilities become available to us.

As with the =importHTML formula in Google spreadsheets, R has a way of scraping data from an HTML table anywhere on the public web:

#First, we need to load in the XML library that contains the scraper function
library(XML)
#Scrape the table
cancerdata=data.frame( readHTMLTable( 'http://www.guardian.co.uk/commentisfree/2011/oct/28/bad-science-diy-data-analysis', which=1, header=c('Area','Rate','Population','Number')))

The format is simple: readHTMLTable(url,which=TABLENUMBER) (TABLENUMBER is used to extract the N’th table in the page.) The header part labels the columns (the data pulled in from the HTML table itself contains all sorts of clutter).

We can inspect the data we’ve imported as follows:

#Look at the whole table
cancerdata
#Look at the column headers
names(cancerdata)
#Look at the first 10 rows
head(cancerdata)
#Look at the last 10 rows
tail(cancerdata)
#What sort of datatype is in the Number column?
class(cancerdata$Number)

The last line – class(cancerdata$Number) – identifies the data as type ‘factor’. In order to do stats and plot graphs, we need the Number, Rate and Population columns to contain actual numbers… (Factors organise data according to categories; when the table is loaded in, the data is loaded in as strings of characters; rather than seeing each number as a number, it’s identified as a category.)

#Convert the numerical columns to a numeric datatype
cancerdata$Rate=as.numeric(levels(cancerdata$Rate)[as.integer(cancerdata$Rate)])
cancerdata$Population=as.numeric(levels(cancerdata$Population)[as.integer(cancerdata$Population)])
cancerdata$Number=as.numeric(levels(cancerdata$Number)[as.integer(cancerdata$Number)])

#Just check it worked…
class(cancerdata$Number)
head(cancerdata)

We can now plot the data:

#Plot the Number of deaths by the Population
plot(Number ~ Population,data=cancerdata)

If we want to, we can add a title:
#Add a title to the plot
plot(Number ~ Population,data=cancerdata, main='Bowel Cancer Occurrence by Population')

We can also tweak the axis labels:

plot(Number ~ Population,data=cancerdata, main='Bowel Cancer Occurrence by Population',ylab='Number of deaths')

The plot command is great for generating quick charts. If we want a bit more control over the charts we produce, the ggplot2 library is the way to go. (ggpplot2 isn’t part of the standard R bundle, so you’ll need to install the package yourself if you haven’t already installed it. In RStudio, find the Packages tab, click Install Packages, search for ggplot2 and then install it, along with its dependencies…):

require(ggplot2)
ggplot(cancerdata)+geom_point(aes(x=Population,y=Number))+opts(title='Bowel Cancer Data')+ylab('Number of Deaths')

Doing a bit of searching for the “funnel plot” chart type used to display the ata in Goldacre’s article, I came across a post on Cross Validated, the Stack Overflow/Statck Exchange site dedicated to statistics related Q&A: How to draw funnel plot using ggplot2 in R?

The meta-analysis answer seemed to produce the similar chart type, so I had a go at cribbing the code… This is a dangerous thing to do, and I can’t guarantee that the analysis is the same type of analysis as the one Goldacre refers to… but what I’m trying to do is show (quickly) that R provides a very powerful stats analysis environment and could probably do the sort of analysis you want in the hands of someone who knows how to drive it, and also knows what stats methods can be appropriately applied for any given data set…

Anyway – here’s something resembling the Goldacre plot, using the cribbed code which has confidence limits at the 95% and 99.9% levels. Note that I needed to do a couple of things:

1) work out what values to use where! I did this by looking at the ggplot code to see what was plotted. p was on the y-axis and should be used to present the death rate. The data provides this as a rate per 100,000, so we need to divide by 100, 000 to make it a rate in the range 0..1. The x-axis is the population.

