With all the complexities facing the world from climate and environment changes to how we feed the world, one thing is clear - we need research in order to plan effectively. And research needs well trained researchers; people who understand agricultural issues and concerns, and who know how to research effectively. GenStat is known as a key research tool for many agricultural and other bioscience researchers, but we were delighted to find GenStat also has an important role to play in the teaching of these areas.

A key user of GenStat is the IAMZ in Zaragoza, Spain, whose main aim is to train people in how to do research. The IAMZ stands (in Spanish) for the Mediterranean Agronomic Institute of Zaragoza, it is one of the 4 sites of the CIHEAM (International Centre for Advanced Mediterranean Agronomic Studies). The main purpose of the CIHEAM is “to develop cooperation between Mediterranean countries through postgraduate training and promotion of cooperative research in the field of agriculture and natural resources.” As a part of this the IAMZ develops Master programmes and advanced courses for professionals designed to update and further the training of researchers in agriculture and its related sciences.

Students come from all over the world to study for the Master programmes, some are straight from their first degree and wish to complete their education, and some are already at work and wish to update their knowledge and understanding of agricultural research. I spoke with Dr Ramzi Belkhodja from the IAMZ, who heads up the Master in plant breeding. The programme covers several areas, one of which being statistics and the use of statistics in plant breeding research. Dr Belkhodja and his colleagues recognised the need for anyone either in plant breeding research or planning on entering the field, to have a good understanding and grounding in statistical methods.

Currently the team teach their statistics course using GenStat. Given GenStat’s history in agricultural research it is perhaps no surprise that it is used as the phraseology and terminology reflects the language used in the biosciences. GenStat contains a huge range of statistical techniques; in fact you would be hard pushed to find a statistical test or routine not included in GenStat. However, it isn’t just GenStat’s inherent statistical strength or its history that makes it so useful to Dr Belkhodja and his colleagues.

GenStat’s straightforward Windows menu system means that the statistics is easy to teach and importantly easy for the students to pick up and understand, indeed Dr Belkhodja told me that the students are up and running with GenStat and statistical techniques within 3 teaching sessions. The self-explanatory menu system means that the statistical methods and concepts are easy to manage and understand. Combined with the speed and ease of importing any data from Excel (for example) into GenStat, and the lecturers at IAMZ can spend less time on the complicated syntax and more time on the analysis itself.

Given the students come from all over the world; GenStat also provides an added advantage for those coming from the developing world. When the students return, they can obtain a free copy of GenStat - as GenStat Discovery, to continue their research. So, in a world where “time is money”, students don’t need to learn a new package in their work environment; they can implement their learning and statistical understanding in a package they already know and trust.

More information on GenStat is available on the VSNi website and for more details on the work and courses of the IAMZ look here.

Product News

ASReml, now at version 2, offers free add-ons for supported ASReml licenses, for S and R. Details on how to download this can be found on the VSNi website. Users will need to install their existing asreml.lic license key in C:\program files\Common Files\VSN International\Licenses which will enable the R and S add on to work, once downloaded. If they do not have this directory then they will need to install the asreml.lic file in the Bin directory within R and or S.

Technical tip - User Support

Whether you are installing a new license key for the first time or a replacement license key because you have changed your PC, you may come across the below error message:

The reason for this error message is generally due to the following:

Sometimes neither of the above has occurred, which means that your PC may be generating a new MAC address each time you reboot, which keeps changing the Host ID every time you use the machine.

The only way that users can overcome the problem if this keeps occurring is by sending us their machine details. The way to display these is by opening up a command Prompt and typing in ipconfig/all and selecting enter. This will display their machine details which they then will need to send us, the Host name and Physical address, for us to send them a license key. This will then solve the problem of the Host ID error message appearing regularly.

Out and about with VSNi

Another successful Australian GenStat User Conference is underway; this year the agenda covers a variety of presentations from developers and users alike based on “Biometrics in Primary Industries and the Environment”. Thank you to the organisers; and all those attending who will help to make a successful event.

We’re always looking for events we can support and sponsor - so please send us details of any events you are organising or involved in, and as we decide on more events for the future we’ll list them on our website.

Latest training courses

The next training course is for Regression, nonlinear and generalized linear models in GenStat, scheduled for 5th and 6th March 2009 at The Paper Trail in Apsley, UK. To find out more or to book please look at the training page on our website.

As a part of our continued update and development of our courses, please let us know if you have any suggestions or topics for future training.

Don’t forget that we also offer specific on-site training if our current schedule doesn’t fit with your requirements. Please email the training team for prices and further information.

As a leading supplier to agricultural research it’s fascinating to watch the stir being created by articles on GM crops and the use of pesticides, especially with the proposed EU legislation. But it’s not necessarily clear which route governments and the industry should be taking…

From fears of poisoning the earth with misuse of pesticides versus the potential reduction in Europe’s food production and food price increases if some pesticides are banned, to the ethical and moral issues over genetically modifying crops at one end of the spectrum to the real need and ability to provide crops that can withstand pests, diseases, droughts or other climatic conditions. And now recent research suggests that some GM crops may even protect neighbouring non GM crops (American
Association for the Advancement of Science (2008 September 19) “Genetically Modified Crops Protect Neighbors from Pests”). Each side of the argument seems compelling, so what should we do?

One thing is clear, sound reliable research is required for sensible future planning. And that is something we at VSNi can help with. By providing outstanding data analysis software, specialising in the biosciences, throughout the world we can assist researchers in each area to come up with results and projections based on solid data analysis.

VSNi software is firmly rooted in the biosciences and agriculture. GenStat, originally developed by statisticians at Rothamsted Research in the UK, is still extensively used there today. Projects range from developing strategies to reduce the use of pesticides, improving production and quality of crops or by using the earth’s natural biodiversity to help improve production or crop yields and
reduce the need for pesticides.

Improving yields covers the simple definition of “more” to the quality of the crop and the ability of the crop to adapt to different environments. For example, researchers in a plant breeding department work on developing hybrids, which then need testing in large multi-year, multi-locations trials. The purpose of these trials is to select the hybrids which have the highest yield potential, and the best adaptation to particular environments. Here it’s clear that whilst crop yields can be
improved, there is very little purpose in doing so if they do not adapt well to their targeted environments. In these analyses GenStat’s REML has been particularly useful for spatial analysis of trials conducted on uneven soils and for meta-analysis of large trial datasets; this allows researchers to evaluate genetic gain and the general and specific combining ability. The crucial issue in this
instance is the ability of the chosen data analysis package to provide complex statistical approaches, in an easy to use way; i.e. experimental design, analysis of variance and mixed model approaches (REML), but in a menu system.

“The experimental design tools of GenStat are really excellent and user-friendly. I think that it is the only statistical program that offers complex statistical approaches that are extremely useful in agricultural research in a friendly, easy-to-use way.”Abelardo de la Vega, Advanta Semillas

Another aspect of increasing yields is how herbicides are used. Researchers in Latvia are testing for the effectiveness of different herbicides to control weeds and maintain crop safety. One such research project centred around surveys on flora in five arable fields in five regions of Latvia aims to assess the effects of crop rotation and crop husbandry practices. These projects are aimed at providing scientifically based information to help agronomists and farmers determine the need for
weed control.

GenStat’s REML techniques were key as the number of contributing factors varied and using this technique allows for the analysis of unbalanced datasets, and produces output equivalent to the analysis of variance. Researchers were able to include over sixty species of weed, and analyse the effect of the use of different herbicides, on different crops including the effect previous crops have on the
trials.

Another customer of VSNi’s is The Organic Research Centre at Elm Farm in the UK. The centre is designed to look at providing solutions that develop and support sustainable agriculture and land use. Based upon organic principles to ensure the environment’s health is as protected as possible, the research programs are conducted at the farm in Berkshire and across 25 other farms in the
UK. GenStat is primarily used in the wheat breeding trials, looking at how Composite Cross Populations (rather than specific varieties) perform under fluctuating environmental conditions.

