Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Using probabilistic graphical models to reconstruct biological networks and linkage maps
Wang, Huange - \ 2017
University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Hans Jansen. - Wageningen : Wageningen University - ISBN 9789463431538 - 150
probabilistic models - models - networks - linkage - mathematics - statistics - quantitative trait loci - phenotypes - simulation - waarschijnlijkheidsmodellen - modellen - netwerken - koppeling - wiskunde - statistiek - loci voor kwantitatief kenmerk - fenotypen - simulatie

Probabilistic graphical models (PGMs) offer a conceptual architecture where biological and mathematical objects can be expressed with a common, intuitive formalism. This facilitates the joint development of statistical and computational tools for quantitative analysis of biological data. Over the last few decades, procedures based on well-understood principles for constructing PGMs from observational and experimental data have been studied extensively, and they thus form a model-based methodology for analysis and discovery. In this thesis, we further explore the potential of this methodology in systems biology and quantitative genetics, and illustrate the capabilities of our proposed approaches by several applications to both real and simulated omics data.

In quantitative genetics, we partition phenotypic variation into heritable, genetic, and non-heritable, environmental, parts. In molecular genetics, we identify chromosomal regions that drive genetic variation: quantitative trait loci (QTLs). In systems genetics, we would like to answer the question of whether relations between multiple phenotypic traits can be organized within wholly or partially directed network structures. Directed edges in those networks can be interpreted as causal relationships, causality meaning that the consequences of interventions are predictable: phenotypic interventions in upstream traits, i.e. traits occurring early in causal chains, will produce changes in downstream traits. The effect of a QTL allele can be considered to represent a genetic intervention on the phenotypic network. Various methods have been proposed for statistical reconstruction of causal phenotypic networks exploiting previously identified QTLs. In chapter 2, we present a novel heuristic search algorithm, namely the QTL+phenotype supervised orientation (QPSO) algorithm, to infer causal relationships between phenotypic traits. Our algorithm shows good performance in the common, but so far uncovered case, where some traits come without QTLs. Therefore, our algorithm is especially attractive for applications involving expensive phenotypes, like metabolites, where relatively few genotypes can be measured and population size is limited.

Standard QTL mapping typically models phenotypic variations observable in nature in relation to genetic variation in gene expression, regardless of multiple intermediate-level biological variations. In chapter 3, we present an approach integrating Gaussian graphical modeling (GGM) and causal inference for simultaneous modeling of multilevel biological responses to DNA variations. More specifically, for ripe tomato fruits, the dependencies of 24 sensory traits on 29 metabolites and the dependencies of all the sensory and metabolic traits further on 21 QTLs were investigated by three GGM approaches including: (i) lasso-based neighborhood selection in combination with a stability approach to regularization selection, (ii) the PC-skeleton algorithm and (iii) the Lasso in combination with stability selection, and then followed by the QPSO algorithm. The inferred dependency network which, though not essentially representing biological pathways, suggests how the effects of allele substitutions propagate through multilevel phenotypes. Such simultaneous study of the underlying genetic architecture and multifactorial interactions is expected to enhance the prediction and manipulation of complex traits. And it is applicable to a range of population structures, including offspring populations from crosses between inbred parents and outbred parents, association panels and natural populations.

In chapter 4, we report a novel method for linkage map construction using probabilistic graphical models. It has been shown that linkage map construction can be hampered by the presence of genotyping errors and chromosomal rearrangements such as inversions and translocations. Our proposed method is proven, both theoretically and practically, to be effective in filtering out markers that contain genotyping errors. In particular, it carries out marker filtering and ordering simultaneously, and is therefore superior to the standard post-hoc filtering using nearest-neighbour stress. Furthermore, we demonstrate empirically that the proposed method offers a promising solution to genetic map construction in the case of a reciprocal translocation.

In the domain of PGMs, Bayesian networks (BNs) have proven, both theoretically and practically, to be a promising tool for the reconstruction of causal networks. In particular, the PC algorithm and the Metropolis-Hastings algorithm, which are representatives of mainstream methods to BN structure learning, are reported to have been successfully applied to the field of biology. In view of the fact that most biological systems exist in the form of random network or scale-free network, in chapter 5 we compare the performance of the two algorithms in constructing both random and scale-free BNs. Our simulation study shows that for either type of BN, the PC algorithm is superior to the M-H algorithm in terms of timeliness; the M-H algorithm is preferable to the PC algorithm when the completeness of reconstruction is emphasized; but when the fidelity of reconstruction is taken into account, the better one of the two algorithms varies from case to case. Moreover, whichever algorithm is adopted, larger sample sizes generally permit more accurate reconstructions, especially in regard to the completeness of the resulting networks.

Finally, chapter 6 presents a further elaboration and discussion of the key concepts and results involved in this thesis.

BasisRegistratie Ondergrond (BRO) Actualisatie Gt/Gd : beschrijving grondwaterkarakteristieken per Gt-klasse voor hoog Nederland
Stuyt, L.C.P.M. ; Knotters, M. ; Walvoort, D.J.J. ; Hoogland, T. ; Brus, D.J. ; Vries, F. de; Heidema, A.H. ; Okx, J.P. - \ 2017
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2797) - 51
grondwater - grondwaterstand - statistiek - nederland - groundwater - groundwater level - statistics - netherlands
Information on the depth and dynamics of the ground water level below the ground
surface, ‘Gt’, associated with the soil map of The Netherlands, is updated incrementally. Only recently
(2014), an updated Gt-map of the lower, western Netherlands was completed. A Gt-map of the higher
grounds was produced in 2016, based on ‘Gd’ information established in 2004. The procedures
followed and the results are reported in this volume. At this time, the compilation of a Gd map for the
lower Netherlands is due. After completion, in conjunction with the update of the ‘Gd’ data for the
higher grounds, a comprehensive, nationwide ‘Gd’ map of The Netherlands will be available.
Statistical methods for QTL mapping and genomic prediction of multiple traits and environments: case studies in pepper
Alimi, Nurudeen Adeniyi - \ 2016
University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Marco Bink. - Wageningen : Wageningen University - ISBN 9789462579361 - 153
capsicum - statistical analysis - statistics - genomics - quantitative trait loci - quantitative traits - quantitative methods - genetics - crop yield - statistische analyse - statistiek - genomica - loci voor kwantitatief kenmerk - kwantitatieve kenmerken - kwantitatieve methoden - genetica - gewasopbrengst

In this thesis we describe the results of a number of quantitative techniques that were used to understand the genetics of yield in pepper as an example of complex trait measured in a number of environments. Main objectives were; i) to propose a number of mixed models to detect QTLs for multiple traits and multiple environments, ii) to extend the multi-trait QTL models to a multi-trait genomic prediction model, iii) to study how well the complex trait yield can be indirectly predicted from its component traits, and iv) to understand the ‘causal’ relationships between the target trait yield and its component traits.