#TH: funnel plot code from:
#TH: http://stats.stackexchange.com/questions/5195/how-to-draw-funnel-plot-using-ggplot2-in-r/5210#5210
#TH: Use our cancerdata
number=cancerdata$Population
#TH: The rate is given as a 'per 100,000' value, so normalise it
p=cancerdata$Rate/100000

p.se <- sqrt((p*(1-p)) / (number))
df <- data.frame(p, number, p.se)

## common effect (fixed effect model)
p.fem <- weighted.mean(p, 1/p.se^2)

## lower and upper limits for 95% and 99.9% CI, based on FEM estimator
#TH: I'm going to alter the spacing of the samples used to generate the curves
number.seq <- seq(1000, max(number), 1000)
number.ll95 <- p.fem - 1.96 * sqrt((p.fem*(1-p.fem)) / (number.seq))
number.ul95 <- p.fem + 1.96 * sqrt((p.fem*(1-p.fem)) / (number.seq))
number.ll999 <- p.fem - 3.29 * sqrt((p.fem*(1-p.fem)) / (number.seq))
number.ul999 <- p.fem + 3.29 * sqrt((p.fem*(1-p.fem)) / (number.seq))
dfCI <- data.frame(number.ll95, number.ul95, number.ll999, number.ul999, number.seq, p.fem)

## draw plot
#TH: note that we need to tweak the limits of the y-axis
fp <- ggplot(aes(x = number, y = p), data = df) +
geom_point(shape = 1) +
geom_line(aes(x = number.seq, y = number.ll95), data = dfCI) +
geom_line(aes(x = number.seq, y = number.ul95), data = dfCI) +
geom_line(aes(x = number.seq, y = number.ll999, linetype = 2), data = dfCI) +
geom_line(aes(x = number.seq, y = number.ul999, linetype = 2), data = dfCI) +
geom_hline(aes(yintercept = p.fem), data = dfCI) +
scale_y_continuous(limits = c(0,0.0004)) +
xlab("number") + ylab("p") + theme_bw()

fp

As I said above, it can be quite dangerous just pinching other folks’ stats code if you aren’t a statistician and don’t really know whether you have actually replicated someone else’s analysis or done something completely different… (this is a situation I often find myself in!); which is why I think we need to encourage folk who release statistical reports to not only release their data, but also show their working, including the code they used to generate any summary tables or charts that appear in those reports.

In addition, it’s worth noting that cribbing other folk’s code and analyses and applying it to your own data may lead to a nonsense result because some stats analyses only work if the data has the right sort of distribution…So be aware of that, always post your own working somewhere, and if someone then points out that it’s nonsense, you’ll hopefully be able to learn from it…

Given those caveats, what I hope to have done is raise awareness of what R can be used to do (including pulling data into a stats computing environment via an HTML table screenscrape) and also produced some sort of recipe we could take to a statistician to say: is this the sort of thing Ben Goldacre was talking about? And if not, why not?

[If I've made any huge - or even minor - blunders in the above, please let me know... There's always a risk in cutting and pasting things that look like they produce the sort of thing you're interested in, but may actually be doing something completely different!]

PS for how to generate reports that can (optionally) also self-document with actually source R code, see How might data journalists show their working? Sweave. The code used in, and comments added to, that post make further refinements to the funnel plot code.

PPS see also this R code for generating funnel plots

Written by Tony Hirst

October 31, 2011 at 1:32 pm

Google Spreadsheets API: Listing Individual Spreadsheet Sheets in R

In Using Google Spreadsheets as a Database Source for R, I described a simple Google function for pulling data into R from a Google Visualization/Chart tools API query language query applied to a Google spreadsheet, given the spreadsheet key and worksheet ID. But how do you get a list of sheets in spreadsheet, without opening up the spreadsheet and finding the sheet names or IDs directly? [Update: I'm not sure the query language API call lets you reference a sheet by name...]

The Google Spreadsheets API, that’s how… (see also GData Samples. The documentation appears to be all over the place…)

To look up the sheets associated with a spreadsheet identified by its key value KEY, construct a URL of the form:

http://spreadsheets.google.com/feeds/worksheets/KEY/public/basic

This should give you an XML output. To get the output as a JSON feed, append ?alt=json to the end of the URL.

Having constructed the URL for sheets listing for a spreadsheet with a given key identifier, we can pull in and parse either the XML version, or the JSON version, into R and identify all the different sheets contained within the spreadsheet document as a whole.

