VSNi is proud to announce the launch of GenStat for Teaching and Learning – a new free product based on the current Genstat 13, but amended to make it suitable for school and undergraduate students. The easy to use GenStat Menu system provides access to a wide range of standard statistical analyses, including: basic statistics, statistical tests (t, chi-square, nonparametric tests etc), regression (general models not just e.g. simple linear regression), generalized linear models, nonlinear models (standard curves and user-defined), analysis of variance, design of experiments and sample size, REML analysis of linear mixed models, multivariate analysis, six-sigma, survival analysis, time series and repeated measurements.

For full details of the key differences between GenStat for Teaching and Learning and the full commercial edition GenStat 13 please visit the website.

GenStat for Teaching and Learning is licenced at an institutional level, but individual trials are available by emailing support.

For researchers working with complex models and larger data sets, the Discovery Programme has been expanded to include ASReml Discovery. Recently launched ASReml Discovery is available to everyone involved in education, and also to non-commercial research organisations based in eligible countries. More details on ASReml Discovery and how to register for a copy can be found on the VSNI website.

Technical Tip – bootstrapping in GenStat

Bootstrapping is now a popular technique for estimating the variability of estimates from a given set of data while making no assumptions about the distribution of the data. The main assumption in bootstrapping is that the observations are exchangeable. In simple circumstances this means exactly that: so, under the “null hypothesis” of no differences between the treatments, the observed data values could have been allocated to any of the observed units. To bootstrap a data set, we draw a new set of observations from the exchangeable units by sampling with replacement from the original units. In each bootstrap sample, the original observations may be omitted or sampled one or more times.

With the launch of the GenStat Teaching and Learning Edition comes a new menu for bootstrapping, which will also be available in the 14th Edition later this year.

We can illustrate the use of the menu with data in the GenStat example spreadsheet Cane.gsh (in the GenStat Data folder). This contains yields of sugar cane under a range of levels of nitrogen fertilizer. The menu is shown in Figure 1.

Figure 1

We need to select the statistics to bootstrap from the choices in the drop-down list at the top of the menu; further boxes then appear to specify the data needed for that analysis. Here we have chosen to look at a linear regression between sugar yield and nitrogen. Running the analysis with the default options produces graphs showing the distributions of slopes and intercepts from the bootstrap resampling.

Figure 2

Figure 2 shows the distribution of the slope, and you can see that a slope of zero is outside the 95% confidence interval. So we can be confident that there is a relationship between sugar yield and the amount of nitrogen fertilizer. The menu produces the output below.

Other statistics available in the menu include means, medians, differences between means and medians, t-statistics and correlations.

The menu uses the BOOTSTRAP procedure, and you can look at the Input log to see how it does this if you want to use the procedure for more complicated analyses.

BOOTSTRAP needs a procedure RESAMPLE to do the analysis and calculate the statistics to be studied. This has a DATA option which passes a pointer containing the resampled data into the procedure. The STATISTICS parameter lists the estimates of the various for this sample, and the EXIT parameter returns a value of 1 if the estimation has failed and 0 otherwise.

The DATA pointer for RESAMPLE is created from the data structures that are listed for the DATA option of BOOTSTRAP. So DATA[1] contains the y-values (Yield), and DATA[2] contains the x-values (Nitrogen). The parameter of BOOTSTRAP lists names to be used to label the statistics in the output.

Figure 3

Figure 4

We can modify RESAMPLE if we want to use this as a template for another analysis, for example, an exponential regression. The easiest way to form the commands is to run the Standard Curves menu (under Stats | Regression Analysis) shown in Figure 3, and then set up the Save dialog (click the Save button) to save the estimated coefficients of the curve, as shown in Figure 4. After running this the Input log contains the following commands:

We can cut and paste this into the RESAMPLE procedure to bootstrap the analysis. We create a new text window (Ctrl+N), cut and paste the original RESAMPLE code to this window, and then paste the code above to replace the linear regression code. We need to make the following changes to exponential regression code we pasted in: change Yield to DATA[1] and Nitrogen to DATA[2], set the PRINT option of FITCURVE to * (unless you want output and graphs from the 100 bootstrap datasets!), return the 3 estimates in STATISTICS, and finally rename the parameters in the BOOTSTRAP statement to give the following amended program (with some additional editing to tidy up the code):

Running this program will now give bootstrap confidences limits for the exponential regression parameters. Figure 5 shows the bootstrap distribution of the parameter R.

Figure 5

So the new menu not only makes bootstrapping a straightforward process for many standard analyses, it also helps you to use the bootstrap for more complicated analyses. For more information you can either look at the on-line help for the Bootstrap menu, or the description of the BOOTSTRAP procedure in the GenStat Reference Manual 3 Procedure Library which can be opened by selecting the Procedure Library sub-option of the Reference Manual option of the Help menu on the menu bar.

Latest training courses

An Introduction to ANOVA and Design in GenStat is scheduled for 28th and 29th July in Pretoria, South Africa. More details can be found on the VSNi website.

Our training schedule is always being updated according to user requests and requirements, so do email support with suggestions and any specific requirements you have and check our website for new courses.

Out and about with VSNi

The 2011 events we are attending or supporting include: SUSAN at the University of Botswana, Gaborone, Botswana from 27 June – 1 July 2011, the Australian Applied Statistics Conference in Palm Cove, Tropical North Queensland from 12-15 July 2011. 58th ISI World Statistics Congress in Dublin, Ireland, from 21- 26 August 2011.

If you would like to meet with the VSNi staff at one of these events please email support to arrange the details.

We’re always updating the list of 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.