The thesis is part of an EU-FP7 project “Smart tools for Prediction and Improvements of Crop Yield” (SPICY- This project generated phenotypic data from four environments using 149 individuals from the sixth generation of recombinant inbred lines obtained from intraspecific cross between large – fruited inbred pepper cultivar ‘Yolo Wonder’ (YW) and the hot pepper cultivar ‘Criollo de Morelos 334’ (CM 334). A total of 16 physiological traits were evaluated across the four trials and various types of genetic parameters were estimated. In a first analysis, the traits were univariately analyzed using linear mixed model. Trait heritabilities were generally large (ranging between 0.43 – 0.96 with an average of 0.86) and mostly comparable across trials while many of the traits displayed heterosis and transgression. The same QTLs were detected across the four trials, though QTL magnitude differed for many of the traits. We also found that some QTLs affected more than one trait, suggesting QTL pleiotropy (a QTL region affecting more than one trait). We discussed our results in the light of previously reported QTLs for these and similar traits in pepper.

We addressed the presence of genotype-by-environment interaction (GEI) in yield and the other traits through a multi-environment (ME) mixed model methodology with terms for QTL-by-environment interaction (QEI). We opined that yield would benefit from joint analysis with other traits and so deployed two other mixed model based multi-response QTL approaches: a multi-trait approach (MT) and a multi-trait multi-environment approach (MTME). For yield as well as the other traits, MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. Many of the detected QTLs were pleiotropic and showed quantitative QEI. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.

The QTL methods considered thus far are not well suited for prediction purposes as only a limited set of QTL-related markers are used. Since the main interest of this research includes improvement of yield prediction, we explored both single-trait and multi-trait versions of genomic prediction (GP) models as alternatives to the QTL-based prediction (QP) models. This was termed direct prediction. The methods differed in their predictive accuracies with GP methods outperforming QP methods in both single and multi-traits situations. We borrowed ideas from crop growth model (CGM) to dissect complex trait yield into a number of its component traits. Here, we integrated QTL/genomic prediction and CGM approaches and showed that the target trait yield can be predicted via its component traits together with environmental covariables. This was termed indirect prediction. The CGM approach seemed to work well at first sight, but this is especially due to the fact that yield appeared to be strongly driven by just one of its components, the partitioning to fruit.

An alternative representation of the biological knowledge of a complex target trait such as yield is provided by network type models. We constructed both conditional and unconditional networks across the four environments to understand the ‘causal’ relationships between target trait yield and its component traits. The final networks for each environment from both conditional and unconditional methods were used in a structural equation model to assess the causal relationships. Conditioning QTL mapping on network structure improved detection of refined genetic architecture by distinguishing between QTL with direct and indirect effects, thereby removing non-significant effects found in the unconditional network and resolving QTL pleiotropy. Similar to the CGM topology, yield was established to be downstream to its component traits, indicating that yield can be studied and predicted from its component traits. Thus, the genetic improvements of yield would benefit from improvements on the component traits.

Finally, complex trait prediction can be enhanced by a full integration of the methods described in the different chapters. Recent research efforts have been channelled to incorporating both multivariate whole genome prediction models and crop growth models. Further research is required, but we hope that the present thesis presents useful steps towards better prediction models for complex traits exhibiting genotype by environment interaction.

Statistical modelling of variability and uncertainty in risk assessment of nanoparticles
Jacobs, R. - \ 2016
University. Promotor(en): Cajo ter Braak, co-promotor(en): Hilko van der Voet. - Wageningen : Wageningen University - ISBN 9789462578197 - 205 p.
modeling - statistics - particles - risk assessment - uncertainty - uncertainty analysis - nanotechnology - probabilistic models - modelleren - statistiek - deeltjes - risicoschatting - onzekerheid - onzekerheidsanalyse - nanotechnologie - waarschijnlijkheidsmodellen

Engineered nanoparticles (ENPs) are used everywhere and have large technological and economic potential. Like all novel materials, however, ENPs have no history of safe use. Insight into risks of nanotechnology and the use of nanoparticles is an essential condition for the societal acceptance and safe use of nanotechnology.

Risk assessment of ENPs has been hampered by lack of knowledge about ENPs, their environmental fate, toxicity, testing considerations, characterisation of nanoparticles and human and environmental exposures and routes. This lack of knowledge results in uncertainty in the risk assessment. Moreover, due to the novelty of nanotechnology, risk assessors are often confronted with small samples of data on which to perform a risk assessment. Dealing with this uncertainty and the small sample sizes are main challenges when it comes to risk assessment of ENPs. The objectives of this thesis are (i) to perform a transparent risk assessment of nanoparticles in the face of large uncertainty in such a way that it can guide future research to reduce the uncertainty and (ii) to evaluate empirical and parametric methods to estimate the risk probability in the case of small sample sizes.

To address the first objective, I adapted an existing Integrated Probabilistic Risk Assessment (IPRA) method for use in nanoparticle risk assessment. In IPRA, statistical distributions and bootstrap methods are used to quantify uncertainty and variability in the risk assessment in a two-dimensional Monte Carlo algorithm. This method was applied in a human health (nanosilica in food) and an environmental (nanoTiO2 in water) risk context. I showed that IPRA leads to a more transparent risk assessment and can direct further environmental and toxicological research to the areas in which it is most needed.