First, the JSON version. I use the RJSONIO library to handle the feed:

library(RJSONIO)
sskey='0AmbQbL4Lrd61dDBfNEFqX1BGVDk0Mm1MNXFRUnBLNXc'
ssURL=paste( sep="", 'http://spreadsheets.google.com/feeds/worksheets/', sskey, '/public/basic?alt=json' )
spreadsheet=fromJSON(ssURL)
sheets=c()
for (el in spreadsheet$feed$entry) sheets=c(sheets,el$title['$t'])
as.data.frame(sheets)

Using a variant of the function described in the previous post, we can look up the data contained in a sheet by the sheet ID (I’m not sure you can look it up by name….?) - I’m not convinced that the row number is a reliable indicator of sheet ID, especially if you’ve deleted or reordered sheets. It may be that you do actually need to go to the spreadsheet to look up the sheet number for the gid, which actually defeats a large part of the purpose behind this hack?:-(

library(RCurl)
gsqAPI = function( key, query,gid=0){ return( read.csv( paste( sep="", 'http://spreadsheets.google.com/tq?', 'tqx=out:csv', '&tq=', curlEscape(query), '&key=', key, '&gid=', curlEscape(gid) ) ) ) }
gsqAPI(sskey,"select * limit 10", 9)

getting a list of sheet names from a goog spreadsheet into R

The second approach is to pull on the XML version of the sheet data feed. (This PDF tutorial got me a certain way along the road: Extracting Data from XML, but then I got confused about what to do next (I still don’t have a good feel for identifying or wrangling with R data structures, though at least I now know how to use the class() function to find out what R things the type of any given item is;-) and had to call on the lazy web to work out how to do this in the end!)

library(XML)
ssURL=paste( sep="", 'http://spreadsheets.google.com/feeds/worksheets/', ssKey, '/public/basic' )
ssd=xmlTreeParse( ssURL, useInternal=TRUE )
nodes=getNodeSet( ssd, "//x:entry", "x" )
titles=sapply( nodes, function(x) xmlSApply( x, xmlValue ) )
library(stringr)
data.frame( sheetName = titles['content',], sheetId = str_sub(titles['id',], -3, -1 ) )

data frame in r

In this example, we also pull out the sheet ID that is used by the Google spreadsheets API to access individual sheets, just in case. (Note that these IDs are not the same as the numeric gid values used in the chart API query language…)

PS Note: my version of R seemed to choke if I gave it https: headed URLs, but it was fine with http:

Written by Tony Hirst

September 7, 2011 at 1:09 pm

Using Google Spreadsheets as a Database Source for R

I couldn’t contain myself (other more pressing things to do, but…), so I just took a quick time out and a coffee to put together a quick and dirty R function that will let me run queries over Google spreadsheet data sources and essentially treat them as database tables (e.g. Using Google Spreadsheets as a Database with the Google Visualisation API Query Language).

Here’s the original function I used:

library(RCurl)
gsqAPI = function(key,query,gid=0){ return( read.csv( paste( sep="",'http://spreadsheets.google.com/tq?', 'tqx=out:csv','&tq=', curlEscape(query), '&key=', key, '&gid=', gid) ) ) }

However, with a move to https, this function kept breaking. The one I currently use is:

library(RCurl)
gsqAPI = function(key,query,gid=0){ 
  tmp=getURL( paste( sep="",'https://spreadsheets.google.com/tq?', 'tqx=out:csv','&tq=', curlEscape(query), '&key=', key, '&gid=', gid), ssl.verifypeer = FALSE )
  return( read.csv( textConnection( tmp ) ) )
}

It requires the spreadsheet key value and a query; you can optionally provide a sheet number within the spreadsheet if the sheet you want to query is not the first one.

We can call the function as follows:

gsqAPI('tPfI0kerLllVLcQw7-P1FcQ','select * limit 3')

In that example, and by default, we run the query against the first sheet in the spreadsheet.

Alternatively, we can make a call like this, and run a query against sheet 3, for example:
tmpData=gsqAPI('0AmbQbL4Lrd61dDBfNEFqX1BGVDk0Mm1MNXFRUnBLNXc','select A,C where <= 10',3)
tmpData

My first R function

The real question is, of course, could it be useful.. (or even OUseful?!)?

Here’s another example: a way of querying the Guardian Datastore list of spreadsheets:

gsqAPI('0AonYZs4MzlZbdFdJWGRKYnhvWlB4S25OVmZhN0Y3WHc','select * where A contains "crime" and B contains "href" order by C desc limit 10')

What that call does is run a query against the Guardian Datastore spreadsheet that lists all the other Guardian Datastore spreadsheets, and pulls out references to spreadsheets relating to “crime”.