“The great aspect of this new analysis is that we can use data from all 12 experiments, i.e. 3 years over 4 sites, to work out which of the varieties and populations are both yielding and reliable,” says Sarah Clarke, ORC, “we can also split the experiments into those that are organic and those that are non-organic, to see if the populations differ between systems.”

The aim is to produce wheat that performs well year after year in differing environments. It is therefore vital that the tools used by these researchers are reliable and provide sound statistical analysis techniques, so that the results from the trials are as trustworthy as possible.

ASReml is another such trusted product. Again born out of agricultural research requirements, this time in the analysis of 12 years of data from over 1000 wheat variety trials, today ASReml is used across the world by plant and animal breeders to help solve some of the big puzzles found in these areas. Its ability to handle the large datasets so often found in agricultural research is one of its main
strengths; indeed the National Variety Trials in Australia, handling data from around 600 trials across Australia in over 250 distinct geographical locations, rely on the results from their trials using ASReml to give reliable predictions on genetic value of different crops in different locations.

“ASReml is the package that helps farmers, breeders and crop variety evaluators obtain the most reliable predictions of genetic value for a range of crops grown in different environments; farmers can get the best information available about performance of varieties in their own location and make an informed decision,” says Professor Brian Cullis, Research
Leader for DPI Biometrics and leader of the SAGI (Statistics for the Australian Grains Industry) project.

Another key strength of ASReml is the accuracy, speed and flexibility of the complex two-stage linear models used in these trials.

But it isn’t just the big Western companies that benefit from our software. Since 2003 we have provided GenStat Discovery, (now at edition 3) to research and teaching institutes across the developing world. As Stewart Andrews, VSNi CEO says “there is no justification for poorer countries to not have access to high quality research tools. Their need for research based on solid,
reliable data analysis tools is as great, if not greater than the West’s; assistance to these countries should come in the form of providing opportunities for self help and self determination, not just aid or gifts.”

GenStat Discovery has become a key tool in the researchers kit bag; relied on by many agricultural institutes throughout the developing world; many of these researchers would not otherwise have access to data analysis software, nor would they be able to share their results and ideas with colleagues around the world.

“I have spent money on other software packages that fall short of my needs.” Ugwu Kenneth Okonkwo, University of Nigeria, Nsukka

For the CGIAR centres this is important, as they work closely with institutes in the developing world such as ILRI, ICRISAT or ICRAF, and need to be able to collaborate on research activities. It is the concept of trust that is so important in these types of trials and research projects; something that VSNi prides itself on. Our software is and has been trusted by
researchers for over 30 years. Trusted because of our history in agriculture - we understand the types of data and the analysis needs within this industry and trusted because of the sound statistical principles on which the software is based.

Technical tip - User Support

Felix Grant’s recent review of GenStat 11th edition mentioned many new features, including the ability to carry out partial or full canonical correspondence analysis (CCA) using a menu based system. Included on the menu is an option to plot a biplot of the results, showing how site or species scores are related to one (or two) of the environmental variables.

Another option could be to run the command CRTRIPLOT to see a plot of species scores, site scores and biplot scores of the environmental variables in a single plot. The user has many options including being able to plot the scores in a three-dimensional environment, add convex hulls and other graphics for grouped data and set the dimensions to be plotted. See the help file for a full list of options.

Read Felix’s full review of GenStat 11th edition, or download your trial copy of the 11th edition.

Out and about with VSNi

As we enter the last quarter of the year, the travel doesn’t stop for VSNi. A key event we are looking forward to is the Australasian GenStat User Conference, from 2-5th December at Marysville, Victoria. A packed agenda on Biometrics in Primary Industries and the Environment, and with many of our developers attending, it’s your chance to share ideas and quiz us face to face. More information and to register is available at their website.

Roger Payne once again attended the Joint Annual Meeting of the GSA, SSSA, ASA, CSSA, GCAGS, and HGS, this year, held in Houston on 5 - 9th October; this year speaking on “A Guide to Analysing Counts and Proportions in Complex Situations”, and specfically covering the methods of analysing counts and proportions from the experiments often found in agriculture and biology. It described the types of biological investigation that have led to the development of methods such as generalized linear
mixed models and hierarchical generalized linear models. His talk also showed how these methods extend the more familiar generalized liner models to allow you to take account of additional sources of error variation. For wrap up information on this event go to the event website.

If you are involved in organising an event which may be of interest to VSNi and our users please let us know.

Latest training courses

The next training course is for REML and multi-level models in GenStat, scheduled for 14th November at The Paper Trail in Apsley, UK. To find out more or to book please look at the training page on our website.

As a part of our continued update and development of our courses, please let us know if you have any suggestions or topics for future training.

Correction

In the last Newsletter we focussed on Dr Brian Miller, of the IOM, and his work in epidemiology; VSNi would like to make a correction to the report number listed, which should have read:IOM research report TM/07/06. Read the article again “http://www.vsni.co.uk/case-studies/the-institute-of-occupational-medicine/”>here.

As a part of VSNi’s on-going commitment to supporting educators across the world, we have launched GenStat for Teaching - a free version of GenStat for educators and students. In today’s world of tightening budgets and justification of spending it’s vital that those at the forefront of teaching and coaching the next generation of scientists can access the best tools for in statistical analysis. With GenStat for Teaching now available free to all students and teachers world-wide, there is no reason why students cannot be taught using the best.

GenStat is known across the globe for its world class statistical tools and data analysis capability; from linear modelling to ANOVA and REML, in fact all that teaching requires. GenStat does, after all, stand for General Statistics! Its history and pedigree provides its users with reliability, trust and security.

On top of this, GenStat is one of the easiest data analysis packages on the market, with a clear and straightforward menu system to guide users through their analyses, backed up with dialogue boxes providing hints and alerts. A Save Session facility allows GenStat to be tailored around teaching sessions, breaking down the steps to fit with the learning path. A snapshot of a session can be taken at any time, and restarted at a later date, with no need to run through all the analyses again. These two benefits alone make GenStat an ideal tool for teaching; couple this with extensive statistical tests included in the software and you have a powerful tool to aid the teaching of statistics and data analysis techniques.

Additionally all users have access to the resources on our website with training available and tutorials for regression and ANOVA.

Download your free copy of GenStat for Teaching here .

New edition dispatch changes

All supported users should by now have received their CD for the GenStat 11th edition, and we hope you are enjoying and benefitting from the new developments.

In an attempt to reduce our carbon footprint, we are hoping to limit the amount we physically dispatch. As such we would like to make future upgrades available as download only from our secure website, and no-longer send out CD’s where possible. Should you still require a CD to be sent please could you email us, otherwise we will email details of any new upgrade and send you the download link.

We hope you see this as a positive step, as we do.

Technical tip - User Support

For more support and assistance don’t forget our on-line user guides for both GenStat and ASReml. These guides have also been updated and revised to include help on GenStat Discovery and GenStat for Teaching. The guides have everything from getting started to detailed statistical analysis, including reviews on the underlying methodology, explaining the output and describing the GenStat commands. Look at the full list of available documentation on our website.

Out and about with VSNi

A list of where VSNi will be this year is on our website.

On 21st July 2008 an enthusiastic group of GenStat users and developers gathered at the Agri-Food & Biosciences Institute (AFBI) in Belfast for the 14th European GenStat Applied Statistics Conference.

The programme of 12 talks was split evenly between developments and applications, with topics ranging from forest fires and salmonella in Australia to sea birds in Scotland. More locally, Irish subjects involved tuberculosis in dairy cattle and sex ratio bias in gall midges. Other application areas included microarrays, microneurography, environmental assessments and the attraction of pollen beetles to oilseed rape flowers.

A broad range of statistical topics were covered, including generalized linear mixed models, hierarchical generalized nonlinear models and meta analysis, in addition to the more usual ANOVA, REML and regression analyses. New GenStat facilities were also described, with talks on survey analysis and the new facilities in the 11th Edition for canonical multivariate analyses, graphics environments and for using mathematical algorithms from the NAG Library.

We enjoyed excellent weather, and those staying on for the Advanced Linear Models workshop on the following day also enjoyed the excellent food, drink and ambiance of Belfast during the intervening evening.