For the second objective, I addressed the problem of small sample size of the critical effect concentration (CEC) in the estimation of R = P(ExpC > CEC), where ExpC is the exposure concentration. First I assumed normality and investigated various parametric and non-parametric estimators. I found that, compared to the non-parametric estimators, the parametric estimators enable us to better estimate and bound the risk when sample sizes and/or small risks are small. Moreover, the Bayesian estimator outperformed the maximum likelihood estimators in terms of coverage and interval lengths. Second, I relaxed the normality assumption for the tails of the exposure and effect distributions. I developed a mixture model to estimate the risk, R = P(ExpC > CEC), with the assumption of a normal distribution for the bulk data and generalised Pareto distributions for the tails. A sensitivity analysis showed significant influence of the tail heaviness on the risk probability, R, especially for low risks.

In conclusion, to really be able to focus the research into the risks of ENPs to the most needed areas, probabilistic methods as used and developed in this thesis need to be implemented on a larger scale. With these methods, it is possible to identify the greatest sources of uncertainty. Based on such identification, research can be focused on those areas that need it most, thereby making large leaps in reducing the uncertainty that is currently hampering risk assessment of ENPs.

Het nieuwe meten
Ramaker, R. ; Khoury, C.K. - \ 2015
Resource: nieuwssite voor studenten en medewerkers van Wageningen UR 9 (2015)15. - ISSN 1389-7756 - p. 18 - 19.
publicaties - publiceren - publiciteit - verspreiding van onderzoek - statistiek - onderzoekers - publications - publishing - publicity - diffusion of research - statistics - research workers
Al decennialang wordt wetenschappelijke kwaliteit en invloed op dezelfde manier gemeten. Maar deugt die methode nog wel in een wereld die door digitalisering en social media ingrijpend is veranderd? Altmetrics biedt een alternatief.
Algae cultivation profitable by 2025
Wijffels, R.H. - \ 2014
voer - diervoedering - diervoeding - voedertechnologie - maling - voedertoevoegingen - ingrediënten - markten - statistiek - veevoederindustrie - voedermiddelbewerking - feeds - animal feeding - animal nutrition - feed technology - milling - feed additives - ingredients - markets - statistics - feed industry - feed processing is tailored towards the information needs of the international feed business community and is complementary to our print publications Feed Tech and Feed Mix. The site offers the worldwide feed industry: news, industry opinions, a newsletter, article archives, market information, and statistics, and much more
Quantifying relationships between governance, agriculture, and nature: empirical-statistical-and pattern-oriented modeling
Mandemaker, M. - \ 2014
University. Promotor(en): Tom Veldkamp, co-promotor(en): Martha Bakker; Jetse Stoorvogel. - Wageningen : Wageningen University - ISBN 9789462571440 - 177
landbouw - governance - natuur - modelleren - modellen - landgebruik - statistiek - agriculture - nature - modeling - models - land use - statistics

Quantifying relationships between governance, agriculture, and nature: empirical-statistical- and pattern-oriented modeling


An improved understanding of complex processes of both socio-political and economic governance may help to abate negative effects of increasing pressures of rising global food demand and agricultural land use on nature. Therefore, in this thesis, relationships between governance, agriculture, and nature were quantified, and it was investigated to what extent governance can be meaningfully included into land-use modeling. As outlined in the general introduction of this thesis, two main approaches to the inclusion of governance were distinguished: a semi-positivistic empirical-statistical approach and a positivistic process-based approach. Therefore, this thesis consists of two parts: one that includes governance through empirical-statistical modeling, and one that includes governance through process-based modeling.

In the first part of this thesis (chapters 2–3), relationships between quantified perceptions of state-centric governance, arable agriculture, and nature were identified through semi-positivistic empirical-statistical approaches. To investigate whether state-centric governance directly drives—and if so, how—expansion and/or intensification of arable agriculture at the global level (chapter 2), empirical-statistical relationships between agricultural production dynamics and state-centric governance indicators were identified for 173 countries between 1975 and 2007. Four groups of countries were distinguished: those with both area and yield increases (“growth” countries); those with increasing yields but decreasing area (“intensifying” countries); those with decreasing yields but a growing area (“expansion” countries); and those with both declines in yields and area (“decline” countries). Differences between these four groups were analyzed, and also governance-production relationships within these groups. The analysis of governance-production relationships within the four groups suggests that countries with a lower quality of governance are more inclined to achieve production increases by expanding agricultural area rather than increasing yields. Moreover, as quality of governance becomes higher, this orientation of countries towards production tends to flip from expansion towards intensification. Overall, higher quality of state-centric governance is more likely to drive the intensification of arable agriculture, while lower quality of state-centric governance is more likely to drive the practicing of cheaper forms of arable agriculture, requiring less financial investment to keep up with the growing demand for food.

To investigate whether state-centric governance directly drives—and if so, how—dominant spatiotemporal processes of fragmentation and expansion of nature, empirical-statistical relationships between overall quality of state-centric governance and such processes were identified through cross-national comparison for 20 European countries for the period 1990–2006 (chapter 3). Land-cover change trends were detected by comparing CORINE land-cover maps from the years 1990 and 2006. Dominant spatiotemporal processes of change in nature were characterized by capturing past developments in two indicators: overall change in nature area and change in average patch size of nature. This resulted in four different dominant spatiotemporal processes of structural change: “Formation of larger-than-average patches of nature and/or Expansion of nature and/or Connection of nature”; “Formation of smaller-than-average patches of nature”; “Removal of smaller-than-average patches of nature”; and “Removal of larger-than-average patches of nature and/or Shrinkage of nature and/or Dissection of nature”. The majority of countries expanded their total nature, although this is likely not to have been the result of deliberate nature restoration alone but also of land abandonment or afforestation for production purposes, which do not necessarily lead to positive development in terms of biodiversity. For the period 1990–2006, overall quality of governance was found to be positively related to expansion of nature, and negatively to increasing patch size of nature. Generally, lower scores of overall quality of state-centric governance are more likely to drive the processes of removal, shrinkage, and dissection of nature through changes in nature area. Higher scores of overall quality of state-centric governance are more likely to drive the processes of formation, expansion, and connection of nature through changes in both nature area and patch size. Overall, it appears that quality of state-centric governance indeed drives the deliberate development of nature for the purposes of restoration and conservation, halting fragmentation and the ongoing decline of biodiversity in Europe.

