Tag Archives: data

Inter-Council Payments and the Google Fusion Tables Network Graph

One of the great things about aggregating local spending data from different councils in the same place – such as on OpenlyLocal – is that you can start to explore structural relations in the way different public bodies of a similar type spend money with each other.

On the local spend with corporates scraper on Scraperwiki, which I set up to scrape how different councils spent money with particular suppliers, I realised I could also use the scraper to search for how councils spent money with other councils, by searching for suppliers containing phrases such as “district council” or “town council”. (We could also generate views to to see how councils wre spending money with different police authorities, for example.)

(The OpenlyLocal API doesn’t seem to work with the search, so I scraped the search results HTML pages instead. Results are paged, with 30 results per page, and what seems like a maximum of 1500 (50 pages) of results possible.)

The publicmesh table on the scraper captures spend going to a range of councils (not parish councils) from other councils. I also uploaded the data to Google Fusion tables (public mesh spending data), and then started to explore it using the new network graph view (via the Experiment menu). So for example, we can get a quick view over how the various county councils make payments to each other:

Hovering over a node highlights the other nodes its connected to (though it would be good if the text labels from the connected nodes were highlighted and labels for unconnected nodes were greyed out?)

(I think a Graphviz visualisation would actually be better, eg using Canviz, because it can clearly show edges from A to B as well as B to A…)

As with many exploratory visualisations, this view helps us identify some more specific questions we might want to ask of the data, rather than presenting a “finished product”.

As well as the experimental network graph view, I also noticed there’s a new Experimental View for Google Fusion Tables. As well as the normal tabular view, we also get a record view, and (where geo data is identified?) a map view:

What I’d quite like to see is a merging of map and network graph views…

One thing I noticed whilst playing with Google Fusion Tables is that getting different aggregate views is rather clunky and relies on column order in the table. So for example, here’s an aggregated view of how different county councils supply other councils:

In order to aggregate by supplied council, we need to reorder the columns (the aggregate view aggregates columns as thet appear from left to right in the table view). From the Edit column, Modify Table:

(In my browser, I then had to reload the page for the updated schema to be reflected in the view). Then we can get the count aggregation:

It would be so much easier if the aggregation view allowed you to order the columns there…

PS no time to blog this properly right now, but there are a couple of new javascript libraries that are worth mentioning in the datawrangling context.

In part coming out of the Guardian stable, Misoproject is “an open source toolkit designed to expedite the creation of high-quality interactive storytelling and data visualisation content”. The initial dataset library provides a set of routines for: loading data into the browser from a variety of sources (CSV, Google spreadsheets, JSON), including regular polling; creating and managing data tables and views of those tables within the browser, including column operations such as grouping, statistical operations (min, max, mean, moving average etc); playing nicely with a variety of client side graphics libraries (eg d3.js, Highcharts, Rickshaw and other JQuery graphics plugins).

Recline.js is a library from Max Ogden and the Open Knowledge Foundation that if its name is anything to go by is positioning itself as an alternative (or complement?) to Google Refine. To my mind though, it’s more akin to a Google Fusion Tables style user interface (“classic” version) wherever you need it, via a Javascript library. The data explorer allows you to import and preview CSV, Excel, Google Spreadsheet and ElasticSearch data from a URL, as well as via file upload (so for example, you can try it with the public spend mesh data CSV from Scraperwiki). Data can be sorted, filtered and viewed by facet, and there’s a set of integrated graphical tools for previewing and displaying data too. Refine.js views can also be shared and embedded, which makes this an ideal tool for data publishers to embed in their sites as a way of facilitating engagement with data on-site, as I expect we’ll see on the Data Hub before too long.

More reviews of these two libraries later…

PPS These are also worth a look in respect of generating visualisations based on data stored in Google spreadsheets: DataWrapper and Freedive (like my old Guardian Datastore explorer, but done properly… Wizard led UI that helps you create your own searchable and embeddable database view direct from a Google Spreadsheet).

Working With Excel Spreadsheet Files Without Using Excel…

One of the most frequently encountered ways of sharing small datasets is in the form of Excel spreadsheet (.xls) files, notwithstanding all that can be said In Praise of CSV😉 The natural application for opening these files is Microsoft Excel, but what if you don’t have a copy of Excel available?

There are other desktop office suites that can open spreadsheet files, of course, such as Open Office. As long as they’re not too big, spreadsheet files can also be uploaded to and then opened using a variety of online services, such as Google Spreadsheets, Google Fusion Tables or Zoho Sheet. But spreadsheet applications aren’t the only data wrangling tools that can be used to open xls files… Here are a couple more that should be part of every data wrangler’s toolbox…

(If you want to play along, the file I’m going to play with is a spreadsheet containing the names and locations of GP practices in England. The file can be found on the NHS Indicators portal – here’s the actual spreadsheet.)

Firstly, Google Refine. Google Refine is a cross-platform, browser based tool that helps with many of the chores relating to getting a dataset tidied up so that you can use it elsewhere, as well as helping out with data reconcilation or augmenting rows with annotations provided by separate online services. You can also use it as a quick-and-dirty tool for opening an xls spreadsheet from a URL, knocking the data into shape, and dumping it to a CSV file that you can use elsewhere. To start with, choose the option to create a project by importing a file from a web address (the XLS spreadsheet URL):

Once loaded, you get a preview view..