The returned data is a bit messy and requires parsing to be properly useful.. but I haven’t started looking at string manipulation in R yet…(So my question is: given a dataframe with a column containing things like <a href=”http://example.com/whatever”>Some Page</a>, how would I extract columns containing http://example.com/whatever or Some Page fields?)

[UPDATE: as well as indexing a sheet by sheet number, you can index it by sheet name, but you'll probably need to tweak the function to look end with '&gid=', curlEscape(gid) so that things like spaces in the sheet name get handled properly I'm not sure about this now.. calling sheet by name works when accessing the "normal" Google spreadsheets application, but I'm not sure it does for the chart query language call??? ]

[If you haven't yet discovered R, it's an environment that was developed for doing stats... I use the RStudio environment to play with it. The more I use it (and I've only just started exploring what it can do), the more I think it provides a very powerful environment for working with data in quite a tangible way, not least for reshaping it and visualising it, let alone doing stats with in. (In fact, don't use the stats bit if you don't want to; it provides more than enough data mechanic tools to be going on with;-)]

PS By the by, I’m syndicating my Rstats tagged posts through the R-Bloggers site. If you’re at all interested in seeing what’s possible with R, I recommend you subscribe to R-Bloggers, or at least have a quick skim through some of the posts on there…

PPS The RSpatialTips post Accessing Google Spreadsheets from R has a couple of really handy tips for tidying up data pulled in from Google Spreadsheets; assuming the spreadsheetdata has been loaded into ssdata: a) tidy up column names using colnames(ssdata) <- c("my.Col.Name1","my.Col.Name2",...,"my.Col.NameN"); b) If a column returns numbers as non-numeric data (eg as a string "1,000") in cols 3 to 5, convert it to a numeric using something like: for (i in 3:5) ssdata[,i] <- as.numeric(gsub(",","",ssdata[,i])) [The last column can be identifed as ncol(ssdata) You can do a more aggessive conversion to numbers (assuming no decimal points) using gsub("[^0-9]","",ssdata[,i])]

PPPS via Revolutions blog, how to read the https file into R (unchecked):

require(RCurl)
myCsv = getURL(httpsCSVurl)
read.csv(textConnection(myCsv))

Written by Tony Hirst

September 2, 2011 at 12:52 pm

The Visual Difference – R and Anscombe’s Quartet

I spent a chunk of today trying to get my thoughts in order for a keynote presentation at next week’s The Difference that Makes a Difference conference. The theme of my talk will be on how visualisations can be used to discover structure and pattern in data, and as in many or my other recent talks I found the idea of Anscombe’s quartet once again providing a quick way in to the idea that sometimes the visual dimension can reveal a story that simple numerical analysis appears to deny.

For those of you who haven’t come across Anscombe’s quartet yet, it’s a set of four simple 2 dimensional data sets (each 11 rows long) that have similar statistical properties, but different stories to tell…

Quite by chance, I also happened upon a short exercise based on using R to calculate some statistical properties of the quartet (More useless statistics), so I thought I’d try and flail around in my unprincipled hack-it-and-see approach to learning R to see if I could do something similar with rather simpler primitives than described in that blog post.

(If you’re new to R and want to play along, I recommend RStudio…)

Here’s the original data set – you can see it in R simply by typing anscombe:

   x1 x2 x3 x4    y1   y2    y3    y4
1  10 10 10  8  8.04 9.14  7.46  6.58
2   8  8  8  8  6.95 8.14  6.77  5.76
3  13 13 13  8  7.58 8.74 12.74  7.71
4   9  9  9  8  8.81 8.77  7.11  8.84
5  11 11 11  8  8.33 9.26  7.81  8.47
6  14 14 14  8  9.96 8.10  8.84  7.04
7   6  6  6  8  7.24 6.13  6.08  5.25
8   4  4  4 19  4.26 3.10  5.39 12.50
9  12 12 12  8 10.84 9.13  8.15  5.56
10  7  7  7  8  4.82 7.26  6.42  7.91
11  5  5  5  8  5.68 4.74  5.73  6.89

We can construct a simple data frame containing just the values of x1 and y1 with a construction of the form: data.frame(x=c(anscombe$x1),y=c(anscombe$y1)) (where we identify the columns explicitly by column name) or alternatively data.frame(x=c(anscombe[1]),y=c(anscombe[5])) (where we refer to them by column index number).

