Posted by Peter Morris on July 23, 2014
John O’Callaghan has successfully defended his thesis entitled “Evidence based hypothermic preservation of the kidney and liver for transplantation” and has now been notified that he has been awarded the DPhil degree. His work in this area has been outstanding and he has produced a number of critically important papers arising from the work of his thesis.
Posted by Simon Knight on July 18, 2014
My pechant for open-source software led me to use the R statistical environment. In this series of blog posts, that I will update over the coming weeks, I will run through the steps of installing R and associated tools and getting set-up for meta-analysis. I will also explain how to create attractive forest and funnel plots for publication, and use some of the more advanced features such as mixed effects meta-analysis and tests for publication bias.
What is R?
R is a statistical programming language, akin to Stata, SPSS and many other statistical software packages. It is based on the S statistical environment, and provides a wide variety of statistical methods and graphical tools which enable the production of publication standard graphics.
The major advantage of R is that it is “open-source” software – it is free to use and distribute unlike the very expensive commercial packages. It is also freely available for Windows, Mac OS X and Unix platforms, and is extensible with downloadable packages and user-defined functions.
Using R for meta-analysis
There are a number of packages available for R which provide functions for meta-analysis, including graphical capabilities such as forest plots and funnel plots, heterogeneity testing, meta-regression and mixed-effects analysis. The most useful of these are the “meta”, “rmeta” and “metafor” packages.
Using R for meta-analysis is slightly more involved than other solutions such as the Cochrane RevMan software, and involves the use of the command-line. However, the number of functions that the user needs to be familiar with is small, and R gives the advantages of much greater flexibility, numerous additional functions and greatly improved graphics suitable for presentations and publication in journals.
Installing the software
Today’s post is all about getting set-up and installing the necessary software and packages. R itself is a command-line programming language that can be installed alone on any platform. Binaries are available from http://cran.r-project.org/. For those of us used to graphical user interfaces (e.g. Windows, OSX) this can be a daunting prospect and for this reason a number of graphical user interfaces have been written that make basic functions such as opening and closing files, exporting graphics etc. much easier for the novice user.
Examples of GUIs for Windows and OSX include R Commander, RKWard, and RStudio. My preference is for RStudio, as it is available for Windows, OSX and Unix platforms and is very easy to install and use.
To install R:
To install RStudio:
Now you are ready to install the RStudio user interface. Visit the RStudio download page and select the Windows or OSX version of RStudio from the list to download.
Once the download is complete, run the installer and follow the instructions.
Running for the first time
In either the Windows program menu or the OSX Application Launchpad, you should now find an icon for RStudio:
Double-click to launch the software. You should now see the default home-screen:
The default panels are as follows:
Left panel: The R console. This is where you type commands and view responses from R.
Top right panel: The environment and history tabs. These show you current datasets and set variables, as well as your command history (commands you have run previously). Buttons here also allow you to import and save data.
Bottom right panel: Here is where you can access files, display plots/graphs, load packages and view help files.
Installing the meta-analysis packages
By default, R comes with just the basic statistical functions loaded. Specialist functions such as those for meta-analysis are available to be downloaded as add-on packages which can be installed and run as needed.
Installing from the RStudio interface
To install packages, select the “Packages” tab on the lower right-hand pane:
From the menu bar, select “Install”:
Enter “metafor” into the box, and click “Install”. You will see some code appear in the console pane as the package is downloaded and installed.
Repeat this for the “rmeta” and “meta” packages.
To load the packages ready for use, simply select each package from the list using the checkbox:
Again, you will see code pass in the console pane as the packages are loaded.
Installing from the command-line
To install the packages, we use the “install.packages()” command. Type the following into the command-line:
The meta package will download and install.
Repeat this for the rmeta and metafor packages:
Once the packages are installed, they must be loaded for use in the current session. For this we use the “library()” command. This must be repeated each time you load RKWard, unless you are using a saved workspace in which they are already loaded. To load, type the following:
All of the necessary software is now loaded and you are ready to start your meta-analysis.