You can tidy up the data that you are going to use in your project via the preview panel. In this case, I’m going to ignore the leading lines and just generate a dataset that I can export directly as a CSV file once I’ve got the data into my project.

If I then create a project around this dataset, I can trivially export it again using a format of my own preference:

So that’s one way of using Google Refine as a simple file converter service that allows you to preview and to a certain extent shape the data in XLS spreadsheet, as well as converting it to other file types.

The second approach I want to mention is to use a really handy Python software library (xlrd – Excel Reader) in Scraperwiki. The Scraperwiki tutorial on Excel scraping gives a great example of how to get started, which I cribbed wholesale to produce the following snippet.

import scraperwiki
import xlrd

#cribbing https://scraperwiki.com/docs/python/python_excel_guide/
def cellval(cell):
    if cell.ctype == xlrd.XL_CELL_EMPTY:    return None
    return cell.value

def dropper(table):
    if table!='':
        try: scraperwiki.sqlite.execute('drop table "'+table+'"')
        except: pass

def reGrabber():
    #dropper('GPpracticeLookup')
    url = 'https://indicators.ic.nhs.uk/download/GP%20Practice%20data/summaries/demography/Practice%20Addresses%20Final.xls'
    xlbin = scraperwiki.scrape(url)
    book = xlrd.open_workbook(file_contents=xlbin)

    sheet = book.sheet_by_index(0)        

    keys = sheet.row_values(8)           
    keys[1] = keys[1].replace('.', '')
    print keys

    for rownumber in range(9, sheet.nrows):           
        # create dictionary of the row values
        values = [ cellval(c) for c in sheet.row(rownumber) ]
        data = dict(zip(keys, values))
        #print data
        scraperwiki.sqlite.save(table_name='GPpracticeLookup',unique_keys=['Practice Code'], data=data)

#Uncomment the next line if you want to regrab the data from the original spreadsheet
reGrabber()

You can find my scraper here: UK NHS GP Practices Lookup. What’s handy about this approach is that having scraped the spreadsheet data into a Scraperwiki database, I can now query it as database data via the Scraperwiki API.

(Note that the Google Visualisation API query language would also let me treat the spreadsheet data as a database if I uploaded it to Google Spreadsheets.)

So, if you find yourself with an Excel spreadsheet, but no Microsoft Office to hand, fear not… There are plenty of other tools other there you can appropriate to help you get the data out of the file and into a form you can work with:-)

PS R is capable of importing Excel files, I think, but the libraries I found don’t seem to compile onto Max OS/X?

PPS ***DATA HEALTH WARNING*** I haven’t done much testing of either of these approaches using spreadsheets containing multiple workbooks, complex linked formulae or macros. They may or may not be appropriate in such cases… but for simple spreadsheets, they’re fine…

Exploring GP Practice Level Prescribing Data

Some posts I get a little bit twitchy about writing. Accessing and Visualising Sentencing Data for Local Courts was one, and this is another: exploring practice level prescription data (get the data).

One of the reasons it feels “dangerous” is that the rationale behind the post is to demonstrate some of the mechanics of engaging with the data at a context free level, devoid of any real consideration about what the data represents, whilst using a data set that does have meaning, the interpretation of which can be used as the basis of making judgements about various geographical areas, for example.

The datasets that are the focus of this post relate to GP practice level prescription data. One datafile lists GP practices (I’ve uploaded this to Google Fusion tables), and includes practice name, identifier, and address. I geocoded the Google Fusion tables version of the data according to practice postcode, so we can see on a map how the practices are distributed:

(There are a few errors in the geocoding that could probably be fixed by editing the correspond data rows, and adding something like “, UK” to the postcode. (I’ve often thought it would be handy if you could force Google Fusion Table’s geocoder to only return points within a particular territory…))

The prescription data includes data at the level of item counts by drug name or prescription item per month for each practice. Trivially, we might do something like take the count of methadone prescriptions for each practice, and plot a map sizing points at the location of each practice by the number of methadone prescriptions by that practice. All well and good if we bear in mind the fact the the data hasn’t been normalised by the size of the practice, doesn’t take into account the area over which the patients are distributed, doesn’t take into account the demographics of the practices constituency (or recognise that a particular practice may host a special clinic, or the sample month may have included an event that drew in a large transient population with a particular condition, or whatever). A good example to illustrate this taken from another context might be “murder density” in London. It wouldn’t surprise me if somewhere like Russell Square came out as a hot spot – not because there are lots of murders there, but because a bomb went off on a single occasion killing multiple people… Another example of “crime hot spots” might well be courts or police stations, places that end up being used as default/placeholder locations if the actual location of crime isn’t known. And so on.

The analyst responsible for creating quick and dirty sketch maps will hopefully be mindful of the factors that haven’t been addressed in the construction of a sketch, and will consequently treat with suspicion any result unless they’ve satisfied themselves that various factors have been taken into account, or discount particular results that are not the current focus of the question they are asking themselves of the data in a particular way.