We would like to thank AFBI for hosting the meeting, and especially the local organiser Alan Gordon (on the right in the picture below with Roger Payne).

On 5-9th October, Roger Payne is again speaking at the Joint Annual Meeting of the GSA, SSSA, ASA, CSSA, GCAGS and HGA in Houston, Texas. Roger will be presenting on A Guide to Analysing Counts and Proportions in Complex Situations, during a session on New Statistical Techniques for the Analysis of Agricultural Experiments. Roger’s talk will describe the types of biological investigation that have led to the development of methods such as generalized linear mixed models and hierarchical generalized linear models. It will show how these methods extend the more familiar generalized linear models to allow you to take account of additional sources of error variation, such as blocking in a field experiment, or parental effects in animal experiments.

If you are involved in organising an event which may be of interest to VSNi and our users please let us know by emailing us.

Latest training courses

We have an ASReml course on 24-25th September. This will be held by Dr Arthur Gilmour and will include an Introduction to Mixed Models and ASReml and on the second day Genetic Analyses for plants and animals. Participants are encouraged to bring their own examples, which can be sent direct to Dr Gilmour a month before the workshop for preparation. A similar workshop will also be taking place in Buenos Aires, Argentina 9-12th September to include the following areas:

An applied workshop on Mixed Models for Plant Improvement using ASReml and r is planned for 2-5th November 2008, at the University of Western Australia, Perth. The workshop will present advanced statistical methods for the design and analysis of data arising from plant improvement programmes. Topics will include the design and analysis of single/multi environment and single/multi-phase experiments. Methods will also be presented for the integration of molecular marker and pedigree information into the analysis (and design) of these experiments.

As a part of our continued update and development of our courses, please let us know if you have any suggestions or topics for future training.

GenStat in Epidemiology

GenStat is well known and highly regarded throughout the world in its historical core area of biosciences, and specifically in agricultural research. The breadth of statistical analysis covered is well documented on websites, review articles and the like. As are the importance of its pedigree, developed, tried, tested and used by agricultural statisticians; the birthplace of GenStat (Rothamsted Experimental Station) being also the birth place of modern statistics with the likes of Sir Ronald Fisher, Frank Yates and Professor John Nelder all giving GenStat a certain kudos in statistical circles and the bioscientist’s world.

More and more disciplines are relying on statistics to uncover trends, causes and to better understand relationships between various factors. One area that has always understood the importance of statistics is epidemiology - the study of factors affecting the health and well-being of populations. Epidemiology is a vital discipline underpinning evidence-based medicine, for identifying risk factors for diseases and health effects.

The epidemiologist’s work ranges from investigations into disease outbreaks, clusters and exposure-response relationships, which may include the development of regression models to test hypotheses and estimate risk coefficients. The epidemiologist’s work at the Institute of Occupational Medicine in Edinburgh is designed to provide reliable information about health effects and risks for occupational and environmental hazards, with a view to addressing public and industry concerns, and providing a scientific basis for policies to limit disease. So it’s easy to see how a statistical analysis system such as GenStat is a vital tool for these researchers.

The IOM has been using GenStat for several decades in their studies on public health in the UK. Originally set up as a charity in 1969 to research coalminers’ lung disease, to continue a research programme set up by the National Coal Board’s medical service, the charity has been independent since 1990, and now provides research, consultancy, laboratory and measurement services in relation to potential health problems caused by occupational and environmental exposures. All the research reports published by the IOM since 1969 are available for free download from the on-line library.

GenStat has been used in a variety of different analyses, including epidemiological or observational data, which typically requires a regression model of some kind (linear, GLM, GAM, LMM, GLMM etc). It is also used for analysing data sets from designed toxicology experiments and for analysing cause-specific mortality data in comparison with reference rates.

A recent study looked at mortality rates in a group of almost 18,000 coalworkers from 10 collieries recruited from the 1950s onwards and followed up until the present time, of whom about two thirds are now deceased. One aim of the study was to compare the observed rates from certain causes of death with the male population rates for those causes in the regions where the coal pits are located. The calculations produce standardised mortality ratios (SMR’s) and their standard errors, using standard epidemiological methods.

GenStat used each individual’s entry and death or censoring dates to amass the person-years in the cohort, tabulating them by region, year and age (using GenStat’s option for sequential tabulation). The SMR calculations then used GenStat’s table manipulation functions to organise observed deaths and calculate expected numbers, ratio of observed to expected (SMR) and its standard error, etc. The outputs included overall SMR, plus a breakdown on 5 year-time groups that show how the healthy worker effect exists in the early part of the follow-up. The study has also been able to show that the risks of developing certain respiratory diseases increase with increased exposure to dust. Detailed results are available in a final report.

The summary results of comparisons of mortality in cohort with external reference rates are shown below. The table shows, for chosen cause groups, numbers of deaths, age- year- and region-standardised mortality ratios (SMR) and 95% confidence interval.

The graph shows the Standardised Mortality Ratio (SMR) for all internal causes over the length of the follow-up period, with years grouped. The solid line is the SMR while the dashed lines represent the 95% confidence interval. The dotted line shows the SMR equal to 100%.

For any complex statistical calculations a software programme that is easy to use and reliable is crucial, but specifically in this instance GenStat’s table functions make the SMR calculations “beautifully simple to program.” (Dr Brian Miller).

The ability to understand the causes of health issues, what factors may lead to ill health or mortality in populations are of critical importance world-wide: so a sound, reliable data analysis system such as GenStat is vital to assist with analysis and help produce scientifically based recommendations and policies.

Our thanks to Dr Brian Miller of The Institute of Occupational Medicine for his help in producing this feature. More information on the IOM can be found here.

Images/Tables with permission from IOM research report TM/07/06.

We’re delighted to announce the release of the 11th Edition of GenStat, proving once again that GenStat is still at the forefront of statistical computing. As the choice for bioscientists around the world, GenStat 11 boasts increased statistical and mathematical modelling capabilities with the inclusion of the NAG routines.

New statistical facilities include canonical correspondence analysis, factor analysis and a new design algorithm to form optimal factorial and fractional designs. Existing facilities have been extended too, for example to provide multinomial regression, robust variogram estimates and least significant differences between REML means. There is a full list of the new features on our website.

Existing supported users can upgrade via our website now and a CD will be sent to the software site representative within 2-3 weeks. For information on upgrading to a supported license please email support .

Why not download and trial a free copy of GenStat 11th Edition.

New website launched

Phase 3 of the VSNi website is here.The driving aim behind this new phase is to be relevant content, we want to make the site an invaluable resource for GenStat users, and you can help. Take a look to see how you can get involved .

Technical tip - User Support

Trouble viewing your help files?

If you are running GenStat from a network server sometimes help pages may not display correctly within the GenStat help system. Instead of the help page an error message saying that the page cannot be found is displayed. This is a known Microsoft security problem and can be easily rectified by altering settings on the local client PC. The Microsoft knowledge base article no. 896054 provides a full description of the problem and a solution for how to configure the local PC to display the help pages.

Out and about with VSNi

Preparations for the 2008 European GenStat Applied Statistics Conference are well under way. The conference is being held at the Agri-Foods and Bioscience Institute (AFBI) in Belfast on Monday 21st July. The conference will focus on developments in the theory and practice of statistics in the context of GenStat. The programme covers a wide range of application areas as well as the development of new methodology. The key themes of the conference are:

• New statistical methodology in GenStat
• Statistical applications and consultancy
• Visualization and graphics

This event provides an excellent opportunity for statistics users with varied backgrounds to share experiences and to explore applications and advances in statistics. It will also bring current and potential users into direct contact with the developers of GenStat from VSN International, and enable them to influence future developments. The conference is followed immediately by a workshop on Advanced Linear Models, also to be held at AFBI on 22nd July 2008, the topics covered include:

• Extensions to generalized linear models such as GLMMs and HGLMs
• REML modelling of spatial and temporal variation
• New methods for design and sample-size calculation

To find out more about the events VSNi are attending in 2008 visit our website.