On the one hand, the combined results of chapters 2–3 may imply that increased inclination toward expansion of agriculture could be commensurate with increased removal, shrinkage, and dissection of nature (i.e., negative change in nature area). On the other hand, the combined results of chapters 2–3 may imply that increased inclination toward intensification of agriculture could be commensurate with increased formation, expansion, and connection of nature (i.e., positive change in nature area). Overall, this would be consistent with the fact that lower scores of quality of state-centric governance are more likely to drive the practicing of cheaper forms of arable agriculture, requiring less financial investment to keep up with growing demands for food. In particular, expansion at the expense of nature, which is common in developing countries where nature is often abundant yet poorly protected (chapter 2).

In the second part of this thesis (chapters 4–5), a positivistic process-based approach was applied to include governance into land-use modeling. To investigate to what extent found the semi-positivistic empirical-statistical relationships could be simulated, a spatially explicit pattern-oriented individual-based land-use-transition model was constructed (chapter 4). Given that conceptualizations of decision-making and other mechanisms controlling behavioral and environmental constraints approach those of a real-world study area sufficiently close, and that land-use change data of this study area permit identification of the degree and composition of systematic influence on aggregate land-use patterns, meaningful comparison of empirical and simulated spatial statistics is possible. Furthermore, it is possible to approximate real-world land-use patterns with simulated ones, by minimizing differences between real-world- and simulated spatial statistics. These differences could be minimized by applying Pattern-Oriented Modeling (POM), iteratively comparing real-world- and simulated land-use patterns, and making systematic adjustments to explore which mechanisms and settings deliver optimal results. It was concluded that the empirical-statistical result that occurrence of agricultural intensification is likely to be more commensurate with higher quality of governance (chapter 2), can be reproduced as an emergent property of aggregated individual behavior of farmers constrained by state-centric governance (by the constructed model).

To investigate under which conditions nature could be protected from agriculture in an optimal way, individual farmers were subjected to different state-centric governance settings in the constructed model (chapter 5). One state-centric governance setting was assumed to be determined by the quality of the investment climate, reflected by the quality of the state-centric governance dimension “Regulatory quality”. Another was assumed to be determined by the level of entrepreneurial awareness, reflected by the quality of the state-centric governance dimension “Government effectiveness”. Together, these assumptions could be combined into four state-centric governance settings: “Low Entrepreneurial Awareness and Low Quality of Investment Climate” (I); “Low Entrepreneurial Awareness and High Quality of Investment Climate” (II); “High Entrepreneurial Awareness and Low Quality of Investment Climate” (III); and “High Entrepreneurial Awareness and High Quality of Investment Climate” (IV). Furthermore, farmers were subjected to two different top-down policy instruments in each state-centric governance setting: subsidies and fines. The most effective- and second-most effective protection of nature was generated by applying fines in state-centric governance settings III and IV, respectively. It was concluded that the empirical-statistical result that better protection of nature is likely to be commensurate with higher quality of governance (chapter 3), can be reproduced as aggregate emergent properties of individual behavior of farmers in different policy scenarios (by the constructed model) (chapter 4). Furthermore, that abstract process-based simulation (pattern-oriented modeling) of spatially explicit agricultural land-use systems allows for identification of different and verifiable governance conditions and policy strategies regarding protection of nature, and for identification of the optimal verifiable governance conditions and policy strategy for protection of nature and the economic interests of farmers in agricultural land-use systems.

It was concluded that governance can be meaningfully included into land-use modeling in both semi-positivistic (i.e., empirical-statistical) and positivistic (i.e., process-based) ways. However, different combinations of empirical specificity and degree of abstraction, i.e., different models, describe the same real-world complexity differently. Therefore, a conceptual representation of land-use models characterized by empirical specificity and degree of abstraction was proposed (chapter 6). According to this representation, there are three main classes of land-use models. There are those models that are more empirically specific than abstract (), indicating increasingly empirical-statistical models. Furthermore, there are those models that are more abstract than empirically specific (), indicating models that are increasingly process-based. It was observed that if a model of a real-world land-use system could optimize the empirical specificity with which this model can be validated and the degree of generality to which this system can be understood, then its predictive power might be maximized. That is, the class of models for which empirical specificity is equal to the degree of abstraction () might represent a class of models for which predictive power is potentially maximal. However, the research in this thesis suggests there is still a considerable gap between the used empirical-statistical models () and the constructed pattern-oriented model (). Therefore, it is recommended that research efforts be devoted to the development of models that further reduce the gap between empirical specificity and degree of abstraction, that is (. Moreover, to apply and validate such models successfully, large amounts of data would be required that are currently unavailable. This is why even more research efforts should be devoted to the development of high-resolution monitoring systems of land use, to allow for larger and better databases.