So when it comes to producing a post like this looking at demonstrating some practical skills, care needs to be taken not to produce charts or maps that appear to say one thing when indeed they say nothing… So bear that in mind: this post isn’t about how to generate statistically meaningful charts and tables; it’s about mechanics of getting rows of data out of big files and into a form we can start to try to make sense of them

Another reason I’m a little twitchy about this post relates to describing certain skills in an open and searchable/publicly discoverable forum. (This is one reason why folk often demonstrate core skills on “safe” datasets or randomly generated data files.) In the post Googling Nasties and Oopses on University and Public Sector Websites, a commenter asked: “is it really ethical to post that information?” in the context of an example showing how to search for confidential spreadsheet information using a web search engine. I could imagine a similar charge being leveled at a post that describes certain sorts of data wrangling skills. Maybe some areas of knowledge should be limited to the priesthood..?

To mitigate against any risks of revealing things best left undiscovered, I could draw on the NHS Information Centre’s Evaluation and impact assessment – proposal to publish practice-level prescribing data[PDF] as well as the risks acknowledged by the recent National Audit Office report on Implementing transparency (risks to privacy, of fraud, and other possible unintended consequences). But I won’t, for now…. (dangerrrrrroussssssssss…;-)

(Academically speaking, it might be interesting to go through the NHS Info Centre’s risk assessment and see just how far we can go in making those risks real using the released data set as a “white hat data hacker”, for example! I will go through the risk assessment properly in another post.)

So… let the journey into the data begin, and the reason why I felt the need to have a play with this data set:

Note: Due to the large file size (over 500MB) standard spreadsheet applications will not be able to handle the volumes of data contained in the monthly datasets. Data users will need to analyse the information using specialist data-handling software.

Hmmm… that’s not very accessible is it?!

However, if you’ve read my previous posts on Playing With Large (ish) CSV Files or Postcards from a Text Processing Excursion, or maybe even the aforementioned local sentencing data post, you may have some ideas about how to actually work with this file…

So fear not – if you fancy playing along, you should already be set up tooling wise if you’re on a Mac or a Linux computer. (If you’re on a Windows machine, I cant really help – you’ll probably need to install something like gnuwin or Cygwin – if any Windows users could add support in the comments, please do:-)

Download the data (all 500MB+ of it – it’s published unzipped/uncompressed (a zipped version comes in at a bit less than 100MB)) and launch a terminal.

>

I downloaded the December 2011 files as nhsPracticesDec2011.csv and nhsPrescribingDataDec2011.CSV so those are the filenames I’ll be using.

To look at the first few lines of each file we can use the head command:

head nhsPrescribingDataDec2011.CSV
head nhsPracticesDec2011.csv

Inspection of the practices data suggests that counties for each practice are specified, so I can generate a subset of the practices file listing just practices on the ISLE OF WIGHT by issuing a grep (search) command and sending (>) the result to a new file:

grep WIGHT nhsPracticesDec2011.CSV > wightPracDec2011.csv

The file wightPracDec2011.csv should now contain details of practices (one per row) based on the Isle of Wight. We can inspect the first few lines of the file using the head command, or use more to scroll through the data one page at a time (hit space bar to move on a page, ESCape to exit).

head wightPracDec2011.csv
more wightPracDec2011.csv

Hmmm.. there’s a rogue practice in there from the Wirral – let’s refine the grep a little:

grep 'OF WIGHT' nhsPracticesDec2011.CSV > wightPracDec2011.csv
more wightPracDec2011.csv

From looking at the data file itslef, along with the prescribing data release notes/glossary, we can see that each practice has a unique identifier. From previewing the head of the prescription data itself, as well as from the documentation, we know that the large prescription data file contains identifiers for each practice too. So based on the previous steps, can you figure out how to pull out the rows from the prescriptions file that relate to drugs issued by the Ventnor medical centre, which has code J84003? Like this, maybe?

grep J84003 nhsPrescribingDataDec2011.CSV > wightPrescDec2011_J84003.csv
head wightPrescDec2011_J84003.csv

(It may take a minute or two, so be patient…)

We can check how many rows there actually are as follows:

wc -l wightPrescDec2011_J84003.csv

I was thinking it would be nice to be able to get prescription data from all the Isle of Wight practices, so how might we go about that. From reviewing my previous text mining posts, I noticed that I could pull out data from a file by column:

cut -f 2 -d ',' wightPracDec2011.csv

This lists column two of the file wightPracDec2011.csv where columns are comma delimited.

We can send this list of codes to the grep command to pull out records from the large prescriptions file for each of the codes we grabbed using the cut command (I asked on Twitter for how to do this, and got a reply back that seemed to do the trick pretty much by return of tweet from @smelendez):

cut -d ',' -f 2 wightPracDec2011.csv | grep nhsPrescribingDataDec2011.CSV -f - > iwPrescDec2011.csv
more iwPrescDec2011.csv

We can sort the result by column – for example, in alphabetic order by column 5 (-k 5), the drugs column:

sort -t ',' -k 5 iwPrescDec2011.csv | head

Or we can sort by decreasing (-r) total ingredient cost:

sort -t ',' -k 7 -r iwPrescDec2011.csv | head

Or in decreasing order of the largest number of items:

sort -t ',' -k 6 -r iwPrescDec2011.csv | head

One problem with looking at those results is that we can’t obviously recognise the practice. (That might be a good thing, especially if we looked at item counts in increasing order… Whilst we don’t know how many patients were in receipt of one or more items of drug x if 500 or so items were prescribed in the reporting period across several practices, if there is only one item of a particular drug prescribed for one practice, then we’re down to one patient in receipt of that item across the island, which may be enough to identify them…) I leave it as an exercise for the reader to work out how you might reconcile the practice codes with practice names (Merging Datasets with Common Columns in Google Refine might be one way? Merging Two Different Datasets Containing a Common Column With R and R-Studio another..?).