Other News from VSNi

Success for the GenStat sponsored Holy Trinity Mariners U9′s football team! After a disappointing 2-0 defeat in the cup final, the Mariners returned to form with a resounding 4-0 victory in their last game of the season making them winners of the Chiltern Church U9′s League. Well done Mariners!

The People’s Trust for Endangered Species has been at the heart of conservation in the UK and across the world since 1977. Despite its focus on raising funds and providing support for conservation projects the PTES still undertakes conservation work itself including a number of surveys. These surveys are as important as the conservation activities themselves and are an integral part of any conservation programme.

The PTES surveys and studies are run in order to help understand population numbers and changes; without understanding how a population is changing over time it is almost impossible to decide what, if any, conservation actions are required. Likewise once a project is underway the conservationists need to see whether the actions are making a difference to the species in question, and it’s here that the conservationists at PTES use statistical analysis, in the form of GenStat.

“It’s too big a task to count all the individuals in a population, so a sample is counted sometimes from sightings, sometimes from signs (tracks or droppings), which comes with its own “statistical error”, explained David Wembridge, of the PTES. “In addition, biological populations are naturally variable – population sizes fluctuate from year to year as prey-predator and environmental interactions change, and in order to spot underlying trends (whether a population is stable or declining in the long-term, for example), it’s necessary to statistical analyses of the data, in particular, so called trend analyses – which is what we use GenStat for.”

The problem with spotting underlying trends is that long datasets are needed, with data collected over a period of ten years or more. Hence the PTES run ongoing surveys, which are repeated annually; for example one such survey – the National Dormouse Monitoring Programme has been running for 22 years.

The graph below is a typical example of how the PTES use the survey data to understand the dormouse population.

Hazel dormice population index 1991-2007

“There is a significant, approximately linear, decline in the years up to 2000. This appears to continue after 2000, but levels off over the last couple of years.”

“From 2005 the population estimate exhibits oscillations of up to 25%. The 2007 population has a strong influence on the shape of the curve, so it will be interesting to see whether the 2008 results are high, suggesting the stabilisation of the population, or low, in which case the curve will be dragged back down again.” (National Dormouse Monitoring Programme, interim report 2008)

Although conservationists at the PTES use a small part of GenStat, it’s another example of how GenStat is an important facet in a bigger picture. Without the trusted and reliable statistical analyses to indicate changes to populations conservationists might struggle to decide where to deploy their efforts and actions.

Our thanks to the PTES for their help and advice with this piece. The PTES run several surveys – to find out more or to get involved look at the PTES website. For more information on other conservation projects using GenStat please go to the GenStat Conservation Pages.

Technical tip – correlation in GenStat

The correlation matrix describes the correlation among a number of different variables. In GenStat you can view this matrix graphically using the DCORRELATION procedure. An example of the correlation within and between two datasets is given below (to replicate go to Help -> Examples -> DCORRELATION).

Using the strip underneath as a key, high positive correlations between variables are given by dark red colours, whilst high negative correlations are given by dark blue colours. Greens, yellows and light blues indicate low correlation. (Note that the diagonal of the correlation matrix is not plotted, though this can be added via the SHOW option.) A key in the upper right hand corner indicates the position of the variables in our calculations, e.g. the red square shows the correlation between N and Axis_2. The dashed black line indicates the separation of our two datasets, so anything within the black lines can be considered the correlation between the datasets; using the PLOT option we can separate the three parts of our plot, as seen below.

Here we have used the COLOURS option to specify the colours we want representing the correlation values -1, 0 and 1 (blue, white and red respectively).

The DCORRELATION procedure can also be used on a single dataset or any symmetric matrix whose values are between -1 and 1, such as similarity matrices.

Latest training courses

Our colleagues from the University of Wageningen are running a three day course on Introduction to Mixed Model QTL Mapping Using GenStat at the Department of Genetics, ESALQ/USP, Piracicaba, SP. Avenida Pádua Dias, 11. Bairro Agronomia, Brazil on 13 to 15 December 2010. The course is designed for graduates and professionals interested in a flexible QTL mapping approach,applicable in standard situations (SIM, CIM) as well as more specialized situations (multi-environment QTL mapping, QTLxE, multi-trait QTL mapping, association mapping, in- and outbreeders). Familiarity with mixed models and quantitative genetics is recommended. For more information and to book your place please go to the website.

Our training schedule is always being updated according to user requests and requirements, so do email support with suggestions and any specific requirements you have and check our website for new courses.

Out and about with VSNi

Carey Biggs is attending and presenting at ASC/OZCOTS, in Fremantle Australia, between 6 and 10 December.

Simon Harding & David Baird, two of the VSN International software developers, will be presenting at the International Biometric Conference in Florianopolis, Brazil between 5 and 10 December.

Other events we are attending or supporting in 2011 include: SUSAN at the University of Botswana, Gaborone, Botswana from 27 June – 1 July 2011, the Australasian Applied Statistics Conference, Palm Cove, Tropical North Queensland from 12-15 July 2011. 58th ISI World Statistics Congress in Dublin, Ireland, from 21- 26 August 2011.

If you would like to meet with the VSNi staff at one of these events please email support to arrange the details.

With at least 1.3 million described species of insect, accounting for at least two-thirds of known organisms, it’s no wonder that entomology fascinates the human race. And yet understanding and studying insects is not just for those with an interest in the creatures; information and knowledge on insects affects farmers and agricultural producers who may wish to be able to control the populations living and feeding on their crops. With such huge numbers of species, it’s easy to imagine the potential damage to crops, and why over the centuries humans have become fascinated with the control of these creatures, particularly in an agricultural setting.