Agronomix are running an AGROBASE Generation II training course at the University of the Free State, Bloemfontaine, South Africa from 25-29th August. Click here to find out more about this event.

If you are involved in organising an event which may be of interest to VSNi and our users please let us know by emailing us.

Royal Statistical Society

On 3rd April the Royal Statistical Society’s Statistical Computing Section held a half-day meeting on Hierarchical Generalized Linear Models (a GenStat speciality!). John Nelder introduced the session with an overview of the theory.

Then our own Roger Payne showed their implementation (in GenStat), and explained his extension to Hierarchical Generalized Nonlinear Models.

He also ran through some examples to show their use in practice. Finally Mike Kenward of London School of Hygiene and Tropical Medicine talked about his collaboration with Youngjo Lee and colleagues on the use of hierarchical likelihood for missing data problems.

If you would like to know more, Roger and Youngjo will be presenting a short course on HGLMs at University College Dublin on 13th July, before the International Biometric Conference there.

Or you can look here to see Roger’s slides.

Latest training courses

Having invested in the best in data analysis, it’s vital that our users know how to make the most of the functionality in our products. With this in mind we are continually developing our training programme to cover both guidance on our software and statistical topics; these now include an Introduction to GenStat, Advanced Course for GenStat, ANOVA and Linear Modelling. In addition VSNi offer bespoke training to cover areas which our existing courses do not include. These courses are often designed around your actual data, helping to provide additional insight to the use of GenStat in your organisation and can be held either in our training rooms or onsite. One such example of this is a recent course held at Rothamsted for Rothamsted International fellows on GenStat Discovery:

“The course went very smoothly and the Fellows were all very appreciative and full of praise. Darren (Murray) did a really good job at getting them to practice tasks rather than just talk to them and this went down very well.”

As a part of the continued update and development of our courses, please let us know if you have any suggestions or topics for future training.

Planned training dates for later this year include an ASREML course on 23-24 September by Dr Arthur Gilmour, consisting of an Introduction to Mixed Models and ASReml, and on the second day Genetic Analyses in ASReml for plants and animals. Participants are encouraged to bring their own examples, which can be sent direct to Dr Gilmour a month before the workshop for preparation. A similar workshop will also be taking place in Buenos Aires, Argentina 9-12 September to include the following areas:

• Introduction to Mixed Models
• Introduction to ASReml
• Spatial Analysis Theory and Practise
• Start OWN analyses
• Factor Analytic Model
• Repeated Measures
• Multi Environment trials
• Basic QTL Theory and practise
• Completion of own analyses

Following the announcement of the opening of our Australian office in March, we’re delighted to announce the latest training courses being run in that region; details can be found on the website.

An applied workshop on Mixed Models for Plant Improvement using ASREML and R is planned for 2-5th November 2008, at the University of Western Australia, Perth. The workshop will present advanced statistical methods for the design and analysis of data arising from plant improvement programmes. Topics will include the design and analysis of single/multi environment and single/multi-phase experiments. Methods will also be presented for the integration of molecular marker and pedigree information into the analysis (and design) of these experiments.

VSNi is proud to announce the opening of a new office, based in Australia to support our customers in Oceania. More information is available on our home pages.

Masterminding REML

Some years ago, on a remote farm in deepest, darkest Lancashire was born a bouncing baby boy named Robin. An unfavourable encounter with an over-friendly cow at an early age didn’t deter the young Robin from an ongoing affinity with animals and the countryside. This affinity combined with an exceptional appreciation of figures eventually led to a very useful statistical advance.In 1971 Robin Thompson and Des Patterson co-authored a paper on the methodology of residual maximum likelihood that extended analysis of variance ideas to the analysis of unbalanced correlated data; and removed the bias in estimation of variance components present in maximum likelihood methods.Whilst on a long haul flight to Australia, before planes doubled as entertainment complexes, the lead in our story sat patiently scribbling what to the untrained eye could only be described as cryptic etchings. Young Robin however was not an early advocate of Dan Brown but toying with the conundrum of how to conduct variety trials with large unbalanced data sets. A flash of insight, a splash of red wine and the Average Information algorithm for REML estimation was born; the algorithm that underpins the mixed model analysis in today’s GenStat and ASReml programs. When asking about his inspiration for such a revolutionary find Robin modestly says “I guess I’m just good with numbers.”

The ongoing achievements of our Dr Robin Thompson, the supreme advancements of the REML methodology and the recognition of all parties involved simply couldn’t be contained in one editorial. Some intriguing chapters, if space were available, would include imperfectly worded application forms, complex travel budgets and the christening of a Spanish Plaza. But we must move swiftly on to the esteemed collaborators, without whom the evolution and accessibility of the REML/ AI algorithm would not have been possible.

Here we recognize the brilliance of Dr Arthur Gilmour and Dr Brian Cullis; who joined forces with Robin in the early 90s. By 1995, with the dawn of larger variety trials and ever expanding data, Brian, Arthur and Robin pioneered techniques that would eventually evolve into ASReml. Over the years ASReml has revolutionized the way we consider problems providing a platform to analyse huge and complex data sets. Today it is used across the globe providing a rich and flexible solution for the analysis of data sets commonly arising in the agricultural, biological, medical and environmental sciences.The ASReml user guide has been cited in over 800 refereed publications.

Despite his recent retirement Robin still spends a great chunk of his time at RRES - when I questioned as to why…. “ASReml 3 my dear” was his ever dedicated reply. ASReml 3 is being developed and we can look forward to many new features including the analysis of grouped data and extra flexibility for defining genetic relationships particularly for inbred varieties.

More information on the current version of ASReml is available here.

Technical tip - User Support

There are two highly useful and often overlooked sections of the website – the User Areas for GenStat and ASReml. They collate resources produced by GenStatters and ASRemlers for you.

We always welcome further additions such as any course notes or libraries you might produce that others could find useful. Please e-mail support with any contributions.

The GenStat area has a link to the vast resource of the GenStat discussion list with over a decade of searchable archives - you can put your questions to the most dedicated, helpful and experienced users of GenStat. If you’re not looking for specific help but are starting out then the kind people of Reading University and their partners have put together various course notes and an introductory guide. Should you want to look at extending what GenStat can do then the researchers from the Biometris department of Wageningen in Holland have put together a procedure library with nearly 50 new procedures for you to use.

The ASReml area contains the wonderful Cookbook by Luis Apiolaza to get you started, with a host of useful ASReml recipes and some real food recipes mixed in for good measure. If genetic analysis is to your taste, then the paper (pdf) by Julius van der Werf shouldn’t be missed. Lastly we have a whole host of user contributed tutorials from getting started to advanced modelling.

We would like to thank all the people who contributed the areas so far which form very much the life blood that keeps GenStat and ASReml successful. Please pass anything that you think might be useful onto us and we will put it up for others to use.

Out and about with VSNi

Our events list is beginning to fill up for 2008, with meetings throughout the world.Don’t forget to register for the European GenStat Applied Statistics Conference at the Agri-Food & Biosciences Institute (AFBI), in Belfast, Northern Ireland, on 21st July 2008, (which takes place immediately after the International Biometrics Conference). It will be followed by a workshop on Advanced Linear Models on Tuesday 22nd July (also at AFBI) for more details see our website.

For those wanting more on HGLM’s John Nelder (Imperial College), Mike Kenward (LSHTM) and Roger Payne (VSNi) will be speaking at an RSS half day meeting on “Hierarchical Generalized Models and Beyond: Theory and Implementation” on 3rd April 2008, for more information or to register look here.

To see where VSNi will be in the future look here.

If you are involved in organising an event which may be of interest to VSNi and our users please let us know by emailing us.

Latest training courses

The latest training courses - An Introduction to GenStat (25th February) and Regression, nonlinear and generalized linear models in GenStat (26-27th February) have just been held in Hemel Hempstead. More courses will be announced soon on the VSNi website, if you have any suggestions for future courses please do contact the VSNi training team.