Using the iwPrescDec2011.csv file, we can now search to see how many items of a particular drug are prescribed across island practices using searches of the form:

grep Aspirin iwPrescDec2011.csv
grep 'Peppermint Oil' iwPrescDec2011.csv

And this is where we now start to need taking a little care… Scanning through that data by eye, a bit of quick mental arithmetic (divide column 7 by column 6) suggests that the unit price for peppermint oil is different across practices. So is there a good reason for this? I would guess that the practices may well be describing different volumes of peppermint oil as single prescription items, which makes a quick item cost calculation largely meaningless? I guess we need to check the data glossary/documentation to confirm (or deny) this?

Okay – enough for now… maybe I’ll see how we can do a little more digging around this data in another post…

PS Just been doing a bit of doing around other GP practice level datasets – you can find a range of them on the NHS Indicator Portal. As well as administrative links up to PCT and Stategic Health Authority names, you can get data such as the size and demographic make up of each practice’s registration list, data relating to deprivation measures, models for incidence of various health conditions, practice address and phone number, the number of nursing home patients, the number of GPs per practice, the uptake of various IT initiatives(?!), patient experience data, impact on NHS services data… (Apparently a lot of this ata is available in a ‘user friendly’ format on NHS Choices website, but I couldn’t find it offhand… as part of the GP comparison service. Are there any third party sites around built on top of this data also?)

Social Interest Positioning – Visualising Facebook Friends’ Likes With Data Grabbed Using Google Refine

What do my Facebook friends have in common in terms of the things they have Liked, or in terms of their music or movie preferences? (And does this say anything about me?!) Here’s a recipe for visualising that data…

After discovering via Martin Hawksey that the recent (December, 2011) 2.5 release of Google Refine allows you to import JSON and XML feeds to bootstrap a new project, I wondered whether it would be able to pull in data from the Facebook API if I was logged in to Facebook (Google Refine does run in the browser after all…)

Looking through the Facebook API documentation whilst logged in to Facebook, it’s easy enough to find exemplar links to things like your friends list (https://graph.facebook.com/me/friends?access_token=A_LONG_JUMBLE_OF_LETTERS) or the list of likes someone has made (https://graph.facebook.com/me/likes?access_token=A_LONG_JUMBLE_OF_LETTERS); replacing me with the Facebook ID of one of your friends should pull down a list of their friends, or likes, etc.

(Note that validity of the access token is time limited, so you can’t grab a copy of the access token and hope to use the same one day after day.)

Grabbing the link to your friends on Facebook is simply a case of opening a new project, choosing to get the data from a Web Address, and then pasting in the friends list URL:

Google Refine - import Facebook friends list

Click on next, and Google Refine will download the data, which you can then parse as a JSON file, and from which you can identify individual record types:

Google Refine - import Facebook friends

If you click the highlighted selection, you should see the data that will be used to create your project:

Google Refine - click to view the data

You can now click on Create Project to start working on the data – the first thing I do is tidy up the column names:

Google Refine - rename columns

We can now work some magic – such as pulling in the Likes our friends have made. To do this, we need to create the URL for each friend’s Likes using their Facebook ID, and then pull the data down. We can use Google Refine to harvest this data for us by creating a new column containing the data pulled in from a URL built around the value of each cell in another column:

Google Refine - new column from URL

The Likes URL has the form https://graph.facebook.com/me/likes?access_token=A_LONG_JUMBLE_OF_LETTERS which we’ll tinker with as follows:

Google Refine - crafting URLs for new column creation

The throttle control tells Refine how often to make each call. I set this to 500ms (that is, half a second), so it takes a few minutes to pull in my couple of hundred or so friends (I don’t use Facebook a lot;-). I’m not sure what limit the Facebook API is happy with (if you hit it too fast (i.e. set the throttle time too low), you may find the Facebook API stops returning data to you for a cooling down period…)?

Having imported the data, you should find a new column:

Google Refine - new data imported

At this point, it is possible to generate a new column from each of the records/Likes in the imported data… in theory (or maybe not..). I found this caused Refine to hang though, so instead I exprted the data using the default Templating… export format, which produces some sort of JSON output…

I then used this Python script to generate a two column data file where each row contained a (new) unique identifier for each friend and the name of one of their likes:

import simplejson,csv

writer=csv.writer(open('fbliketest.csv','wb+'),quoting=csv.QUOTE_ALL)

fn='my-fb-friends-likes.txt'

data = simplejson.load(open(fn,'r'))
id=0
for d in data['rows']:
	id=id+1
	#'interests' is the column name containing the Likes data
	interests=simplejson.loads(d['interests'])
	for i in interests['data']:
		print str(id),i['name'],i['category']
		writer.writerow([str(id),i['name'].encode('ascii','ignore')])

[I think this R script, in answer to a related @mhawksey Stack Overflow question, also does the trick: R: Building a list from matching values in a data.frame]

I could then import this data into Gephi and use it to generate a network diagram of what they commonly liked:

Sketching common likes amongst my facebook friends

Rather than returning Likes, I could equally have pulled back lists of the movies, music or books they like, their own friends lists (permissions settings allowing), etc etc, and then generated friends’ interest maps on that basis.