Crop pests can take on different forms through their lifecycle, from larvae through to the final adult stage, and can cause havoc for farmers both above and below ground. The damage caused by insects living above the ground is often more easily identified and treated than the insects living below ground on the roots of plants, so crop losses from soil insects are often underestimated, and sometimes even not recognised as being caused by insects. White grubs, the larvae of chafer beetles, are one group of species for which this is true, with below-ground damage to plants often being extensive and in some cases causing the death of the plants. This complexity is further compounded by the fact that some soil pests feed on different plants at the different stages of their lifecycle, both above and below the ground. Scientists in India noted devastating effects on teak (Tectona grandis) seedlings in the nursery beds at the Ramdongari Forest Nursery in central India associated with the presence of white grubs, with the plant destruction causing severe economic effects. Little is often known about the biology and ecology of such white grubs, making them one of the toughest pests to manage, often leading to the high use of chemical insecticides, rather than Integrated Pest Management (IPM) schemes.

Teak is an important part of India’s economy by virtue of its timber quality, popularity and ever-increasing demand; it is highly prized by ship builders and manufacturers of outdoor furniture (amongst others) due to its ability to withstand most weather conditions. Combine this with the difficulty of managing white grubs, and it’s no surprise that Dr Nitin Kulkarni from the Tropical Forest Research Institute in Jabalpur, India chose to investigate the effect of the larvae of the chafer beetles Holotrichia rustica and H. mucida on teak seedlings. The area studied (Ramdongari Forest Nursery) accounts for around 500,000 to 800,000 teak seedlings per year and supplies seedlings for state forest departments and non-governmental organisations, including small farmers, across central India, so is of significant economic importance to the region.

The researchers observed and recorded data on the adult beetle emergence, their host preferences and populations, as well as the grub populations and damage to the teak seedlings. They found that typically the seedlings wilt due to the roots having been eaten, and often die. The insect count and plant damage data collected over the four years of the study were analysed in GenStat Discovery Edition 3, the free version of GenStat available to the developing world, using analysis of variance followed by the multiple comparison of means. Dr Kulkarni said “GenStat covers most of the statistical analyses and yet, is very user friendly with appropriate demonstrations.”

It was noted that the adult beetles emerged from the teak beds and became active at the onset of the monsoon season, when humidity had risen rapidly after pre-monsoon showers, and remained active for approximately 18 days. Importantly, they observed that whilst the adult beetles fed and mated on the leaves of jujube and other Ziziphus species, immature grubs of both species fed on the fine rootlets and main roots of teak seedlings. It has therefore led to the suggestion that it may be possible to control this pest with an IPM approach by targeting adults rather than applying chemicals against the larvae. With adult activity triggered by measurable weather conditions – falling temperatures and increased humidity – manual collection of the adults on the shrubs growing on nursery field edges appears one viable option for managing the pests without use of toxic chemicals, as part of an IPM program.

Information and results from research such as this has wider reaching impacts for entomologists looking at other white grub species, many of which are pests of food crops across the developing world. As well, the research progresses research into effective pest-management techniques, in this case on the chafer beetles in Indian teak nurseries.

Imagine needing to conduct research of this nature but with limited access to the appropriate tools, specifically appropriate data analysis software. Unfortunately researchers and scientists in the developing world don’t always have access to the tools they need for their work; however data analysis software is something they do have access to. With GenStat Discovery edition 3 these researchers were able to use high quality, respected and appropriate software to conduct their analysis, and so provide farmers – and in this case, teak nurseries – with relevant advice and assistance on the cultivation and protection of their crops.

GenStat Discovery edition 3, is widely used across the developing world to assist in analysing and visualising data. It is free to non commercial establishments across the developing world. For more details or to download look at the VSNi website.

Our thanks to Dr Rogers of Research Connections and Consulting and to Dr Kulkarni of the Tropical Forest Research Institute. Dr Rogers provides pesticide-efficacy data analysis services to the crop-protection industry and also assists authors with the preparation and submission of scientific publications.

The original paper (abstract) is available from Wiley Interscience

Technical tip – registration of GenStat Discovery

The GenStat Discovery licence is valid for one calendar year, but a new licence key will be automatically sent to you in December, irrespective of when you originally downloaded it if you register, meaning you never need be without it, nor do you need to download another version, at the end of the year.

Users who have obtained their copy of GenStat Discovery through an old or a colleague’s CD, may find they need to request a new licence key from support, if the GenStat Discovery CD was made prior to the current year.

To register your copy of GenStat Discovery visit the registration webpages.

Latest training courses

VSNi run training courses throughout the year on a variety of topics, and we are always updating the schedule. Our next courses on GenStat are scheduled for April 2010.

Introduction to GenStat will take place on Monday 19th April 2010 at Apsley Paper Trail in Apsley, Hertfordshire, UK. This course is aimed for those who need an overview of GenStat and the sklls to start them analysing and visualising data.

For users who are confident with the menu system and wish to develop their skills in programming in GenStat, the Introduction to the GenStat Command Language is being held on Tuesday 20th April 2010, again at the Apsley Paper Trail.

For more details or to book your place on either of these courses please register on line, or email support.

Courses at the Statistical Services Centre, University of Reading

We’re pleased to tell you of additional courses in statistics run by colleagues at the Statistical Services Centre at the University of Reading; all of which allow time for practicals for the attendee to put into practise what they have learnt:

E-SMS – a popular online course about understanding variability (next run scheduled 22nd March-10 May). It includes the essentials needed to describe data well (descriptive statistics) and to make good generalisations (statistical inference). It also covers the concept and uses of p-values, and establishes the groundwork for statistical modelling based on simple linear regression. Find out more at e-SMS website.

Review of Basic Statistics (19-20 April) – this course covers the basic ideas of statistcs needed in research systematically and quickly. Mathematical details are kept to a minimum, but concepts such as hypothesis tests, t tests, different distributions are all covered.