x y
1 10 8.04
2 8 6.95
3 13 7.58
4 9 8.81
5 11 8.33
6 14 9.96
7 6 7.24
8 4 4.26
9 12 10.84
10 7 4.82
11 5 5.68

A tidier way of writing this is as follows:
with(anscombe,data.frame(x1Val=c(x1),y1Val=c(y1)))

In order to call on, or refer to, the data frame, we assign it to a variable: g1data=with(anscombe,data.frame(xVal=c(x1),yVal=c(y1)))

We can then inspect the mean and sd values: mean(g1data$xVal), or sd(g1data$yVal)

> mean(g1data$xVal)
[1] 9
> sd(g1data$xVal)
[1] 3.316625
>

To plot the data, we can simply issue a plot command: plot(g1data)

R- getting started with anscombe's quartet

It would be possible to create similar datasets for each of the separate groups of data, but R has all sorts of tricks for working with data (apparently…?!;-) There are probably much better ways of getting hold of the statistics in a more direct way, but here’s the approach I took. Firstly, we need to reshape the data a little. I cribbed the “useless stats” approach for most of this. The aim is to produce a data set with 44 rows, and 3 columns: x, y and a column that identifies the group of results (let’s call them myX, myY and myGroup for clarity). The myGroup values will range from 1 to 4, identifying each of the four datasets in turn (so the first 11 rows will be for x1, y1 and will have myGroup value 1; then the values for x2, y2 and myGroup equal to 2, and so on). That is, we want a dataset that starts:

1 10 9.14 1
2 8 8.14 1

and ends:

43 8 7.91 4
44 8 6.89 4

To begin with, we need some helper routines:

- how many rows are there in the data set? nrow(anscombe)
– how do we create a set of values to label the rows by group number (i.e. how do we generate a set of 11 1’s, then 11 2’s, 11 3’s and 11 4’s)? Here’s how: gl(4, nrow(anscombe)) [typing ?gl in R should bring up the appropriate help page;-) What we do is construct a list of 4 values, with each value repeating nrow(anscombe) times]
– to add in a myGroup column to a dataframe containing x1 and y1 columns, set with just values 1, we simply insert an additional column definition: data.frame(xVal=c(anscombe$x1), yVal=c(anscombe$y1), mygroup=gl(1,nrow(anscombe)))
– to generate a data frame containing three columns and the data for group 1, followed by group 2, we would use a construction of the form: data.frame(xVal=c(anscombe$x1,anscombe$x2), yVal=c(anscombe$y1,anscombe$y2), mygroup=gl(2,nrow(anscombe))). That is, populate the xVal column with rows from x1 in the anscombe dataset, then the rows from column x2; populate yVal with values from y1 then y2; and populate myGroup with 11 1’s followed by 11 2’s.
– a more compact way of constructing the data frame is to specify that we want to concatenate (c()) values from several columns from the same dataset: with(anscombe,data.frame(xVal=c(x1,x2,x3,x4), yVal=c(y1,y2,y3,y4), mygroup=gl(4,nrow(anscombe))))
– to be able to reference this dataset, we need to assign it to a variable: mydata=with(anscombe,data.frame(xVal=c(x1,x2,x3,x4), yVal=c(y1,y2,y3,y4), mygroup=gl(4,nrow(anscombe))))

This final command will give us a data frame with the 3 columns, as required, containing values from group 1, then group 2, then groups 3 and 4, all labelled appropriately.

To find the means for each column by group, we can use the aggregate command: aggregate(.~mygroup,data=mydata,mean)

(I think you read that as follows:”aggregate the current data (.) by each of the groups in (~) mygroup using the mydata dataset, reporting on the groupwise application of the function: mean)

To find the SD values: aggregate(.~mygroup,data=mydata,sd)

R-playing with anscombe

Cribbing an approach I discovered from the hosted version of the ggplot R graphics library, here’s a way of plotting the data for each of the four groups from within the single aggregate dataset. (If you are new to R, you will need to download and install the ggplot2 package; in RStudio, from the Packages menu, select Install Packages and enter ggplot2 to download and install the package. To load the package into your current R session, tick the box next to the installed package name or enter the command library("ggplot2").)