In the next part of this series, I will cover the basics of meta-analysis of binary data.
Posted by Simon Knight on July 10, 2014
The Royal Melbourne Hospital is arguably the major teaching hospital of the University of Melbourne and Melbourne Health now forms a complex not only comprising the Royal Melbourne Hospital, but the Royal Children’s Hospital, the Royal Women’s hospital as well as a number of research institutes (e.g. Walter and Eliza Hall Institute of Medical Research, Howard Florey Institute). As they launch the Parkville precinct as Australia’s leading biomedical research complex (it is right opposite the Medical School) they have established a Research Hall of Fame. The inaugural inductees on the 21st of June included Sir Peter Morris, Sir Gustav Nossal, Professor Priscilla Kincaid-Smith, Professor Ian Mackay, Professor Don Metcalf, the late Sir Macfarlane Burnet (Nobel Laureate), the late Dr John Cade and the late Sir Benjamin Rank as well as the first Professors of Surgery and Medicine at the University of Melbourne, namely the late Maurice Ewing and Richard Lovell. Other equally distinguished inductees were honoured at the Medical Foundation dinner on this special occasion.
Posted by Simon Knight on July 7, 2014
This month’s top ten trials include a systematic review of tuberculosis prophylaxis in renal transplantation, rituximab for desensitisation of cadaveric kidney recipients and the use of albuterol in DBD donors.
Posted by Liset Pengel on July 2, 2014
The deadline is approaching for ESOT’s European Transplant Fellow Workshop (ETFW), which is an advanced ESOT course for young professionals in transplantation about improving communication skills.
You can register for this course through the ESOT website.
Posted by Liset Pengel on June 26, 2014
From this month the Transplant Library includes invited commentaries by transplantation experts. The commentary includes a clinical impact rating and also indicates whether the trial is considered practice changing.
The randomised controlled trial “De novo sirolimus and reduced-dose tacrolimus versus standard-dose tacrolimus after liver transplantation: the 2000-2003 phase II prospective randomized trial” by Asrani and colleagues is considered practice changing by our expert and received a 5/5 clinical impact rating score.
You can read the full commentary in the Transplant Library. Get a trial account today!
Posted by Simon Knight on June 23, 2014
The next Frontiers in Transplantation course at King’s College will be held on the 1st and 2nd September 2014. The 2-day program includes discussion on recent developments in basic transplantation immunology alongside the latest cutting-edge clinical research.
If you are interested in attending, you can register at the King’s College website.
Posted by Peter Morris on June 20, 2014
Erik Compton, an American golfer, came second in the US Open last week at the age of 34. Why does this warrant a Blog? Well he has had two heart transplants, the first as a child for viral myocarditis at the age of 12 and the second a few years ago in 2007 after suffering a major heart attack. What a story of adversity and triumph! You do not get much notice for coming second usually but in this case he has had nearly as much as the winner, Martin Kaymer from Germany, who won by 8 strokes in four magnificent rounds. This is a great advertisement for what transplantation can achieve, but undoubtedly the courage shown by Compton throughout most of his life was illustrated by his last round performance in the Open when he was struggling but came back to finish equal second!
Posted by Peter Morris on June 18, 2014
I went to an excellent lecture on PROs by Professor Melanie Calvert from the University of Birmingham as part of the Doll Seminar series today. She talked about the incorporation of PROs in randomised controlled trials but the quality of the reporting which was quite dismal. Many analyses that she and her group have done were presented and all in all it was a first class coverage of PROs and the challenges they present in getting it right. There is now an extension to the CONSORT statement, known as the CONSORT PRO extension which gives excellent guidance on how one might use PROs as primary or secondary outcomes as well as discussing the methodology for developing appropriate PRO guidelines and questionnaires. She suggests that improved reporting of PRO data should make for a robust interpretation of the results of clinical trials as defined by the trialist and that are more relevant to patient care.
Posted by Peter Morris on June 17, 2014
Dr Liset Pengel, the CEO of the CET and a member of the staff of the Nuffield Department of Surgery, has been granted a distinction award by the NDS for her work with the CET.