Regression Analysis: A Hands-on Approach (21-22 July) – Regression is a powerful technique for studying relationships between quantitative variables. Summarising relationships by the most appropriate equation (modelling) is very quick using Genstat. Find out more about the details on this course.

Introduction to ANOVA – (21-22 April) is a key technique popularly used in analysing research data. Every serious researcher needs to acquire skills in using this technique, and to have a good appreciation of the underlying concepts.

What Sample Size do I need? (1 December) Choosing an appropriate sample size is a common problem and should be given due consideration in any research proposal, as an inadequate sample size invariably leads to wasted resources. This course aims to give a practical introduction to sample size determination in the context of some commonly used significance tests.

More details on these courses and the Statistical Services Centre is available at the SSC website.

Out and about with VSNi

From 11-16 July 2010, VSNi’s CEO, Stewart Andrews will be presenting GenStat for Teaching at ICOTS8 in Slovenia. ICOTS8 in Ljubljana in Slovenia.

If you would like to meet with Stewart at one of this event please email Stewart Andrews to arrange the details.

We’re always updating the list of 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.

Our plans for 2010 and beyond are to continue to provide outstanding software for the biological sciences, across the world, and specifically to assist in areas where funding is limited – the developing world and education. As the Copenhagen talks come to a close we are mindful of all our responsibilities to support scientists and researchers working to understand and suggest solutions to the issues, by providing the best and most appropriate data analysis software.

To find out more about our software, and how it assists scientists and researchers visit our webpages, or email us for a free 60 day trial at support, with your name and organisation quoting reference VISION17CB, and we will arrange one for you.

We wish you all a very happy Christmas and successful New Year. This year we have opted not to send any Christmas cards, and to support the World Food Programme, Gift of Hope .

Please note our offices will be closed from 25th December to 28th December 2009, and on 1st January 2010 – we look forward to meeting and talking with you in the new year.

Best wishes,

Stewart Andrews
CEO, VSN International

ASReml 3, the outstanding data analysis software designed for fitting linear mixed models is now available for download.

Already widely used by scientists and researchers in the biosciences the new procedures and functionality added to version 3 further extend ASReml’s ability to analyse large datasets and complex statistical models. Since its original launch ASReml has enabled scientists to investigate and understand relevant factors in breeding and genetics leading to for example, the identification of superior grain varieties for farmers in Australia (based on the National Variety Trials system) and generating herd heritability estimates (based on research at the Pennsylvania State University).

ASReml is vital for researchers with very large datasets, who may need to apply complex statistical models. Unlike other software systems ASReml can easily and efficiently handle large datasets. ASReml is unique in that it uses the Average Information (AI) algorithm for the fitting of linear mixed models and it is optimised for working with genetics data and hence performs considerably faster than other generic data analysis software. The superior range of variance models are specifically suited to the analysis of data arising from genetic applications in animal and plants, so ASReml is chosen by researchers and scientists who need these specific analysis tools provided in ASReml. It also has an in-built link with R for scientists and researchers who prefer to use the r programming environment rather than more generic windows based systems.

It was and continues to be developed by researchers working in bioscience, so the statistics are sound, valid and most importantly relevant to the needs of bioscientists. Users are supported by VSNi (if they have a support contract), a range of tutorials and user guides and by an active user community through the ASReml Forum, available through the VSNi webpages.

For a free 60 day trial of ASReml please email support with your name and organisation quoting reference VISION16CB, and we will arrange one for you.

For more details on ASReml, look at the new features.

Technical tip – New supported platforms for ASReml 3

ASReml has now been updated to run on both 32 bit and 64 bit applications of Linux both as the stand alone command driven ASReml and as the ASReml-R add on. Additionally Apple Macintosh users can run also run ASReml in a batch mode.

Windows (32 and 64 bit) users can use ASReml 3 as the command driven version, Windows interface or as an add-on to R.

For a more detailed explanation see the ASReml webpages.

Latest training courses

VSNi run training courses throughout the year on a variety of topics, and we are currently planning the schedule for 2010. Please email support with any specific training requests or go to the training pages on our website to keep updated on the latest courses.

Out and about with VSNi

From 29th November to 3rd December, the GenStat developer Dr David Baird will be presenting at the International Biometric Society Australasian Region Conference. Dr Alison Smith, a keen ASReml user, based at Wagga Wagga Agricultural Institute is also presenting her work on grain quality testing with ASReml at the conference.

If you would like to meet with VSNi staff at one of these events please email Carey Biggs to arrange the details.

We’re always updating the list of 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 here.

The latest version of GenStat, the pioneering data analysis tool for bioscientists, is now available for download. This latest edition has been updated and enhanced to include a host of new and improved statistical techniques of particular use and interest to plant breeders and scientists working in genetic research.

Specific new features include the addition of stability co-efficients and genotype + genotype-by- environment biplots for use in variety trials, quantile regression and a suite of menus for QTL analysis. Enhancements to the GenStat graphics features include facilities to allow interactive selection between plotting components, which will assist with the interpretation of data – see the Technical Tip below for more details. GenStat’s existing core areas such as regression, REML and multivariate analysis have also been enhanced ensuring GenStat’s statistical techniques remain relevant, reliable and current.

“GenStat 12 is an outstanding achievement in terms of statistical capability,” says Stewart Andrews, CEO, VSNi, “and, importantly, demonstrates VSNi’s appreciation of the need to assist with solving the issues we all face. In an era of climate change, food shortages and food security, we have upgraded GenStat with statistical routines needed by scientists working to solve problems in world agriculture today.”