VSNi photography competition

Congratulations to our winner, VP Prasanth from ICRISAT in India, with this beautiful picture of a uniform sprinkler entitled “A big leap towards Green from Grey”. Our winner receives £150 of Amazon vouchers.To see some of the other entries please look here. Once again thank you to all those who entered, we really enjoyed seeing so much of where you work and what you do.

Statistics and animal welfare

This donkey is seriously suffering with lesions on the spine. Obviously it must be the pack saddle that is causing the sores so let’s add extra padding under its pack saddle to make it better. If we’re lucky this might reduce the problem, but what if the problem is actually more complicated than that? What if the padding is important, but only when coupled with being dirty, or with rough handling from the owner, or a particularly awkward load? Then increasing the padding would be unlikely to make much impact, and besides, what type and thickness of padding would it be best to change it to? Many such welfare issues are faced by working equines in developing countries and the fact that they may be caused not by one obvious factor, but by many factors which are not always obvious and may interact with each other, is the underlying principle of the Risk Assessment project developed by the Brooke.

Historically animal welfare work abroad, has typically assumed the causes of such problems, but not necessarily known them or had evidence to support them. Hence treatment or prevention interventions may have been based more on assumption than fact.

However the Brooke takes a different approach. The Brooke is the UK’s leading overseas equine welfare charity, committed to improving the welfare of horses and donkeys in some of the poorest countries in the world. Countries where families are dependant on their donkeys, horses or mules for their work, and therefore the welfare of these animals can mean life or death for the family. And yet, many suffer through malnutrition, disease and injury due to poverty, misguided intention or lack of accessible or affordable veterinary care. Since 1934, the Brooke has been providing free treatment and training through their teams of mobile vets and animal welfare workers. They have been working hard to underpin their work with scientific evidence.

The Brooke believes in sustainable support. That is they look to finding long-term solutions to the problems and not just fixing them in the short term. To fully achieve this they need to understand what these welfare issues are and what causes them. This scientifically based approach is unique to the Brooke amongst animal welfare NGO’s abroad.

A Risk Assessment Team, headed up by Amanda Childs, studies welfare issues individually to identify and understand the root causes of the problem. Her team visit the communities and observe, measure and record data on all sorts of issues surrounding the problem being assessed. This data is then collated and analysed using GenStat to understand which are the key factors contributing to the welfare issue. The long term aim being to eliminate these welfare issues by designing specifically targeted interventions.

For example, a study in Mardan and Gujranwala in Pakistan found that 70% of the horses, mules and donkeys pulling carts had lip lesions. The animals were in considerable pain from the lesions alone, let alone any secondary effects such as lack of ability to eat adequate feed.

The assessments are always incredibly detailed, and this one in Pakistan was no exception: 203 measurements and observations were made on more than 370 animals in a month. The data included many characteristics of the bit in the animal’s mouth, from its overall design to its rustiness, size and cleanliness. Close observations of the driving behaviour were made, such as the frequency with which the reins were pulled, any beating and the style of loading, as well as many other measurements taken from the working environment, the cart and bridle, and of course the animal itself.

The Brooke Risk Assessment staff has been training in statistics and the use of Genstat for the last two years. Their knowledge of Genstat not only allows them to present their work graphically and descriptively, but to analyse the relationships between the welfare issue (outcome) variables and explanatory variables, predominantly using linear and logistic regression analyses. The ’screening test’ facility enables them to explore both univariate and multivariate relationships far more quickly than with any other software, while the ability to calculate both conditional and marginal tests for linear models makes it quick and easy to identify potentially confounded variables.

The results of the lip lesion assessment were fascinating and showed that 20 different factors contributed to the lesions. Specifically these factors could be split into 4 groups:

1. the bit

2. the attitude and behaviour of the owner

3. the animal itself

4. the cart and harness.

The detail of the results mean specific advice and help can be offered to the animal’s owner, who depend on these animals for their livelihoods. Information about the type of bit to use, the use of a nose band and the best ways to drive the animals…in all 17 recommendations have been made by the risk assessment team, which can be used in the animal owning communities to dramatically reduce if not eradicate the problem of lip lesions on these animals.

The ease of use of GenStat’s menu system has meant that the Brooke’s field staff can now produce their own statistical analysis of the issues and are increasingly keen to do so, despite not being statisticians by training. Indeed most of the staff has veterinary or bioscience backgrounds. Therefore a system which provided world class statistics at the drop of a menu was vital. The aim for all these staff is that with GenStat all the Brooke’s field centres will be independent and able to perform their own analysis, where previously the data was sent to UK consultants.

“When choosing a statistical programme we presented 3 different programmes to our field workers and let them decide which one they felt would be most suitable. The final decision, based on the ease with which data could be manipulated and the ability to clearly see how the programme would be used in our specific context, was unanimously in favour of GenStat.” Amanda Childs, Head of Risk Assessment, the Brooke.

GenStat has made an enormous difference to the Brooke’s ability to easily and quickly analyse their own data and in Amanda’s words has provided the opportunity to “bridge a huge gap” between the need to provide quality data analysis and the need to get that done in a way that is locally sustainable.

Our thanks to the Brooke for their help with this article. All photographs in this article are courtesy of the Brooke.

More information on the Brooke.

Imagine being a painter with no brushes, or a builder with no trowel, or a chef with no wooden spoon… It would be very difficult to do your job; there are ways around it - but it might make your job much harder and take twice as long. All of us need the right tools to make our jobs easier and make the results better.Now let’s imagine being a researcher or scientist, but not be able to access professional software to help with your analysis. Well, strictly speaking you can access the software, but the cost is too great for you or your organisation. This unfortunately is the reality for many universities and research stations in the Developing World; the repeated cry is inadequate infrastructure, lack of funding and little access to literature.

“This problem has now been solved with the release of GenStat Discovery Edition 3, professional statistical software that is free for non-commercial users such as government researchers, lecturers and students in developing countries” says Ric Coe, who heads the Research Methods Group in Nairobi, Kenya. This is a joint unit across two CGIAR centres that trains and gives advice to researchers on how to improve their research.

I spoke to Stewart Andrews (CEO of VSNi) to find out more:

What is GenStat Discovery and what is the story behind it?

Stewart: GenStat Discovery is the full version of GenStat but available only to non-commercial organisations in the Developing World; it’s as simple as that. We know that GenStat is a very powerful and easy to use statistical software system; and that it has features that are useful when doing research on agriculture, biosciences and related disciplines, including climate change. Africa is a continent where the effects of climate change are noticeable and can be dramatic i.e. even a small reduction in rainfall can affect the crop yields dramatically. We also know that many African institutes cannot afford to buy professional statistical software; so in 2003 we launched the first GenStat Discovery Edition - a free version of GenStat, initially only in Africa. The response was so positive that we made it available to all developing countries the following year, and we have continued to support this since.

But why are VSNi giving their software away? Surely a charitable donation would be easier?

Stewart: We believe that we have a social and moral responsibility to assist where we can. A single charitable donation would provide financial aid at that time, but we believe that it is better to give people the ability to solve their own problems in the long term; and therefore be able to plan for the future better…for example one of my great frustrations is when my computer stops working and I ask for help; what I actually want is the ability to solve the problem in the future, not a one off fix. By providing researchers and scientists in the Developing World with a tool for analysis and prediction and the support that goes with that I believe we are giving everyone a fair and equal chance to access the best in data analysis systems so no matter where you are in the world you need not necessarily be hampered by lack of resource.

So who pays for it?

Stewart: The supported users from the developed world essentially pay for it - as without them and their business we could not provide GenStat Discovery for free. We are a commercial organisation, not a charity; therefore we have commitments to our employees and our board. However, the more business we do - the more we can help organisations from developing countries, who do not have the financial capacity to purchase GenStat. Having said that, our prices are not inflated to cover this project; GenStat is priced fairly throughout the world - we see this as putting our ethics into practice.

Research is about giving information to people so that they can make decisions based on hard evidence and at the same time have an idea about risks and uncertainties. If people have access to information, they can start to make informed decisions; information can open minds to ideas and doors to the future.