[See also: Getting Started With The Gephi Network Visualisation App – My Facebook Network, Part I and how to visualise Google+ networks]

PS dropping out of Google Refine and into a Python script is a bit clunky, I have to admit. What would be nice would be to be able to do something like a “create new rows with new column from column” pattern that would let you set up an iterator through the contents of each of the cells in the column you want to generate the new column from, and for each pass of the iterator: 1) duplicate the original data row to create a new row; 2) add a new column; 3) populate the cell with the contents of the current iteration state. Or something like that…

PPS Related to the PS request, there is a sort of related feature in the 2.5 release of Google Refine that lets you merge data from across rows with a common key into a newly shaped data set: Key/value Columnize. Seeing this, it got me wondering what a fusion of Google Refine and RStudio might be like (or even just R support within Google Refine?)

PPPS this could be interesting – looks like you can test to see if a friendship exists given two Facebook user IDs.

Mapping the New Year Honours List – Where Did the Honours Go?

When I get a chance, I’ll post a (not totally unsympathetic) response to Milo Yiannopoulos’post The pitiful cult of ‘data journalism’, but in the meantime, here’s a view over some data that was released a couple of days ago – a map of where the New Year Honours went [link]

New Year Honours map

[Hmm… so WordPress.com doesn’t seem to want to let me embed a Google Fusion Table map iframe, and Google Maps (which are embeddable) just shows an empty folder when I try to view the Fusion Table KML… (the Fusion Table export KML doesn’t seem to include lat/lng data either? Maybe I need to explore some hosting elsewhere this year…]

Note that I wouldn’t make the claim that this represents an example of data journalism. It’s a sketch map showing which parts of the country various recipients of honours this time round presumably live. Just by posting the map, I’m not reporting any particular story. Instead, I’m trying to find a way of looking at the day to see whether or not there may be any interesting stories that are suggested by viewing the data in this way.

There was a small element of work involved in generating the map view, though… Working backwards, when I used Google Fusion tables to geocode the locations of the honoured, some of the points were incorrectly located:

Google Fusion Tables - correcting fault geocoding

(It would be nice to be able to force a locale to the geocoder, maybe telling it to use maps.google.co.uk as the base, rather than (presumably) maps.google.com?)

The approach I took to tidying these was rather clunky, first going into the table view and filtering on the mispositioned locations:

Google Fusion Tables - correcting geocoding errors

Then correcting them:

Google Fusion Table, Correct Geocode errors

What would be really handy would be if Google Fusion Tables let you see a tabular view of data within a particular map view – so for example, if I could zoom in to the US map and then get a tabular view of the records displayed on that particular local map view… (If it does already support this and I just missed it, please let me know via the comments..;-)

So how did I get the data into Google Fusion Tables? The original data was posted as a PDF on the DirectGov website (New Year Honours List 2012 – in detail)…:

New Year Honours data

…so I used Scraperwiki to preview and read through the PDF and extract the honours list data (my scraper is a little clunky and doesnlt pull out 100% of the data, missing the occasional name and contribution details when it’s split over several lines; but I think it does a reasonable enough job for now, particularly as I am currently more interested in focussing on the possible high level process for extracting and manipulating the data, rather than the correctness of it…!;-)

Here’s the scraper (feel free to improve upon it….:-): Scraperwiki: New Year Honours 2012

I then did a little bit of tweaking in Google Refine, normalising some of the facets and crudely attempting to separate out each person’s role and the contribution for which the award was made.

For example, in the case of Dr Glenis Carole Basiro DAVEY, given column data of the form “The Open University, Science Faculty and Health Education and Training Programme, Africa. For services to Higher and Health Education.“, we can use the following expressions to generate new sub-columns:

value.match(/.*(For .*)/)[0] to pull out things like “For services to Higher and Health Education.”
value.match(/(.*)For .*/)[0] to pull out things like “The Open University, Science Faculty and Health Education and Training Programme, Africa.”

I also ran each person’s record through Reuters Open Calais service using Google Refine’s ability to augment data with data from a URL (“Add column by fetching URLs”), pulling the data back as JSON. Here’s the URL format I used (polling once every 500ms in order to stay with the max. 4 calls per limit threshold mandated by the API.)