“One of the guiding principles behind GenStat’s development from its conception has always been careful consideration for scientific validity,” says Professor Roger Payne, CTO, VSNi, “GenStat’s history and pedigree provides users with the security of knowing that the results from GenStat analysis are founded on sound statistical principles. GenStat’s intelligent and well-planned menu system and comprehensive suite of diagnostic messages work together to guide users to the most correct and appropriate analyses for their data. In short, you can use GenStat with complete confidence.”

Also new in the 12th Edition is an interface to CycDesigN, the package for computer generation of experimental designs which constructs optimal or near-optimal block and row-column designs, via the GenStat menus. CycDesigN has been developed for scientists and researchers conducting experiments in field, glasshouse or laboratory trials, incorporating the latest research developments in experimental design. To obtain the CycDesign interface download the relevant files from the VSNI website, or for more information on CycDesign go to the CycDesign website.

For more details on GenStat, including a full list of new features and capabilities look at the VSNi website.

Technical tip – Interactive graphics in GenStat 12

Amongst the myriad of new features for the 12th Edition of GenStat, one of the more exciting is the ability to use the graphics interactively by making use of the ‘HOT’ components within the command DGRAPH, which allow the user to start with a basic plot and add elements to aid interpretation.

For example, the graph below shows a canonical variates biplot (figure 1) which makes use of another new feature for the 12th Release, the ability to plot oblique axes (see the command AXIS for further details).

Of the four groups here, we may be interested in plotting some extra features around one, or more, of the groups. For this, a hotmenu can be created and displayed in the Graphics toolbar giving you a drop-down menu of extra features that can be plotted (figure 2).

For this example we have several options, namely plotting the convex hulls or group means. If we select ‘Convex hull West’, ‘Group mean North’ and ‘Group mean South’ they will be added to the existing plot, as seen below. (figure 3)

Another element of the ‘hot’ components is the ability to select a point and plot extra information about that point. For this, we would use the hotdefinition parameter of DGRAPH. Selecting Hotchoice mode (the, new, rightmost button in the Graphics toolbar) (figure 4) allows us to select any hotpoints.

In the example we selected points 1 and 22 and we can now see the orthogonal projections from those points onto the four oblique axes. (figure 5)

More information about the ‘hot’ components can be found in the help for DGRAPH.

Latest training courses

On 15th September we’ll be running a course on REML and multi-level models in GenStat. The course is designed to introduce the user to REML in GenStat, and provide the underlying knowledge and confidence to use it correctly and effectively. It highlights how the REML menus guide the user through very complicated analysis and explains the REML commands so that users can program any non-standard analyses.

The course covers 4 main sessions:

• Analysis of variance
• Meta analysis
• Spatial analysis
• Repeated measurements

For more details on both courses and to book email support or go to the training pages on our website.

Out and about with VSNi

From 22-25th September Stewart Andrews (CEO) and Carey Biggs (Commercial Director) will be in Bangkok at the ABIC Conference 2009.

From 27th September to 2nd October we are back in Australia at the Barossa Valley for the Association for the Advancement of Animal Breeding and Genetics Conference.

Professor Roger Payne, our Chief Technical Officer is speaking at the ASA-CSSA-SSSA, in Pittsburgh between 1st and 5th November.

If you would like to meet with VSNi staff at one of these events please email Carey Biggs to arrange the details.

We’re always updating the list of 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.

Since starting work at VSNi it’s no surprise to find so many applications of our software, be it GenStat or ASReml, are working within some aspect of agricultural research; projects that range from development of new plants to new herbicides or pesticides. But this isn’t just a race to find the best, most productive type of grain, or the most effective pesticide, in so many cases this is linked to the welfare of the local ecology. More and more agricultural producers can now see a benefit of using the earth’s natural resources to assist in crop production.

Researchers at the New South Wales Department of Primary Industry in Australia highlight the complexities of farming using one of the more traditional methods of crop production. Southern Australian farms have long used annual legumes in the pasture phase of crop rotation methods. These act as natural disease breaks and restore soil structure and nitrogen in the soil, as well as providing valuable, high quality feed for livestock. Fantastic! In the panic of today’s world on pesticide poisoning this seems an ideal solution, and has certainly been a good one – here we are using the earth’s natural resources and traditional crop rotation methods to help increase production, and as a bonus create livestock feed.. however it is not that straightforward.

The problem with annual pastures and crops, is that they are often shallow rooted and therefore use less rainfall than the deeper rooted perennial species. This has led to a significant increase in groundwater recharge with higher water tables and dry land salinisation in parts of Australia where the agricultural production has meant a change from perennial deep-rooted species to annual crops and pastures. Simple answer! Surely we just swap the annual pastures and crops for perennial ones… but which one? Australia is a big country with a diverse range of climates. How then do you determine which perennial legumes and herbs are best suited to Australian conditions, with so much variation between regions?

A team of researchers headed by Guangdi Li took on the challenge. The purpose of their study was to evaluate a wide range of herbaceous perennial species as potential new species for incorporation into the farming system of Southern Australia. Guangdi Li’s team needed to identify species with an ability to adapt to a broad range of environments, and species which are particularly suited to specific soil conditions, environments and climatic patterns. They evaluated 91 perennial legumes and herbs (entries) at 10 sites across Southern Australia. There were originally 17 sites but 7 were abandoned because of weeds or poor establishment leaving 4 in Western Australia, 1 in South Australia and 5 sites in New South Wales. Only a subset of the 91 was sown at each site, local conditions not being conducive to the successful establishment of many of the varieties. In fact only a handful of the entries were sown at all the sites. Some of the sites were chosen because they posed environmental constraints to plant growth and hence could be used to identify alternate species that may be better adapted to these more demanding environments. Those constraints were saline or waterlogged soils, although drier than usual conditions minimised the effects of waterlogging. Over the three years of the experiment there were a number of occasions that herbage mass and plant frequency was assessed across the ten sites, creating 67 and 21 ‘environments’. Each environment provides information about the performance of the varieties, but of course successive samplings from the same site are not independent of each other, and a high correlation was expected.