Wettelijke Onderzoek Taken WOT-05 Visserijonderzoek: Werksafspraken en werkplan 2015
Verver, S.W. - \ 2014
IJmuiden : Centrum voor Visserijonderzoek (CVO rapport 14.006)
visserijbeleid - visserij - zeevisserij - kustwateren - aquacultuur - binnenwateren - visserijbeheer - visstand - bijvangst - statistiek - monitoring - onderzoek - duurzaamheid (sustainability) - recreatieactiviteiten - palingen - schaaldieren - fishery policy - fisheries - marine fisheries - coastal water - aquaculture - inland waters - fishery management - fish stocks - bycatch - statistics - research - sustainability - recreational activities - eels - shellfish
Dit rapport beschrijft het werkplan voor 2015 van cluster WOT-05 Visserijonderzoek van Wageningen UR. Wageningen UR voert voor het Ministerie van Economische Zaken (EZ) een aantal programma’s met Wettelijke Onderzoek Taken (WOT) uit. Binnen WOT-05 worden Wettelijke Onderzoek Taken uitgevoerd die betrekking hebben op het beheer van de visserij op zee, in Nederlandse kust- en binnenwateren en de aquacultuur. Het werkplan is een uitwerking van de Uitvoeringsovereenkomst tussen het Ministerie van EZ en de Stichting Dienst Landbouwkundig Onderzoek (DLO), onderdeel van Wageningen UR, voor diensten vanwege wettelijke taken op het terrein van visserijonderzoek voor de periode 2011-2015. Bij deze uitvoerings-overeenkomst zijn voor deze periode werkafspraken gemaakt welke de basis vormen voor de jaarlijkse werkplannen. Daarnaast zijn in deze overeenkomst afspraken gemaakt over de KennisBasis (KBWOT) die specifiek aan dit programma is gekoppeld.
Agrimatie : informatie over de agrosector
Fernhout, C.Y. ; LEI, - \ 2013
Den Haag : LEI Wageningen UR
landbouwsector - statistiek - overheidsbeleid - prijzen - informatiesystemen - economische indicatoren - duurzaamheidsindicatoren - agricultural sector - statistics - government policy - prices - information systems - economic indicators - sustainability indicators
Deze website toont diverse onderzoeksresultaten die LEI Wageningen UR in het kader van Wettelijke onderzoekstaken publiceert voor het Ministerie van Economische Zaken.
Pacioli 20: Complex farms and sustainability in farm level data collection
Vrolijk, H.C.J. - \ 2013
The Hague : LEI, onderdeel van Wageningen UR (LEI proceedings : Onderzoeksveld Agriculture & entrepreneurship ) - ISBN 9789086156344 - 239
agrarische economie - boekhouding van landbouwbedrijf - european farm accounting network - statistiek - datacommunicatie - landbouwbeleid - gegevens verzamelen - agricultural economics - farm accounting - statistics - data communication - agricultural policy - data collection
For the 20th time, LEI organised the yearly Pacioli workshop. This year it took place in Rome, Italy, from 30 September to 3 October 2012. There were a record number of 48 participants from EU countries, non-EU countries such as Switzerland and Norway, candidate countries and from international organisations such as OECD, USDA, FAO and the European Commission. They discussed innovations and developments in the collection and use of farm level data. Important topics were the measurement of sustainability indicators, the specific problems of collecting information on large complex farms and the use of data for policy analysis and research. The Italian research institute INEA hosted the meeting and took care of the local organisation. LEI was responsible for organising the content of the programme and chairing the meetings.
Concurrentiekracht van de Nederlandse eiersector
Horne, P.L.M. van - \ 2012
Den Haag : LEI, onderdeel van Wageningen UR (LEI-rapport : Onderzoeksveld Markt & ketens ) - ISBN 9789086155996 - 74
dierlijke producten - eieren - pluimvee - markten - statistiek - prijzen - economische productie - productiekosten - marktconcurrentie - animal products - eggs - poultry - markets - statistics - prices - economic production - production costs - market competition
Het LEI heeft op verzoek van het ministerie van Economische Zaken (EZ) en het Productschap Pluimvee en Eieren (PPE) een onderzoek uitgevoerd naar de concurrentiekracht van de Nederlandse eiersector. Centrale vraag daarbij is of de Nederlandse eierketen concurrerend is. Belangrijk onderdeel van de studie is een vergelijking van de huidige en toekomstige positie van de Nederlandse eierketen ten opzichte van de belangrijkste concurrerende productielanden. In deze studie zijn de productiekosten van eieren in Nederland vergeleken met de productiekosten in het belangrijke afzetgebied Duitsland en met die van enkele concurrerende landen in Noordwest Europa. Ook is een vergelijking gemaakt van productiekosten van eieren met enkele landen buiten Europa.
Quantitative methods for sampling of germplasm collections : getting the best out of molecular markers when creating core collections
Odong, T.L. - \ 2012
University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Theo van Hintum; Hans Jansen. - [S.l.] : s.n. - ISBN 9789461732095 - 152
bemonsteren - germplasm - genenbanken - genetische bronnen van plantensoorten - statistiek - moleculaire merkers - statistische steekproeftechnieken - gewassen - sampling - gene banks - plant genetic resources - statistics - molecular markers - statistical sampling techniques - crops