"http://api.opencalais.com/enlighten/rest/?licenseID=<strong>MY_LICENSE_KEY</strong>&content=" + escape(value,'url') + "&paramsXML=%3Cc%3Aparams%20xmlns%3Ac%3D%22http%3A%2F%2Fs.opencalais.com%2F1%2Fpred%2F%22%20xmlns%3Ardf%3D%22http%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%22%3E%20%20%3Cc%3AprocessingDirectives%20c%3AcontentType%3D%22TEXT%2FRAW%22%20c%3AoutputFormat%3D%22Application%2FJSON%22%20%20%3E%20%20%3C%2Fc%3AprocessingDirectives%3E%20%20%3Cc%3AuserDirectives%3E%20%20%3C%2Fc%3AuserDirectives%3E%20%20%3Cc%3AexternalMetadata%3E%20%20%3C%2Fc%3AexternalMetadata%3E%20%20%3C%2Fc%3Aparams%3E"

Unpicking this a little:

licenseID is set to my license key value
content is the URL escaped version of the text I wanted to process (in this case, I created a new column from the name column that also pulled in data from a second column (the contribution column). The GREL formula I used to join the columns took the form: value+', '+cells["contribution"].value)
paramsXML is the URL encoded version of the following parameters, which set the content encoding for the result to be JSON (the default is XML):

<c:params xmlns:c="http://s.opencalais.com/1/pred/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<c:processingDirectives c:contentType="TEXT/RAW" c:outputFormat="Application/JSON"  >
</c:processingDirectives>
<c:userDirectives>
</c:userDirectives>
<c:externalMetadata>
</c:externalMetadata>
</c:params>

So much for process – now where are the stories? That’s left, for now, as an exercise for the reader. An obvious starting point is just to see who received honours in your locale. Remember, Google Fusion Tables lets you generate all sorts of filtered views, so it’s not too hard to map where the MBEs vs OBEs are based, for example, or have a stab at where awards relating to services to Higher Education went. Some awards also have a high correspondence with a particular location, as for example in the case of Enfield…

If you do generate any interesting views from the New Year Honours 2012 Fusion Table, please post a link in the comments. And if you find a problem with/fix for the data or the scraper, please post that info in a comment too:-)

More Dabblings With Local Sentencing Data

In Accessing and Visualising Sentencing Data for Local Courts I posted a couple of quick ways in to playing with Ministry of Justice sentencing data for the period July 2010-June 2011 at the local court level. At the end of the post, I wondered about how to wrangle the data in R so that I could look at percentage-wise comparisons between different factors (Age, gender) and offence type and mentioned that I’d posted a related question to to the Cross Validated/Stats Exchange site (Casting multidimensional data in R into a data frame).

Courtesy of Chase, I have an answer🙂 So let’s see how it plays out…

To start, let’s just load the Isle of Wight court sentencing data into RStudio:

require(ggplot2)
require(reshape2)
iw = read.csv("http://dl.dropbox.com/u/1156404/wightCrimRecords.csv")

Now we’re going to shape the data so that we can plot the percentage of each offence type by gender (limited to Male and Female options):

iw.m = melt(iw, id.vars = "sex", measure.vars = "Offence_type")
iw.sex = ddply(iw.m, "sex", function(x) as.data.frame(prop.table(table(x$value))))
ggplot(subset(iw.sex,sex=='Female'|sex=='Male')) + geom_bar(aes(x=Var1,y=Freq)) + facet_wrap(~sex)+ opts(axis.text.x=theme_text(angle=-90)) + xlab('Offence Type')

Here’s the result:

Splitting down offences by percentage and gender

We can also process the data over a couple of variables. So for example, we can look to see how female recorded sentences break down by offence type and age range, displaying the results as a percentage of how often each offence type on its own was recorded by age:

iw.m2 = melt(iw, id.vars = c("sex","Offence_type" ), measure.vars = "AGE")
iw.off=ddply(iw.m2, c("sex","Offence_type"), function(x) as.data.frame(prop.table(table(x$value))))

ggplot(subset(iw.off,sex=='Female')) + geom_bar(aes(x=Var1,y=Freq)) + facet_wrap(~Offence_type) + opts(axis.text.x=theme_text(angle=-90)) + xlab('Age Range (Female)')

Offence type broken down by age and gender

Note that this graphic may actually be a little misleading because percentage based reports donlt play well with small numbers…: whilst there are multiple Driving Offences recorded, there are only two Burglaries, so the statistical distribution of convicted female burglars is based over a population of size two… A count would be a better way of showing this

PS I was hoping to be able to just transmute the variables and generate a raft of other charts, but I seem to be getting an error, maybe because some rows are missing? So: anyone know where I’m supposed to post R library bug reports?

Accessing and Visualising Sentencing Data for Local Courts

A recent provisional data release from the Ministry of Justice contains sentencing data from English(?) courts, at the offence level, for the period July 2010-June 2011: “Published for the first time every sentence handed down at each court in the country between July 2010 and June 2011, along with the age and ethnicity of each offender.” Criminal Justice Statistics in England and Wales [data]

In this post, I’ll describe a couple of ways of working with the data to produce some simple graphical summaries of the data using Google Fusion Tables and R…

…but first, a couple of observations:

– the web page subheading is “Quarterly update of statistics on criminal offences dealt with by the criminal justice system in England and Wales.”, but the sidebar includes the link to the 12 month set of sentencing data;
– the URL of the sentencing data is http://www.justice.gov.uk/downloads/publications/statistics-and-data/criminal-justice-stats/recordlevel.zip, which does not contain a time reference, although the data is time bound. What URL will be used if data for the period 7/11-6/12 is released in the same way next year?

The data is presented as a zipped CSV file, 5.4MB in the zipped form, and 134.1MB in the unzipped form.