GenStat Discovery 3 was launched in November 2007 in Nairobi, Kenya and Kampala, Uganda. This picture is of Wim Buysse (Flemish Association for Development Cooperation and Technical Assistance), Professor Adipala (RUForum) and Ric Coe (ILRI). GenStat Discovery 3 is available direct from VSNi, simply follow the link below to download your copy. In Africa, a free CD-Rom is available from RUForum, the Regional Universities Forum for Capacity Building in Agriculture. The license key for GDE3 is automatically installed from the download version and CD-Rom, but expires at the end of 2008. To renew your license key and receive information on Discovery and related projects, register on the VSNi website - see below.

RUForum is an initiative by a consortium of 12 universities in east and southern Africa, to develop and strengthen human resource capacity for inter-disciplinary problem-solving. For more information go to or email.

For more information on GenStat Discovery 3 go here

Graphics environments, a new feature in GenStat for Windows® - Tenth Edition

GenStat provides control over the appearance of graphs so that they can be customized to suit your needs. Amongst other things, you can choose tick mark positions, axes label directions, line styles, colours and symbols of points, and switch grid lines on or off. Together these settings define a graphics environment. You can modify the graphics environment by using the menu provided (Tools | Graphics Environments) or by using the GenStat commands FRAME, XAXIS, YAXIS, ZAXIS, PEN and COLOUR. Graphics environments can be saved to files that can be loaded back into GenStat using the DSAVE and DLOAD commands. So, you can create a graphics environment to suit a specific project or publication and save it to a file so it can be shared with colleagues and used again when similar plots are required.

Here is an example where the same data is plotted using the default graphics environment and again using a customized one. This customized graphics environment uses larger sizes for symbols, axes labels and the plot title as well as adding gridlines, sub tick marks and a box around the plot and placing the tick marks on the inside.

Out and about with VSNi

We’re pleased to report back on Professor Roger Payne’s (VSNi’s CSTO) invited talk at the International Annual Meeting of the American Society of Agronomy, held in New Orleans. The ASA had invited Roger to give a special lecture entitled “Fisher, Yates, Nelder and Thompson: The Development of Statistical Design and Analysis Concepts at Rothamsted”. The lecture was the first of three in a symposium called “The Role of Statistics in Agricultural Research: Past, Present and Future”. Rothamsted Research, probably the oldest research station in the world, saw the beginnings of statistics. This led to the development of GenStat, now of course developed by us at VSNi. Go here to see Roger’s slides. While at the conference, Roger also met with Dieter Mulitze of Agronomix, developers of the Gen II database, and demonstrated the links between Gen II and GenStat to visitors at the Agronomix stand.

Biometricians the world over would no doubt have wanted to join the IBS Australian Region Conference - Biometrics by the Beach, where an exciting scientific programme included Professor Ari Verbyla talking on Whole genome analysis of QTL, including analyses of various experiments presented using an implementation of the approach in the ASReml software. This picture shows Ari with VSNi technical developer David Baird and our good friend Maryann Ebsworth.Don’t forget to register for the European GenStat Applied Statistics Conference at AFBI, in Belfast, Northern Ireland, from 21st- 22nd July 2008, for more details see the event page.

To see where VSNi will be in the future look here.

If you are involved in organising an event which may be of interest to VSNi and our users please let us know by emailing us.

Latest training courses

Don’t forget to check out the latest VSNi training course schedule to find out when your nearest course will be held, or email us to request a specific event.Another new course has been developed and is being held in February 2008 in Hemel Hempstead on using Regression, non-linear and generalized linear models in GenStat. The course shows how GenStat’s menus guide you from simple to very complicated analyses. It aims to familiarize you with these techniques, and give you the underlying knowledge and confidence to use them correctly and effectively.

Some familiarity of GenStat is necessary and a practical experience of the standard probability distributions (Normal, binomial and Poisson), but there will be no need for any complicated maths. On each day the lectures will be interspersed with practicals to introduce you to real-life data sets and illustrate the methods. The practicals also give you the opportunity to discuss your own problems and investigations with the presenter.

For more details on this Regression, nonlinear and generalized linear models in GenStat course, or to book a place and for more information view the current course schedule, or contact the VSNi training team.

VSNi photography competition

The photography competition has now closed and we will be announcing the winner in the next Newsletter. Thank you to all who entered.

Why Piglet needs GenStat

For those who know and love the Christopher Robin stories by A. A. Milne, you’ll know that Piglet’s favourite food is acorns. Given that Piglet, like all of Christopher Robins’ friends, lives in The Hundred Acre Wood, you would think that Piglet’s food should be easy to find…after all The Hundred Acre Wood is in England, acorns come from oak trees, and oak trees are common enough in England…But what if it wasn’t that simple? A typical English woodland usually comprises a variety of different deciduous and evergreen trees…all of whom are fighting for survival against each other, against groundcover/vegetation and damage from squirrels, deer etc …so how can Piglet be sure that the mighty oak will survive and regenerate to produce more of his beloved acorns?

Well, perhaps GenStat holds the key…a recent study undertaken by Forest Research[1] on oak regeneration indicates that a number of factors can affect the regeneration of oak trees - such as the amount and type of groundcover that is best suited for oak seedlings to survive, how far the seedlings are from the parent tree, and therefore how much the canopy might need cutting back…and so the list goes on. But with the help of GenStat’s Generalised Linear Models, Piglet could investigate the relationships between location and vegetation variables, and seedling data; linear regression could be used to analyse the height and diameter of seedlings and vegetation cover. Piglet would need to analyse this experiment over many years and take many measurements, therefore the mixed model facilities in GenStat would help to manage the issues of unbalanced data…

So with a little statistical analysis, time and a great software package like GenStat, Piglet could learn to manage the woodland for optimum acorn production…well, providing Christopher Robin lets him borrow his computer…

[1] Development of Quercus robur advance regeneration following canopy reduction in an oak woodland, Ralph Harmer & Geoff Morgan, Forestry 2007 80(2): 137-149

The original article featured in Forestry and Timber News (Dec 07): Statistical software in forestry research, can be found here (as a pdf):

Seasons Greetings from VSNi

Finally, we wish you all a very Merry Christmas and Happy and prosperous New Year from all at VSNi

VSNi were lucky enough to attend and be involved with the TIES 07 conference, held in beautiful Mikulov in the Czech Republic from 15 - 19th August. It was an interesting event for VSNi, and here’s a brief interview with the VSNi attendees (Stewart Andrews and Darren Murray) about it:

Why did VSNi attend TIES?

Stewart: The environment and climate change is an issue for all of us, and as human beings we have a moral obligation to investigate and understand changes that may be occurring to our environment and to assist in stopping, or alleviating the devastating effects to the globe.

What did VSNi do at the conference?

Stewart: Darren, our principle developer specializing in ecology and the environment, presented a talk on GenStat and the environment in the opening session of the conference; and I was delighted to be invited to chair the session on Software for Environmental Data Processing. As with many other sessions during the conference, we both found that the questions and comments stimulated from the presentations and afterwards were extremely interesting and valuable in understanding how we can help our colleagues in these fields in the future.

Who goes to TIES?

Stewart: Statisticians, modellers, bioscientists, environmental scientists, lecturers, students - a whole range of people who are interested in this area. And it was great to meet up again with our users in these fields. It’s always fascinating to see GenStat being used in real life issues and to understand more of what and how it works in different subjects.

So was GenStat the only tool being used?

Darren: Wherever you look you always come across R, but as people are aware GenStat can run R scripts, allowing researchers to use both products in tandem; similar to WinBUGS added in the 10th edition.

What happens next?

Darren: We made many new friends and started new collaborations, which we are really looking forward to working with and on. These collaborations will inevitably lead us to expand GenStat’s tools to aid all our users. And, there is always the TIES conference in Vancouver next year, which we hope to be deeply involved in so we can continue our collaboration with all the people we met this year.

If you are working in environmental research or related topic, VSNi would be very interested to hear about what you’re working on, methods you are using, software used, and how you feel the current software available is answering your needs. Please email us with your comments and questions.