This thesis addresses the issue of how special players (crisis entrepreneurs)
try to generate attention to a latent crisis and how government communication
can contribute to identifying and interpreting such a crisis.
In chapter 1, I show how crisis communication is an activity that is often
associated with organizations. This study takes a different view. It is based
on the concept that strategic crisis communication is used by those in
the immediate environment to achieve certain goals. In society, certain
individuals and groups can decide to oppose and denounce a given crisis.
Some of those involved often start signalling the risk of an impending
crisis before any such crisis has actually developed. In this study, I refer
to individuals who generate signals of this kind as ‘crisis entrepreneurs’.
These crisis entrepreneurs typically take the initiative when it comes to
airing their concerns about a potential crisis situation. However, such individuals
often have to deal with certain interactional problems that make it
difficult for them to raise the issue of a crisis. They have to deal with certain
‘interactional’ challenges, while running the risk that their signals will
not be picked up. For instance, they can be held responsible for raising the
problem in question. They can be accused of bearing some degree of personal
responsibility for the problem, through negligence, incompetence,
or laziness, for example. In this study, I have explored the way in which
crisis entrepreneurs issue signals. This is an attempt to identify the problems
that they encounter as they attempt to draw people’s attention to a
given crisis. The goal of this study is to enhance our understanding of crisis
entrepreneurs’ interactional problems. The study makes use of the ‘discursive
perspective’, which is based on the discursive psychological approach
developed in the 1990s by two British social psychologists, Derek Edwards
and Jonathan Potter. To date, this interaction-based approach has seldom
been used in the context of crisis communication.
Chapter 2 underlines the value of examining the way in which stakeholders
within an organization’s environment raise the issue of a crisis.
In terms of crises as a phenomenon, it is important to do justice to
the dynamics of risks and crises. In essence, this is about what happens
in the course of interactions. In such an environment, it is vital for an
organization to keep pace with those in its surroundings if it is to observe
signals in interaction with this dynamic environment. This requires a
view of crisis communication that allows sufficient scope for the interactional
Chapter 3 explores various elements that characterize crises in general,
while describing a particularly significant phase - the latent crisis. I have
identified two forms of latent crisis, a lingering form and a creeping form.
These two forms differ chiefly in terms of the dynamics involved. While
the dynamics of both types exhibit both peaks and troughs, there are differences.
Lingering crises are entirely lacking in dynamism for extended
periods of time. The dynamics of creeping crises, on the other hand, tend to
increase gradually.
After describing the theoretical framework of the study, chapter 4 proceeds
to explore the theoretical and methodological scope of discursive
psychology, in terms of an interactional approach to crisis communication.
Discursive psychology offers the valuable option of using discourse analysis
to examine the social context of risks from the standpoint of everyday
reality. A discursive perspective characteristically focuses on a) everyday
interactions that are not shaped by the study itself and b) the transactions
that, either consciously or unconsciously, feature in such interactions.
The discursive perspective offers a specific form of discourse analysis that
communications professionals can use to understand how those in the
environment express their ideas relative to others. The significance of this
is that it can help professionals to understand the specific interactional
problems facing crisis entrepreneurs. These involve dealing with certain
‘interactional’ challenges, while running the risk that their signals will not
be picked up.
Chapter 5 discusses the two cases selected for this study. The selected
case domain is education in the Netherlands. I have investigated the ways
in which crisis entrepreneurs have signalled problems in this sector. I used
discourse analysis (Edwards, 1997; Potter, 1992) to first examine the interactional
efforts of those behind collective social movements, then those of
individual whistleblowers. To this end, I studied an interview with Matthé
Sjamaar, the rector of a secondary school, which was published in Onderwijsblad
(education journal) in May 1998. I also examined the manifesto of
Beter Onderwijs Nederland (better education for the Netherlands; BON),
which was published in the NRC Handelsblad newspaper in June 2006. Both
sources raised the issue of a crisis. One of the criteria that I used in selecting
these texts was whether the crisis entrepreneur in question had the ability
to influence the public debate. In both cases, both local and national media
responded to the statements made by these crisis entrepreneurs. Using a
discursive response analysis, I explored the way in which newspapers dealt
with the interactional problems faced by these crisis entrepreneurs.
Chapters 6 and 7 form the empirical part of this study. The analysis identified
three important discursive activities that are carried out by crisis
entrepreneurs. These are: 1. demonstrating the validity of the problem,
2. establishing the messenger’s credibility, and 3. creating the belief in a
solution. The analysis showed that Matthé Sjamaar creates indirectly undetermined
others in the environment as being partly responsible for the
cause of the problem, while exhibiting a degree of fatalism and holding out
no prospect of a solution. He makes an indefinite-side group responsible
for the problems. He shows he can not control the problem because it is
too large. He creates the crisis as an isolated entity. They are merely the
facts which he shows, which are independent of him. He suggests that he
has done a lot of hard work and now others have to do something.
The media portrayed Rector Sjamaar as symbolizing a problem that was
primarily a personal issue. BON, on the other hand, presents itself as a collective
that is committed to achieving better education in the Netherlands.
The writers display insight and overview of the education problem and
create the association to BON as a group consisting of ‘outspoken thinkers’
who are not hindered by doubts. The authors set themselves superior
in their attitude towards the education reformers. The writers poses the
problem as clear and relevant to everyone and so they create their own
need for existence. So now they start a movement and give voice to something
that has long been going on: BON is the solution to turn the tide. We
can jointly fate a twist. Various media sources reinforced this image, portraying
this social movement as the solution to the problem.
The study has shown that crisis entrepreneurs may differ in terms of the
strategies used and the interactional problems encountered. The solutions
put forward by BON have proved more effective than those suggested by
Rector Sjamaar. As a result, the discursive activities pursued by the former
have been more successful than those of the latter. The diverse reactions
exhibited by the media sources in this study serve to underline the precarious
nature of a crisis entrepreneur’s operation. For instance, the analysis
shows that rather than focusing on the authenticity of his signal, the
responses to Matthé Sjamaar’s article dismiss his views as a purely private
emotion. Based on this study, I show that the Rector’s initiative was undermined
by his presentation of the problem. It failed to trigger a general
sense of crisis as a result of segregation. BON fared very differently, as the
problem of educational reform is already widely recognized. Moreover, as
the analysis shows, BON’s spokespersons are important actors in this connection.
Ad and Marijke Verbrugge have put forward polarizing arguments,
in which they distance themselves from the New Learning concept. These
views have clearly been taken on board by supporters and opponents in the
debate triggered by these authors. The study has also shown that certain
interactional problems are not necessarily inevitable, but that such problems
can be triggered by crisis entrepreneurs themselves. Its content is
inextricably linked to people’s goals in making specific comments.
Chapter 8 summarizes the main observations in this thesis. It shows
that the problems created by raising the issue of a latent crisis are not
purely substantive in nature (‘is this crisis genuine?’), there is also an interactional
aspect (for example, ‘how do I get people to accept the urgency
and validity of the problem?’). My study provides a greater understanding
of the course that crises can take. It also shows that crisis entrepreneurs
can be seen as dynamic elements within society. They express dissenting
views, and launch new initiatives through various forms of traditional and
electronic media. This process can be very instructive. Communications
professionals can better understand how crises develop among those in
their environment if they are aware of the types of interactional problems,
and the types of responses, that can result from raising the issue of a crisis.
Moreover, this might also help communications professionals to achieve
better outcomes in their dealings with crisis entrepreneurs.
A discursive approach is valuable in this respect because it shows how
certain themes in communication can deal with policy development. This
approach can lead to a better hold on these themes in practice and can
provide another perspective to widespread failure of interaction between
government and citizens. The government is often unable to understand
what the citizen means, because their interactional problems are not recognized.
Knowledge of their doubts on an issue, can help the organization
to acquire a better understanding of objections – from inside and
out – against a particular policy. A discourse analysis of the interactional
contributions of crisis entrepreneurs may give a rich and structured insight
into latent crisis supply, including the strategies, interactional problems
and reactions of the actors involved and how they are able to recognize a
potential crisis.