ASReml was chosen to analyse this data because it can handle the estimation of the genetic correlations between pairs of environments. The analysis involves a mixed model in which the variance-covariance matrix of the entries in different environments is modelled using a factor analytic (FA) structure. The FA model facilitates the accurate prediction of entry means for individual environments using best linear unbiased prediction. Selection across a range of environments, be it the saline or waterlogged sites or even for those samplings taken in Summer for instance, is easily achieved by using the Predict facility in ASReml. Entries that showed potential in saline or waterlogged conditions can be targeted for inclusion in future breeding programs.

The complexities of this study very much reflect the complexities faced by the agricultural producers. In farming there are often no straightforward, obvious answers to the questions posed and the problems faced. This is why research and studies such as Guandi Li’s are so important; they give evidence based on sound science and statistical analysis techniques which show the importance of specific types of plants; in this instance Lucerne, which performed well over a broad range of environments. This in itself suggests projects are needed to fully exploit this plant so that its limiting factors (susceptibility to acid conditions and heavy grazing) can be overcome. Additionally Guangdi Li and his team showed that there is a range of deep-rooted perennial legumes and herbs which could be used in the Southern Australian farming system, rather than relying on a narrow range. The impact of the results of this and future trials are huge, it is yet another step closer to even better planned farming policies and methods, and hence to a true understanding of how we best feed ourselves and the world.

There is no doubt that sound scientific research is needed on which to base future crop, farming methods or policy decisions; research that is built using proven scientific tools. VSNi are a key provider of these tools; we know this because many agricultural scientists rely on us to continue providing high quality, relevant statistical analysis software built by statisticians who understand the complexities of agricultural research and data.

For more details on ASReml, its capability and why over 41% of papers presented at the last meeting of the Australian Association for the Advancement of Breeding and Genetics cited ASReml look at the VSNi website.

Technical tip – New Guide for Analysing Climatic Data in GenStat

We are delighted to announce a new guide which is available for download from the VSNi website. The new guide titled Analysing Climatic Data using GenStat, covers an introduction to GenStat, data input and basic data manipulation, simple statistical inference, including the use of boxplots and comparison of means and basic regression. After mastering the basics, the guide explains the summary and presentation of climatic data and then more detailed explanation of statistical methods including linear, non-linear, multiple regression and multivariate analysis. Finally, the guide assists users with GenStat programming for those who want to move from menus to more complex modelling and analysis.

Our thanks to the Statistical Services Centre at the University of Reading for this guide.

Latest training courses

New courses coming over the summer include:

• Introduction to ANOVA, 9th-10 July, Apsley, Hertfordshire, UK
• Introduction and Intermediate ASReml, 12-13 August, Apsley, Hertfordshire, UK
• REML and multi-level models in GenStat, 15 September, Apsley, Hertfordshire, UK

GenStat users who are looking for assistance with Analysis of Variance should book onto the Introduction to ANOVA on 9th to 10th July, in Apsley, Hertfordshire, UK.

The aim of the course is to introduce ANOVA techniques and develop the fundamental knowledge and skills to use them correctly and effectively. The basic principles of experimental design will also be included to aid the effective planning of experiments and investigations.

By the end of the course users will be able to:

• Select an experimental design appropriate to the requirement of your investigations.
• Use randomization to avoid bias in the allocation of units to treatments, to ensure that results are reliable and unaffected by any systematic patterns in the units.
• Determine how many replicates are required for your designs.
• Use blocking to increase the accuracy of an experiment by forming the basic units (e.g. plots or subjects) into groups with similar properties.
• Analyse simple to sophisticated designs, explaining ideas such as balance, and to recognise the GenStat features available for the analysis of unbalanced designs.
• Compare several types of treatment in the same experiment.
• Interpret experimental results and produce relevant tables, graphs and figures for publication in reports and papers.

Dr Arthur Gilmour is running Introduction and Intermediate ASReml Courses on 12-13 August again in Apsley, Hertfordshire. Participants will gain an insight into the concepts underlying ASReml and hands on experiences relevant to their own applications. Participants are welcome to prepare examples they would like analysed during the workshop and forward them before the end of July to support, so that the courses can be tailored to include specific user examples.

Day one will cover an Introduction to ASReml and simple univariate models. On day two participants will cover variance structures and be able to bring their own examples for discussion.

On 15th September we’ll be running a course on REML and multi-level models in GenStat. To take advantage of the early bird discount book before 31st July 2009. The course is designed to introduce the user to REML in GenStat, and provide the underlying knowledge and confidence to use it correctly and effectively. It highlights how the REML menus guide the user through very complicated analysis and explains the REML commands so that users can program any non-standard analyses.

The course covers 4 main sessions:

• Analysis of variance
• Meta analysis
• Spatial analysis
• Repeated measurements

For more details and to book email support or go to the training pages on our website.

Out and about with VSNi

We are delighted to be sponsoring two events in Italy – the ICORS 09 (International Conference on Robust Statsitics) in Parma from 14-19 June, and then later the EUCARPIA conference in Bergamo on 21-24 June.

This year we are looking forward to visiting old and meeting new friends when our CEO Stewart Andrews speaks on GenStat Discovery and the importance of agricultural research in Africa at the ISI 2009, in Durban (16-22nd August). Stewart will also lead a session on data analysis software for the developing world; more details to follow.

August is looking a busy time as we are also speaking and sponsoring the 14th Australasian Plant Breeding & 11th SABRAO Conference from 10-14th August at Cairns Convention Centre in Queensland.