Out and about with VSNi

VSNi will be attending a number of events in the coming months - to find out where we will be click here. Professor Roger Payne, VSNi’s CSTO is an invited speaker at the ASA-CSSA-SSSA Annual Meeting in New Orleans from 4-8th November for more information check the website. Roger will be speaking on “Fisher, Yates, Nelder and Thompson: The Development of Statistical Design and Analysis Concepts at Rothamsted” and describes how agricultural research at Rothamsted has provided a stimulus to statistical research - for the benefit of biologists everywhere.

We’re also delighted to announce the European GenStat Applied Statistics Conference at AFBI, in Belfast, Northern Ireland, from 21st- 22nd July 2008, for more details see the website.

If you are involved in organising an event which may be of interest to VSNi and our users please let us know by emailing us.

Latest training courses

Don’t forget to check out the latest VSNi training course schedule to find out when your nearest course will be held, or email us to request a specific event.We’re pleased to announce a new course being held on 29th November in Hemel Hempstead on using REML within GenStat. The course is designed to introduce you to REML in GenStat, and give you the underlying knowledge and confidence to use it correctly and effectively. It shows how the REML menus guide you through even very complicated analyses, and also explains the REML commands so that you can program any non-standard analyses that you need.

Practical experience of ordinary analysis of variance is necessary, but there will be no need for any complicated maths. On each day the lectures will be interspersed with practicals to introduce you to real-life data sets and illustrate the methods. The practicals also give you the opportunity to discuss your own problems and investigations with the presenter.

For more details on this REML course, or to book a place and information visit the current course schedule, or contact the VSNi training team.

VSNi photography competition

Fancy yourself as a photographer? Well, don’t forget now is your chance to show us your skills, and to show us how you use our software. The VSNi photo competition is now open. For a chance to win £150 worth of Amazon vouchers, send us your photos via the online competition form. For full terms and conditions see terms.

GenStat 10th edition

GenStat 10 is now available for download or email us. This latest update covers new statistical functionality, improved graphical capabilities and current compatibility with Excel 2007 ® and Windows Vista ®. The new features, menus and extensions to existing functionality further broaden and develop the level of statistical and data analysis tools within GenStat. Visit the VSNi website for a full list of new features.

“GenStat 10th Edition, cements its position as tool of choice for bioscientists the world over,” says Roger Payne, CSTO VSNi, “this latest edition will be of interest to existing and new users across the wide biological science spectrum. This is evidence of our commitment to ensure scientists have access to the best in statistical analysis.”

Existing customers with support contracts should have received an upgrade CD, if you haven’t received this please email us.

VSNi are delighted to be involved in the exciting developments in teaching in Africa, and we’re pleased to include the following report from John Rowlands, one of the developers of the Biometrics and Research Methods Teaching Resource CD.

John Rowlands

“ The primary reason for producing the CD was associated with the knowledge that the teaching of statistics/biometrics at universities in some sub-Saharan African universities tends to be somewhat theoretical and not directly related to the real applied problems of biological research. One of the problems has been the lack of relevant text books. The Biometrics & Research Methods Teaching Resource has been developed to help fill this gap by providing statistical, biometric and research method knowledge in interactive, electronic form. A key feature of the CD is it contains 13 case studies drawn from a variety of real-life agricultural studies across East and Southern Africa. The Teaching Resource is for use by the teacher in class and allows him/her to take the students through the process that they are likely to encounter in developmental or applied research, namely Research strategy, Study design, Data management, Exploration & description, Statistical modelling and Reporting.

“Teaching guides are also included in the CD to describe these processes. These guides are not complete course notes. Rather their aim is to provide supplementary notes to lecturers and their students that cover some of the more practical aspects of biometrics. Each case study has a set of questions and a data set that the teacher can use with his/her students. Various photographs are included to illustrate the environments in which the case studies took place, and some case studies also contain short videos to illustrate study design and methods of data collection in the field. The CD also contains the CAST for Africa software (Computer Assisted Statistical Teaching) developed by Doug Stirling (Massey University, New Zealand) that enhances in an elegant and graphical way the understanding of elementary statistical concepts. Two of the case studies use InStat+, a useful teaching statistical package developed by the Statistical Services Centre, University of Reading, and this software is included in the CD too. Also Harvey Dicks (University of Kwazulu-Natal) has kindly provided a number of GenStat data sets drawn from a wide number of agricultural experiments.

“An important feature of the Teaching Resource is that it uses the GenStat statistical software for much of the data analysis. Each case study not only illustrates how to apply GenStat but also shows users how to interpret the outputs. A free version of the software known as GenStat Discovery has been produced by the developers VSN International Ltd , Hemel Hempstead, UK for non-commercial use in a number of developing countries. The software is available to lecturers, researchers and students to help alleviate the problem of limited access to professional statistical software. It is distributed in Africa by the ICRAF-ILRI Research Methods Group (RMG) on their Research Methods Resources CD. So far, over 7,000 CDs have been distributed across sub-Saharan Africa.

“The Biometrics & Research Methods Teaching Resource CD is also free and can be obtained from the RMG, contact Agnes Odanga. A web-based version is due for release shortly. With the recent introduction of the Teaching Resource these two CDs provide the opportunity for appropriate and effective use of statistical methods and, together, will help to improve the quality, not only of biometric teaching, but also of design and analysis of agricultural research.

The development of the Biometrics & Research Methods Teaching Resource was funded by the Rockefeller Foundation. Further information about the Teaching Resource can be obtained from either me or from Jane Poole of the RMG.”

Read more about GenStat’s support for African agriculture.

Out and about with VSNi

VSNi will be attending a number of events later this year - to find out where we will be click here. If you are involved in organising an event which may be of interest to VSNi and our users please let us know by emailing us.

Latest training courses

Don’t forget to check out the latest VSNi training course schedule to find out when your nearest course will be held, or email us to request a specific event. In addition to our own training courses, we’re delighted to report on courses led by some of our colleagues world-wide.The second in a series of workshops on “Statistics for Plant Breeding and QTL Analysis” was held at the Joodoburri Conference Centre on Bribie Island, Queensland, Australia, from 16-19 April. The thirty-four participants were drawn from diverse backgrounds in the disciplines of Statistics, Plant Physiology, Plant Breeding, Cereal Chemistry and Molecular Biology. Course presenters Brian Cullis, Ari Verbyla and David Butler presented informative and challenging sessions covering the latest developments in statistical methodology with applications in plant breeding and genetics. ASReml-R was the chosen package for workshop demonstrations and hands-on sessions.

The third workshop in this series will be held in Canberra on 23-26 July. This workshop will cover both the phenotypic and genetic aspects necessary for analysis of plant breeding and marker data. The workshop spans 4 days and includes:

• phenotypic analysis of individual one and two phase experiments
• combined phenotypic analysis of a series of experiments
• foundation concepts in genetics
• linkage analysis and QTL analysis
• practical computing sessions with the opportunity to analyse your own data
• the use of the R statistical package throughout the workshop, with learning of the package integrated and relevant to the material covered

For more information on this workshop contact the organisers. For the current course schedule visit the VSNi website, or contact the VSNi training team.

VSNi photography competition

Fancy yourself as a photographer? Well, don’t forget now is your chance to show us your skills, and to show us how you use our software. The VSNi photo competition is now open. For a chance to win £150 worth of Amazon vouchers, send us your photos via the online competition form. For full terms and conditions see terms.

Staff Changes

VSNi are pleased to announce the appointment of two new staff members, who join our technical team: Ian Channing and Alex Glaser. Ian Channing joined us in April from Credit Suisse where he spent five years working in the Risk Measurement and Management technology department. He has a breadth of experience across web design, database (including data warehousing) and desktop application development. He joined Credit Suisse from Imperial College where he did a four year undergraduate Masters in Mathematics and Computer Science. He continued his studies whilst at work, spending the past three years completing a Postgraduate Certificate (conversion course) and Masters in Economics at Birkbeck College. He is currently working on extensions to the website, including the e-store and the infrastructure for web demos etc. He will also be closely involved in ADVISE.