Pacioli 19; The role of FADN after the CAP reform
Vrolijk, H.C.J. - \ 2012
The Hague : LEI, part of Wageningen UR (LEI Memorandum / LEI Wageningen UR : Agriculture & entrepreneurship ) - ISBN 9789086155729 - 186
agrarische economie - boekhouding van landbouwbedrijf - statistiek - european farm accounting network - datacommunicatie - landbouwbeleid - gegevens verzamelen - agricultural economics - farm accounting - statistics - data communication - agricultural policy - data collection
The international Pacioli network shares knowledge on the management and use of agricultural microeconomic databases (such as the Farm Accountancy Data Network in Europe). Each year LEI, part of Wageningen UR, organizes a Pacioli workshop in close cooperation with a local organizer. The 19th Pacioli workshop took place in Tallinn, Estonia in October 2011
Sampling efficiency of national, EU and global stratifications : exploring by using CL2000
Metzger, M.J. ; Brus, D.J. ; Ortega, M. - \ 2012
Wageningen : Alterra (Alterra report 2279) - 26
bemonsteren - statistiek - landclassificatie - terrestrische ecosystemen - sampling - statistics - land classification - terrestrial ecosystems
Stratification, dividing the statistical population into less heterogeneous subgroups before sampling, can help improve sampling efficiency by improving representativeness and reducing sampling error. This report explores the added sampling efficiency that is achieved by using the European Environmental stratification for estimating the area covered by the 25 Corine Land Cover (CLC) categories occurring in the semi-natural and managed terrestrial habitats of the wider-countryside. Although the dataset is not ideally suited to assess stratification efficiency for EBONE, the results give some encouragement. The analysis indicates that the pan-European stratification improves sampling efficiency for several land cover categories and performs similar to four more detailed national stratifications, supporting their use as a basis for designing a pan-European biodiversity observation network.
Models to relate species to environment: a hierarchical statistical approac
Jamil, T. - \ 2012
University. Promotor(en): Cajo ter Braak. - S.l. : s.n. - ISBN 9789461731395 - 146
statistiek - lineaire modellen - interacties - kenmerken - bayesiaanse theorie - plantenecologie - biostatistiek - statistics - linear models - interactions - traits - bayesian theory - plant ecology - biostatistics

In the last two decades, the interest of community ecologists in trait-based approaches has grown dramatically and these approaches have been increasingly applied to explain and predict response of species to environmental conditions. A variety of modelling techniques are available. The dominant technique is tocluster the species based on their functional traits and then summarize the response of the clusters to environmental change. In general, fitting explicit models to data is always more informative and powerful than more informal approaches. The central theme of the thesis is how to quantify the relation of traits with the environment using three data tables, data on species occurrence and abundance in sites, data on traits of species and data on the environmental characteristics of sites. In this thesis, we place the challenge of quantifying trait-environment relationships in the context of species distribution modelling, so in the context of species-environment relationships. We present a hierarchal statistical approach to species distribution modelling that efficiently utilize the trait information and that is able to automatically select the relevant traits and environmental characteristics. This model-based approach, coupled with recent statistical developments and increased computing power, opens up possibilities that were unimaginable before.

In the present study a hierarchical statistical approach is introduced for modeling and explaining species response along environmental gradients by species traits. The model is an extension of the generalized linear model with random terms that express the between-species variation in response to the environment. This so-called generalized linear mixed model (GLMM)is derived byintegrating a two-step procedure into one. As the basic GLMM we take the random intercept and random slope model. To introduce traits, the regression parameters (intercept and slope) are made linearly dependent on the species traits. As a consequence the trait-environment relationship is represented as an interaction term in the model. The method is illustrated using the famous Dune Meadow Data using Ellenberg indicator values as species traits.

Niche theory proclaims that species response to environmental gradients is nonlinear. Each species has preferred an environmental condition in which it can survive and reproduce optimally. Thus each species tends to be most abundant around a specific environmental optimum and the distribution of species along any environmental gradient is usually unimodal, with the maximum at some ecological optimum.For presence-absence data, the simplest unimodal (non-negative) species response curve is the Gaussian logistic response curve with three parameters that characterize the niche: optimum (niche centre), tolerance (niche width) and maximum (expected occurrence at the centre). Niches of species differ between species and species are assumed to be evolutionary adapted. It is difficult to fit the Gaussian logistic model with linear trait submodels for the parameters with the available (generalized) nonlinear mixed model software.

We develop the trait-modulated Gaussian logistic model in which the niche parameters are made linearly dependent on species traits. The model is fitted to data in the Bayesian frameworkusing OpenBUGS (Bayesian inference Using Gibbs Sampling).A Bayesian variable selection method is used to identify which species traits and environmental variables best explain the species data through this model. We extended the approach to find the best linear combination of environmental variables.

We explained why and when (generalized) linear mixed models can effectively analyse unimodal data and presented a graphical tool and statistical test to test for unimodality while fitting just a generalized linear mixed model without any squared or other polynomial term. A GLMM is, of course, a linear model. Despite this fact, it can be used to detect unimodality and to fit unimodal data, with the provision that the differences in niche widthsamongspecies are not too large. As graphical tool we suggested to plot the random site effects against the environmental variable. There is an indication for unimodality, when this graph shows a quadratic relationship. The efficacy of GLMM to analyse unimodal data is illustrated by comparing the GLMM approach with an explicit unimodal model approach on simulated data and real data that show unimodality.