From 2-4th September we’ll be in Dundee at the EUCARPIA 2009 XIV meeting of the Biometrics in Plant Breeding Section.

If you would like to meet directly with a VSNi attendee at these events please email Carey Biggs to make the arrangements.

We’re always updating the list of 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.

The links between GenStat and NAG go back many years, but did you know that you can now access many of NAG’s numerical algorithms from within GenStat?

For example, to solve the polynomial in Figure 1 (poly1) for y = 0, set the NAG option name equal to c02agf, the algorithm for solving zeros of polynomials.

Bee Breeding Secrets.

There is something about bees that trigger happiness in people. Whether it’s the thought of honey dripping on toast or admiration for the organisation and industry of the little insects, you don’t have to be a bee keeper to like these pretty and industrious insects. Honey in itself is also highly regarded, be it for the taste, or the health-giving properties that are increasingly being assigned to it. But bees are also important for the pollination in nature and therefore agriculture.

But a bee is not just a bee; different strains and species of bee have different characteristics and behaviour patterns, so bee keepers and breeders need to be able to identify specific strains in order that they breed the most suitable bees for their requirements. There are obvious physical aspects that can be used such as size, colour or shape, but these methods are not foolproof and often hide specific strain differences. Another option is DNA testing, but this is an expensive and time consuming exercise, therefore a method first identified and introduced before the 1960′s can be used, known as morphometry.

Morphometry is a study of bee anatomy to establish race or strain characteristics, that are otherwise difficult to ascertain. The types of anatomy studied are the wings, tongue length, Tomentum width (width of the band of hair on the body segments) and hair length. The most common test and study is on the bee wings, looking at vein formation. Specifically bee breeders look at the “cubital index”, which is the ratio between two vein segments of the cubital cell in a bee’s wing, and the “discoidal shift”, which measures the position of the discoidal joint in relation to the perpendicular through the distal lower joint in the radial cell.

The concept of understanding which bee strain or race is important for bee breeding; as the more purer bee strains can have a better temper (this is not always true, as some inbred bees can be very cross), and therefore there is a less chance of being stung, likewise they seem to keep cleaner and more organised hives than their hybrid cousins. Beyond these “housekeeping” issues there is the bees actual performance, for example researchers have found that certain strains of bee respond quicker to Spring stimulation than others, this is important if the bees are being used for pollination, as it means some strains of bees are more active earlier than others.

The more a bee keeper or bee breeder knows about his bees the more sure he can be about how they will perform and behave. And it seems beewing morphometry can give an indication of the strain or subspecies of Apis mellifera.

The Dark European honey bee, or Apis mellifera mellifera, is defined by having a cubital index of no more than 1.9 and the discoidal shift angle of no more than 0 (although these are ideal standards and not always attainable). Results from the measurements from any hive or colony are displayed on a scattergram and bee keepers and breeders can see how pure their bees are. Jacob Kahn has taken this research further and used GenStat to analyse the measurements more in keeping with quantitative population genetics. He doubled the sample size of 30, normally used by honey bee morphometrists, to a sample size of 60 . 10 of these have had their measurements checked for goodness of fit of normal distribution, and the results showed that only one did not conform to normality. He then looked at any correlation between the cubital index and discoidal shift and found that 6 samples displayed correlation. Jacob hopes that further research and work on this will verify his findings, which would suggest that any correlation indicates genetically purer samples. Jacob suspects that there is a misconception, especially among amateurs, as to what is pure and what is a hybrid. “The term hybrid is generally misunderstood by beekeepers,” says Jacob, “We can talk here about two levels of hybridization: a cross between species can be termed hybridization, but a cross between two strains within a subspecies carrying different alleles of particular loci can also be said to be hybrids. and it is this aspect of population genetics which I am hoping to clarify with the help of GenStat.”

At the moment bee keepers and breeders are content with looking at simple scattergrams to check for bee purity, however Jacob’s work shows that there maybe even more details to discover about bee species or strains. Either way GenStat’s sound statistics has enabled Jacob to dig deeper into the data and initial analysis to find out more about the bees. This additional level of information should allow better definition of variants of Apis m. mellifera which in turn gives bee keepers and breeders greater information on their hives and colonies so they can breed better performing bees.

For more details on GenStat and its capability look at the VSNi website.

Likewise to integrate the polynomial between the values -4 and 3, set the option name to d01ahf, the algorithm for simple integration.

At present many of the algorithms with regards linear programming problems, differentiation, integration and ordinary differential equations have been included. Integral equations and partial differential equations will be included in the 12th edition.

Go to the Help menu, select Examples, then Commands and open the NAG topic to see the full list of routines available as well as examples for each one.

For more information on this, look at Simon Harding’s (VSNi software developer) talk at the Australasian GenStat User Conference.

Latest training courses

For the more advanced GenStat users who are looking for assistance with Analysis of Variance, book onto the Introduction to ANOVA on 9th to 10th July, in Apsley, Hertfordshire, UK. For more details and to book email support or go to the training pages on our website.

The aim of the course is to introduce ANOVA techniques and develop the fundamental knowledge and skills to use them correctly and effectively. The basic principles of experimental design will also be included to aid the effective planning of experiments and investigations.

By the end of the course users will be able to:

Out and about with VSNi

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.

Elephants – their sheer size, incredible looks combined with intelligence, shyness and gentle nature are awe inspiring to most people; indeed is there a child in the world who is not wowed by them…so can you imagine a world without them?

It’s not news that elephants are endangered; for literally thousands of years ivory has driven hunters to kill these magnificent beasts. Combine this deliberate destruction with increased land use change and habitat transformation by private enterprise, international aid and government expansion across Africa and these magnificent beasts are still under threat even within the national parks and other protected areas set aside for them.