Alex Glaser joined us in February after completing his PhD at the universities of Surrey and Cambridge under the supervision of Professor Steve Brooks. His PhD involved computational routines for the calculation of time series models and he has had many routines incorporated into the Fisheries Science in R project. Previous work experience has included working in the Operational Research unit of the Department of Transport and teaching statistics modules to final year undergraduates at the University of Surrey. Since joining VSNi he has worked on Redundancy Analysis, False Detection Rates in microarray analysis and is currently involved in the analysis of Joint Regression and Associative modelling (with dropout) for longitudinal data.

Sadly we also have two staff departures to announce: Many of you have worked closely with Anna Kane, our long-time Customer Support Manager and more recently Training Manager and Carey Biggs, our Business Development Manager. With sadness we announce that both Anna and Carey have decided that it is time for them to move on from VSNi.

Anna’s relationship with GenStat predates VSNi from her NAG days when Anna joined NAG in 1994. Carey has been with VSNi for five years and as some of you may be aware has recently been on a 3 month sabbatical helping in an Orphanage in Africa and Carey has decided that she will not be returning to the UK. I know many of you have developed long standing relationships with both Anna and Carey and you may well miss them as much as we will.

Anna and Carey have been valuable members of our team and we are very sorry to see them go. With a heavy heart we wish them every success in their new ventures.

We are in the process of appointing new members to our commercial team, we are always interested to hear from interested candidates and should you be interested would be happy to hear from you. Our first vacancy can be found here.

We have recently changed the software we use for email newsletters, marketing bulletins etc. The previous software was not 100% reliable; particularly when removing contacts who no longer wish to be mailed. We have made every attempt to ensure those of you who have already requested not to receive the VSNi Newsletter, do not; however some of you may have inadvertently been emailed. We offer our sincerest apologies if this is the case for you, and ask that you follow the links below to remove yourselves again from the list for future Newsletters.

VSNi Appoints Industry-Leading Member to its Board of Directors

VSNi have announced the appointment of its first non-executive Chairman, Jim Cooper. As CEO and President of Maplesoft Inc., the leading developer of interactive mathematical software, Jim brings a wealth of technical and commercial expertise to help guide and steer VSNi in its future growth and development. Read the full press release.

Australian GenStat User Conference 2006

The recent Australasian GenStat User Conference was held in the idyllic surroundings of Victor harbour, SA from the 5th - 8th December. It was a demanding week with the striking scenery, perfect temperatures and fascinating sessions - but thankfully most people seemed to cope well.Enormous thanks to the organisers; these events are not easy to pull together - particularly when you have a day job. Thanks also to the invited speakers particularly Professor John Nelder for his intriguing discussions on HGLM’s and Roger Stern for his thought provoking insights into African statistics and the disturbing realities of global climate change.

Forums like this provide the perfect setting for us to meet and exchange ideas with the GenStat community as you continuously offer encouragement and suggestions for future releases. So folks, if you have any additions you may have thought of since the conference (our brains no longer hindered by the aftermath of free wine!) then do please let us know.

Here’s the wrap up of the conference, including pictures.

GenStat and climate change

Those of you who attended the Australasian GenStat conference will no doubt recall the provocative talks on climate change expertly delivered by Roger Stern. Roger, a member of Reading University, has many years experience in statistical climatology, statistical methods in agriculture and a strong involvement with Africa and many other developing countries. His topic of choice, climate change, is certainly the issue of the moment and rightly so. So what might be the impact of climate change in our future research? Tackling climate change begins with appreciation and awareness of climate variability - and the tools to analyse and begin to understand such. GenStat began addressing this issue some years ago with the incorporation of statistics of extremes and the processing of circular data in our 7th Edition release.Whether you are concerned with soya, pines or Israeli Friesian’s; from Africa to Australia to Ayshire and all those in between, climate change is expected to affect us all and we need to start considering the ramifications on our research.

If you wish to discuss this topic with the GenStat team or are working with climatic data and have any suggestions for future releases why not email us.

Latest training courses

Check out the latest VSNi training course schedule to see a few new additional courses in our training portfolio. Our public Core Skills, HGLM workshops, Introduction to ANOVA and GenStat Language courses are not the only activities keeping our trainers busy however. Our on-site courses, 1:1 coaching and bespoke training activities make sure that they rarely have a chance to rest on their laurels!If you have immediate training needs, a number of colleagues who all need GenStat training and would benefit from on-site training or you simply want some tailored coaching on a specific analysis you are having problems with, we are sure to have the training solution that’s right for you.

For the current course schedule visit the VSNi website, or contact the VSNi training team.

VSNi photography competition

Fancy yourself as a photographer? Well, now is your chance to show us your skills, and to show us how you use our software. The VSNi photo competition is now open. For a chance to win £150 worth of Amazon vouchers, send us your photos via the online competition form. For full terms and conditions see terms.

New starters

We welcome Rhianne Cosby, the newest member of the VSNi team. Her background is in customer service and her role within VSNi is Customer Support and Sales Administrator. She is working within the customer support, sales and marketing teams and also helping out in other commercial activities.

Rhianne says: “Over the last few weeks I have had the pleasure of corresponding with many of you on support issues and I look forward to dealing with the rest of you in the future. I am already struck by how nice and how incredibly enthusiastic VSNi software users are, and I look forward to being part of this lively community.”

GenStat in Africa

VSNi are supporting the following event taking place in Nairobi, Kenya in February 2007:”Teaching Biometrics and Research Methods: The Latest Resources” and includes the launch of the Rockerfeller funded Biometrics and Research Methods Teaching Resource CD which has recently been completed by John Rowlands and the WorldAgroforestry Centre.

This CD provides a rich resource of case studies throughout African agriculture with its problems, applications and use not limited to the needs of Africa. Researchers throughout the world will find this teaching resource a valuable aid to understanding the use of GenStat statistical analysis within their work.

Read more about GenStat’s support for African agriculture.

GenStat to AGROBASE Generation II Link

VSNi has collaborated with Agronomix Software, Inc., to develop a direct software link so that registered users of both software packages can achieve the significant benefits of using them together. Since the focus of AGROBASE Generation II is field research data, this collaboration offers some exciting possibilities for agronomists, plant breeders, and plant scientists.Specifically, VSNi has developed a suite of GenStat procedures so that users can store means and related statistics from ANOVA and REML analyses directly in Generation II through a special interface developed in Generation II by Agronomix Software. The procedure library and associated Help documentation are available for download and can be run within GenStat 8th Edition or later. This new feature is available in AGROBASE Generation II as of version 14.

The benefits of this software link are significant, and include the following:

• Access to mixed model (REML) analyses within GenStat for users of Generation II;
• Benefit from other analyses in GenStat;
• AGROBASE Generation II users may access other analyses in GenStat, although the means will not be stored, results can be printed as usual, or saved;
• Relational storage of field trial and plant breeding data.GenStat users who would like to ‘warehouse’ all their research data in a fully relational software system, and not worry about managing many files, can now benefit from AGROBASE Generation II in an efficient and direct manner. This will undoubtedly improve the productivity of GenStat users.The Agronomix website provides further information on AGROBASE Generation II and a trial version of AGROBASE Generation II.

Stewart Andrews, CEO

Hierarchical Generalized Linear Models HGLMs have been a feature of GenStat’s advanced statistics for several editions now, but until recently their use seems to have been restricted to a small group of specialists. This year, however, that looks set to change.The book Generalized Linear Models with Random Effects: Unified Analysis by H-likelihood by Youngjo Lee, John Nelder & Yudi Pawitan has been published by Chapman & Hall to give a full account of the theory. John and Youngjo’s HGLM algorithms have been reimplemented in a more efficient form, with the assistance of Roger Payne, in the 9th Edition of GenStat for Windows. There is also a menu in the 9th Edition allowing you to access and run many of the examples from the book.Finally, Youngjo and Roger have been running workshops on HGLMs at locations ranging from Spain to South Africa. So, if you need to allow for several sources of random variation but your data are not from a Normal distribution, why not give them a try?

Roger Payne, Chief Science & Technology Officer