When a system is described by a statistical model, model complexity leads to a very large computing time and poor estimation, especially if the number of predictors is large relative to the data size. As an alternative to and improvement over stepwise methods, shrinkage methods have been proposed. One of these is the Relevance vector machine (RVM). RVM assigns individual precisions to weights of predictors which are then estimated by maximizing the marginal likelihood (Type-II ML or empirical Bayes). We also investigated the selection properties of RVM both analytically and by experiments. We found that RVM is rather tolerant for predictors to stay in the model and concluded that RVM is not a real solution in high-dimensional data problems.

By further study the multi-trait and multi-environmental variablemodel selection method developed that used our previous study in a linear mixed model context. The method is called tiered forward selection. In the first tier, the random factors are selected, in the second, the fixed effects are selected and in the final tier non-significant terms are removed based on a modified Akaike information criterion. The linear mixed model with the tiered forward selection is compared with Type-II ML and existing methods for detecting trait-environment relationships that are not based on mixed models, namely the fourth corner method and the linear trait-environment method (LTE).

Gebruikers handleiding rekenmodel Kwantitatieve Informatie Glastuinbouw
Vermeulen, P.C.M. - \ 2011
Bleiswijk : Wageningen UR Glastuinbouw (Rapporten GTB 1108) - 32
glastuinbouw - kosten-batenanalyse - agrarische bedrijfsvoering - statistiek - nederland - wiskundige modellen - handleidingen - greenhouse horticulture - cost benefit analysis - farm management - statistics - netherlands - mathematical models - guide books
In dit verslag wordt een model beschreven waarmee studenten van het agrarisch onderwijs, mbo, hbo en universitair kennis kunnen maken met de bedrijfseconomische aspecten van de glastuinbouw. Het model bevat verschillende niveaus van diepgang, die aansluiten bij het onderwijsniveau. Dit model, “Model kwantitatieve informatie Glastuinbouw” is een Excel bestand waarin de achterliggende rekenregels voor de berekening van het bedrijfsresultaat, het rendement en de jaar rond kostprijs zijn opgenomen. Het model levert daarnaast een arbeidsbegroting en voor depotplanten een ruimteplanning. In overleg met docenten van de verschillende schooltypen kan er gewerkt worden op 3 niveaus: norm niveau, het niveau van eigen bedrijfsgegeven en het model kan als startpunt dienen voor een eigen te ontwikkelen model. Er zijn gewas specifieke versies voor: Komkommer, tomaat, paprika, chrysant, gerbera en roos en twee uitgebreidere versies met teeltplanning voor bloeiende en groen planten. Dit verslag kan als gebruikershandleiding gezien worden voor mensen met achtergrond kennis.
Bayesian Markov random field analysis for integrated network-based protein function prediction
Kourmpetis, Y.I.A. - \ 2011
University. Promotor(en): Cajo ter Braak, co-promotor(en): Roeland van Ham. - [S.l.] : S.n. - ISBN 9789085859598 - 113
statistiek - bayesiaanse theorie - markov-processen - netwerkanalyse - biostatistiek - toegepaste statistiek - bio-informatica - eiwitten - genen - moleculaire biologie - statistics - bayesian theory - markov processes - network analysis - biostatistics - applied statistics - bioinformatics - proteins - genes - molecular biology

Unravelling the functions of proteins is one of the most important aims of modern biology. Experimental inference of protein function is expensive and not scalable to large datasets. In this thesis a probabilistic method for protein function prediction is presented that integrates different types of data such as sequences and networks. The method is based on Bayesian Markov Random Field (BMRF) analysis. BMRF was initially applied to genome wide protein function prediction using network data in yeast and in also in Arabidopsis by integrating protein domains (i.e InterPro signatures), expressions and protein protein interactions. Several of the predictions were confirmed by experimental evidence. Further, an evolutionary discrete optimization algorithm is presented that integrates function predictions from different Gene Ontology (GO) terms to a single prediction that is consistent to the True Path Rule as imposed by the GO Directed Acyclic Graph. This integration leads to predictions that are easy to be interpreted. Evaluation of of this algorithm using Arabidopsis data showed that the prediction performance is improved, compared to single GO term predictions.

Oefenmateriaal statistiekonderwijs
Janssen, A.P.H.M. ; Berg, W. van den - \ 2011
lesmaterialen - statistiek - agrarisch onderwijs - oefening - teaching materials - statistics - agricultural education - practice
In het project worden 16 onderzoekcasussen verzameld voor gebruik in het statistiek onderwijs in het HAO. Het betreft 8 casussen uit onderzoek van Praktijkonderzoek Plant en Omgeving voor Akkerbouw, Groene ruimte en Vollegrondsgroenteteelt (PPO-AGV) en 8 uit onderzoek van Livestock Research. Elke casus bestaat uit het verslag van een onderzoeksproject en bijbehorende data verzameld binnen het project.
The biology of plant metabolomics
Hall, R.D. - \ 2011
Oxford : Blackwell/Wiley (Annual plant reviews vol. 43) - ISBN 9781405199544 - 420
planten - metabolomica - genexpressieanalyse - plantenfysiologie - genetica - statistiek - bio-informatica - plants - metabolomics - genomics - plant physiology - genetics - statistics - bioinformatics
Following a general introduction, this book includes details of metabolomics of model species including Arabidopsis and tomato. Further chapters provide in-depth coverage of abiotic stress, data integration, systems biology, genetics, genomics, chemometrics and biostatisitcs. Applications of plant metabolomics in food science, plant ecology and physiology are also comprehensively covered.
Biometris GenStat Procedure Library Manual 13th Edition
Goedhart, P.W. ; Thissen, J.T.N.M. - \ 2010
Wageningen : Wageningen Universiteit (Biometris report 18.08.10) - 126
statistiek - handleidingen - computer software - computertechnieken - statistics - guide books - computer techniques
The Biometris GenStat Procedure Library contains procedures in which new and existing statistical methodology is implemented, as well as procedures to make GenStat more user-friendly. The Biometris library can be used and distributed freely. The Library is standardly distributed over the Dutch agricultural research sites.
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