However, before we get too carried away with horrific idea that elephants may well become extinct; there is another side to this. Two separate taxa, or races, of elephants exist in Africa today: the savannah elephant, which is well known and has been studied and valued by the international tourist trade for decades, and the diminutive forest elephant, which until recently has remained in obscurity beneath the trees. In the Congo Basin, an area noted for being one of the great wilderness areas with the second largest rainforest on earth – it is home to an outstanding range of biological diversity; forest elephants have until recent decades thrived. These types of wildernesses have always been recognised for their high conservation value, being home to a wide variety of flora and fauna, and as such provide invaluable resources of timber, minerals and other natural resources. The Congo Basin is a typical case where the resources available are in high demand in rich, industrial nations and are also critical to the economies of poor nations. And it is at this point we in the Western developed world need to be very careful about conservation and conservation techniques; the international conservation efforts are aimed at managing and promoting sustainable natural resource exploitation and functional ecosystems. It is incredibly important that we recognise the needs of people in the developing world, and try to ensure they are able to exploit their natural resources in ways that do not fundamentally alter the ecology of the environment, upon which millions of rural people still depend.

The high value of resources in these wilderness areas means that it is only fair that Africans have an opportunity to exploit and benefit from them and are encouraged to do so legally, ethically and with an eye on their own local ecology.

Complications occur as industrial expansion pushes into the wildernesses to obtain these natural resources, an expansion that relies on a network of roads and rail infrastructure. It is this increase in roads that appears to be causing some of the biggest threats to the forest elephants. Illegal elephant killings tend to occur close to roads, since these areas are easily accessible, so the density of forest elephants in the protected areas is determined, not by the size of the area but by how many roads criss-cross through the wilderness.

Elephants are by their nature, shy and avoid human contact as much as possible, so how are they reacting to the increasing number of roads across their home ranges? Will they adopt a “siege” mentality and reduce their home range to avoid roads, or a “skirmish” strategy, where they will continue to range widely, irrespective of the number of roads?

I spoke with Stephen Blake of the Wildlife Conservation Society and Max Planck Institute of Ornithology who has recently headed up a study into this very issue. His team fitted a large sample of forest elephants in the Congo Basin with GPS telemetry collars, so that they could track their roaming behaviour. They collected data from 28 elephants located in conservation areas in the Congo, Central African Republic and Gabon.

Figure 1: Relationship between area of MCP home range and the area of road-less polygon; y axis – Home range size (kmsq), x axis roadless polygon size (kmsq).

Figure 2:Maximum linear displacement versus area of road-less polygon; y axis maximum linear distance moved (km), x axis roadless polygon size (kmsq).

“The data we collected covered the sex of the elephant, the site (the protected area in which the elephants were collared, the number of roads in the area, the number of days the elephants were collared,” explained Stephen, ” I initially analysed the result collected in GenStat, using linear regression for data exploration followed by fitting standard curves to the data (Figures 1 and 2). GenStat was vital in the research programme as I can trust the statistical procedures, I was able to talk directly with developers when I came up against any queries. I have found the Genstat support team to be extremely helpful, I usually get a response to a query within 24 hours and often much sooner. We could have gone much further with the analysis, but in order to understand the influence of roads on forest elephant ranging, the regression options in the Genstat menu showed us clear statistical patterns.”

Results indicated that the forest elephants routinely crossed protected roads, however only 1 elephant crossed an unprotected road, and of these one did so, as far away from the nearest village as she could, and her speed increased as she crossed the road.

“Our study showed that elephants seem to adopt a siege mentality with the encroaching roads”, said Stephen Blake, “and the issue with this is that over time the elephants will have less and less access to food, in quantity and variety, leading to food competition and aggression; both of which are likely to lead to a reduction in population.”

The main issue seems to be that elephants are risk averse, hence why they avoid roads where they can…so here we have a problem…central African states need the income earned from the natural resources found in their countries; but not only do we not want to see the elephants themselves to disappear, a change like that to any ecosystem is likely to have more wide ranging impacts.

“There are options for policies to overcome the issues, before it is too late,” says Stephen, “based on our research, we recommend that no new roads are built on existing forest elephant conservation areas, but to access the natural resources near these sites temporary roads should be built, so that once the resources are exhausted the area can easily return to natural wilderness. The other option is to try to reduce the elephants fear of roads, by preventing settlements on the roads, enforcing anti-poaching. These are of course expensive options, but without addressing this we face losing these beautiful creatures.”

More information on the Wildlife Conservation Society and its forest elephant project visit the Wildlife Conservation Society; and for more details on GenStat and its capability.

Find out more about the role GenStat plays in understanding elephants and their behaviour – this time in Kenya with Save the Elephants – as featured on the BBC, January 2009.

Technical tip – GGEbiplot procedure

A recent enquiry to VSNi’s forum asked about a procedure for GGEbiplot, based on GGE Biplot Analysis (2003) by W Yan and M S Kang (CRC Press). The procedure will be included in GenStat 12th edition, but several users have requested and received a sneak preview.

The procedure carries out a principal components analysis, to examine genotype (G) and genotype-by-environment interaction (GE) effects. Many different forms of plots are available to help determine how genotypes perform in certain environments. A simple scatter plot can have convex hulls added, which then can be used to divide the plot into sectors (Figure 1).

Alternatively, a comparison plot can plot many concentric circles, to ascertain the best performing genotypes in certain environments (Figure 2).

To obtain an advance copy, mail Support or register your interest on the Forum.

Out and about with VSNi

Look out for us at the World Potato Congress, from 22nd to the 25th March at Christchurch, New Zealand.

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.

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.