The unzipped CSV file is too large to upload to a Google Spreadsheet or a Google Fusion Table, which are two of the tools I use for treating large CSV files as a database, so here are a couple of ways of getting in to the data using tools I have to hand…

Unix Command Line Tools

I’m on a Mac, so like Linux users I have ready access to a Console and several common unix commandline tools that are ideally suited to wrangling text files (on Windows, I suspect you need to install something like Cygwin; a search for windows unix utilities should turn up other alternatives too).

In Playing With Large (ish) CSV Files, and Using Them as a Database from the Command Line: EDINA OpenURL Logs and Postcards from a Text Processing Excursion I give a couple of examples of how to get started with some of the Unix utilities, which we can crib from in this case. So for example, after unzipping the recordlevel.csv document I can look at the first 10 rows by opening a console window, changing directory to the directory the file is in, and running the following command:

head recordlevel.csv

Or I can pull out rows that contain a reference to the Isle of Wight using something like this command:

grep -i wight recordlevel.csv > recordsContainingWight.csv

(The -i reads: “ignoring case”; grep is a command that identifies rows contain the search term (wight in this case). The > recordsContainingWight.csv says “send the result to the file recordsContainingWight.csv” )

Having extracted rows that contain a reference to the Isle of Wight into a new file, I can upload this smaller file to a Google Spreadsheet, or as Google Fusion Table such as this one: Isle of Wight Sentencing Fusion table.

Isle fo wight sentencing data

Once in the fusion table, we can start to explore the data. So for example, we can aggregate the data around different values in a given column and then visualise the result (aggregate and filter options are available from the View menu; visualisation types are available from the Visualize menu):

Visualising data in google fusion tables

We can also introduce filters to allow use to explore subsets of the data. For example, here are the offences committed by females aged 35+:

Data exploration in Google FUsion tables

Looking at data from a single court may be of passing local interest, but the real data journalism is more likely to be focussed around finding mismatches between sentencing behaviour across different courts. (Hmm, unless we can get data on who passed sentences at a local level, and look to see if there are differences there?) That said, at a local level we could try to look for outliers maybe? As far as making comparisons go, we do have Court and Force columns, so it would be possible to compare Force against force and within a Force area, Court with Court?

R/RStudio

If you really want to start working the data, then R may be the way to go… I use RStudio to work with R, so it’s a simple matter to just import the whole of the reportlevel.csv dataset.

Once the data is loaded in, I can use a regular expression to pull out the subset of the data corresponding once again to sentencing on the Isle of Wight (i apply the regular expression to the contents of the court column:

recordlevel <- read.csv("~/data/recordlevel.csv")
iw=subset(recordlevel,grepl("wight",court,ignore.case=TRUE))

We can then start to produce simple statistical charts based on the data. For example, a bar plot of the sentencing numbers by age group:

age=table(iw$AGE)
barplot(age, main="IW: Sentencing by Age", xlab="Age Range")

R - bar plot

We can also start to look at combinations of factors. For example, how do offence types vary with age?

ageOffence=table(iw$AGE, iw$Offence_type)
barplot(ageOffence,beside=T,las=3,cex.names=0.5,main="Isle of Wight Sentences", xlab=NULL, legend = rownames(ageOffence))

R barplot - offences on IW

If we remove the beside=T argument, we can produce a stacked bar chart:

barplot(ageOffence,las=3,cex.names=0.5,main="Isle of Wight Sentences", xlab=NULL, legend = rownames(ageOffence))

R - stacked bar chart

If we import the ggplot2 library, we have even more flexibility over the presentation of the graph, as well as what we can do with this sort of chart type. So for example, here’s a simple plot of the number of offences per offence type:

require(ggplot2)
#You may need to install ggplot2 as a library if it isn't already installed
ggplot(iw, aes(factor(Offence_type)))+ geom_bar() + opts(axis.text.x=theme_text(angle=-90))+xlab('Offence Type')

GGPlot2 in R

Alternatively, we can break down offence types by age:

ggplot(iw, aes(AGE))+ geom_bar() +facet_wrap(~Offence_type)

ggplot facet barplot

We can bring a bit of colour into a stacked plot that also displays the gender split on each offence:

ggplot(iw, aes(AGE,fill=sex))+geom_bar() +facet_wrap(~Offence_type)

ggplot with stacked factor

One thing I’m not sure how to do is rip the data apart in a ggplot context so that we can display percentage breakdowns, so we could compare the percentage breakdown by offence type on sentences awarded to males vs. females, for example? If you do know how to do that, please post a comment below 😉

PS HEre’s an easy way of getting started with ggplot… use the online hosted version at http://www.yeroon.net/ggplot2/ using this data set: wightCrimRecords.csv; download the file to your computer then upload it as shown below:

yeroon.net/ggplot2

PPS I got a little way towards identifying percentage breakdowns using a crib from here. The following command:
iwp=tapply(iw$Offence_type,iw$sex,function(x){prop.table(table(x))})
generates a (multidimensional) array for the responseVar (Offence) about the groupVar (sex). I don’t know how to generate a single data frame from this, but we can create separate ones for each sex as follows:
iwpMale=data.frame(iwp['Male'])
iwpFemale=data.frame(iwp['Female'])

We can then plot these percentages using constructions of the form:
ggplot(iwp2)+geom_bar(aes(x=Male.x,y=Male.Freq))
What I haven’t worked out how to do is elegantly map from the multidimensional array to a single data.frame? If you know how, please add a comment below…(I also posted a question on Cross Validated, the stats bit of Stack Exchange…)

Sports Data Journalism and “Datatainment”

Over the last couple of years, you’ve probably noticed that data has become a Big Thing in commerce (Big Data for business advantage) as well as in the openness/transparency community, with governments and the media joining the party particularly in the context of the latter. But if you’re looking to develop data journalism skills, it’s probably also worth remembering the area of sports journalism, and the wealth of data produced around sporting events.