The single command to plot xy scatterplots for each of the four groups in the combined 3 column dataset is as follows:

ggplot(mydata,aes(x=xVal,y=yVal,group=mygroup))+geom_point()+facet_wrap(~mygroup)

And here’s the result (remember, the statistical properties were the same…)

R - anscombe's quartet

To recap the R commands:

mydata=with(anscombe,data.frame(xVal=c(x1,x2,x3,x4), yVal=c(y1,y2,y3,y4), group=gl(4,nrow(anscombe))))
aggregate(.~mygroup,data=mydata,mean)
aggregate(.~mygroup,data=mydata,sd)
library(ggplot2)
ggplot(mydata,aes(x=xVal, y=yVal)) + geom_point() + facet_wrap(~mygroup)

PS this looks exciting from an educational and opendata perspective, though I haven’t had a chance to play with it: OpenCPU: a server where you can upload and run R functions. (The other hosted R solutions I was aware of – R-Node – doesn’t seem to be working any more? online R-Server [broken?]. For completeness, here’s the link to the hosted ggplot IDE referred to in the post. And finally – if you need to crucnh big files, CloudNumbers may be appropriate (disclaimer: I haven’t tried it))

PPS And here’s something else for the data junkies – an easy way of getting data into R from Datamarket.com: How to access 100M time series in R in under 60 seconds.

Written by Tony Hirst

August 30, 2011 at 9:24 pm

Posted in Anything you want, Rstats, Tinkering, Uncourse

Tagged with

Creating Simple Interactive Visualisations in R-Studio: Subsetting Data

Watching a fascinating Google Tech Talk by Hadley Wickham on The Future of Interactive Graphics in R – A Joint Visualization and UseR Meetup, I was reminded of the manipulate command provided in R-Studio that lets you create slider and dropdown widgets that in turn let you dynamically interact with R based visualisations, for example by setting data ranges or subsetting data.

Here are a couple of quick examples, one using the native plot command, the other using ggplot. In each case, I’m generating an interactive visualisation that lets me display as a line chart two user selected data series from a larger data set.

manipulate UI builder in RStudio

[Data file used in this example]

Here’s a crude first attempt using plot:

hun_2011comprehensiveLapTimes <- read.csv("~/code/f1/generatedFiles/hun_2011comprehensiveLapTimes.csv")
View(hun_2011comprehensiveLapTimes)

library("manipulate")
h=un_2011comprehensiveLapTimes

manipulate(
plot(lapTime~lap,data=subset(h,car==cn1),type='l',col=car) +
lines(lapTime~lap,data=subset(h,car==cn2 ),col=car),
cn1=slider(1,25),cn2=slider(1,25)
)

This has the form manipulate(command1+command2, uiVar=slider(min,max)), so we see for example two R commands to plot the two separate lines, each of them filtered on a value set by the correpsonding slider variable.

Note that we plot the first line using plot, and the second line using lines.

The second approach uses ggplot within the manipulate context:

manipulate(
ggplot(subset(h,h$car==Car_1|car==Car_2)) +
geom_line(aes(y=lapTime,x=lap,group=car,col=car)) +
scale_colour_gradient(breaks=c(Car_1,Car_2),labels=c(Car_1,Car_2)),
Car_1=slider(1,25),Car_2=slider(1,25)
)

In this case, rather than explicitly adding additional line layers, we use the group setting to force the display of lines by group value. The initial ggplot command sets the context, and filters the complete set of timing data down to the timing data associated with at most two cars.

We can add a title to the plot using:

manipulate(
ggplot(subset(h,h$car==Car_1|car==Car_2)) +
geom_line(aes(y=lapTime,x=lap,group=car,col=car)) +
scale_colour_gradient(breaks=c(Car_1,Car_2),labels=c(Car_1,Car_2)) +
opts(title=paste("F1 2011 Hungary: Laptimes for car",Car_1,'and car',Car_2)),
Car_1=slider(1,25),Car_2=slider(1,25)
)

My reading of the manipulate function is that if you make a change to one of the interactive components, the variable values are captured and then passed to the R command sequences, which then executes as normal. (I may be wrong in this assumption of course!) Which is to say: if you write a series of chained R commands, and can abstract out one or more variable values to the start of the sequence, then you can create corresponding interactive UI controls to set those variable values by placing the command series with the manipulate() context.

Written by Tony Hirst

August 5, 2011 at 1:05 pm

Posted in Anything you want

Tagged with , , , , ,

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