Part of the attraction of developing learning activities around sports data is that there’s a good chance that it’ll keep on delivering… If you develop a way of analysing or displaying sports data that pulls out interesting features or story elements from a set of sports data, you should be able to keep on using it… To set the scene, here’s a example: Driven By Data: Data Journalism in Sports. For a peek at my own fumblings, I’ve started exploring the automatic creation of F1DataJunkie Stats Graphics reports (still a lot to be done, but it’s a start…)

In the extreme case, you might be able to generate story outlines, or even canned prose… For example, in certain computer games in the sports genre, you might find you’re playing a game along to a “live commentary”, generated from the data being produced by the game. Automatic commentary generation is a form of sports journalism. And automated article generation is already here, as @RobbieAllen describes in How I automated my writing career, a brief overview of Automated Insights, a company that specialises in computer generated visualisations and prose.

See also: Automated Storytelling in Sports: A Rich Domain to Be Explored, Automated Event Recognition for Football Commentary Generation, Three RoboCup Simulation League Commentator Systems, and so on…

Getting hold of data is always an issue, of course, but I suspect that many larger newsrooms will take a subscription to the Press Association sports data feeds, for example…

Anyway, as an exercise, here’s some data to start with, from the Guardian datastore: Premier League’s top scorers: who is scoring the most goals? Is there a correlation with age, perhaps? (Where would you find the age data…?)

As well as sports reporting, I think we’re also likely to see an increase in what Head of Digital at Manchester City FC, Richard Ayers, referes to as datatainment: “where you use data as the primary source of entertainment. You might choose to make the visualisation of raw data entertaining or perhaps use data visualisation as part of the process of entertainment – but there’s definitely a strong editorial control which is focussed on entertaining the audience rather than exposing data.” (Data? Entertainment? You need Datatainment and Defining Data Visualisation, Data Journalism & Data Entertainment).

Devices such as FanVision already blend video and audio streams with data feeds, for example, more and more sports have “live stats apps” associated with them, and it’s not hard to imagine the data crunching that goes on under the hood in things like Optiplay making an appearance on sports analysis and review sites?

I also think that the “data as entertainment” line might work well as a second screen activity. Things like the F1 Live Timing app already demonstrate this:

On the other hand, there’s an opportunity for data focussed sites that go into deep analysis for the hardcore fan. Again looking at Formula One, the Intelligent F1 blog features a data-powered model developed by a rocket scientist that provides engagment oaround a particular race over an extended period, from predicting Sunday race behaviour based on Friday practice data and previous outings, through analysis of practice and qualifying data, to a detailed series of post-race analyses. (Complement this with technical analyses applied to the cars on the Scarbs F1, and you have the ultimate F1 geeks paradise!;-)

PS This also caught my eye: Gametime [Assistant]: Girls’ Lacrosse Game Data, which steps through the design of a “datatainment” app…

PPS as the Lacrosse app suggests, the data collection thing can also improve engagement with a live event. For example, my own doodlings around a motorsport lapcharting app (Thoughts on a Couple of Possible Lap Charting Apps, initial code experiment)

How Might Data Journalists Show Their Working? Sweave

If part of the role of data journalism is to make transparent the justification behind claims that are, or aren’t, backed up by data, there’s good reason to suppose that the journalists should be able to back up their own data-based claims with evidence about how they made use of the data. Posting links to raw data helps to a certain extent – at least third parties can then explore the data themselves and check the claims the press are making – but you could also argue that the journalists should also make their notes available regarding how they worked the data. (The same is true in public reports, where summary statistics and charts are included in a report, along with a link to the raw data, but no transparency in how the summary reports/charts were actually produced from the data.)

In Power Tools for Aspiring Data Journalists: R, I explored how we might use the R statistical programming language to replicate a chart that appeared in one of Ben Goldacre’s Bad Science columns. I included code snippets in the post, along with the figures they generated. But is there a way of getting even closer to the source, as it were, and produce documents that essentially generate their output from some sort of “source code”?

For example, take this view of my working relating to the production of the funnel chart described in Goldacre’s column:

You can find the actual “source code” for that document here: bowel cancer funnel plot working notes If you load it into something like RStudio, you can “run” the code and generate your own PDF from it.

The “source” of the document includes both text and R code. When the Sweave document is processed, the R code contained within the document is executed and the results also included in the document. The charts shown in the report are generated directly from the code included in the document, using data pulled in to the document form a source referenced within the document. If the source data is changed, or the R code is changed, what’s contained in the output document will change as well.

This sort of workflow will be familiar to many experimental scientists, but I wonder: is it something that data journalists have considered, at least as a way of keeping working notes about data related projects they are working on?

PS as well as Sweave, see dexy.it, which generalises the Sweave approach to allow you to create self-documenting software/code. Educators, also take note…;-)

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!]