A Guide to CoCo

CoCo is a program for estimation, test and model search among hierarchical interaction models for large complete contingency tables. The name CoCo is derivated of "Co"mplete "Co"ntingency tables, since the initial program could only handle complete tables, but the program has been enhanced to handle incomplete tables. CoCo works especially efficiently on graphical models, and some of the commands are designed to handle graphical models.

Spiser kvæg som en grønthøster, eller er de kræsne

De fire arter, som studene selekterede positivt, var alle naturarter, nemlig alm. kvik, manna-sødgræs, alm. hønsetarm og fløjlsgræs. Af de arter, som studene selekterede negativt, var der to kulturarter, rød svingel og engrapgræs, samt to naturarter, mosebunke og knæbøjet rævehale. Studenes selektion var ikke knyttet til kvalitet for foderværdi i form af fordøjeligt organisk stof, råprotein eller cellevægsindhold (NDF)

Organic Food and Health: A new project to study the effects of plant cultivation methods (organic and conventional) on nutritional value, health and reproduction in an animal experiment

Many consumers believe that food from plants grown under certain conditions, such as organic agriculture, will benefit health more than conventional food. This cannot be determined simply by analysing the material, since our understanding of the connections between food components and health is still to imprecise for such a purpose. Rather than waiting until basic research provides the knowledge needed for this approach, in the spring of 2001 we have initiated a project to study physiological effects of plant quality directly, in an animal experiment. The following cultivation treatments are used to grow plants that are typical ingredients for a human diet (potato, mature peas, kale, spring wheat, oilseed rape, carrots and apples): 1. A model of a distinct conventional cultivation system, with high input of mineral nutrients and use of as much pesticides as is allowed. 2. A model of a distinct organic cultivation system, with low input of organic plant nutrients and no use of pesticides. 3. A combination of model 1 and 2, with low input of nutrients and use of pesticides. The materials from each cultivation treatment will be thoroughly characterised, by measuring contents of nutrients (protein, minerals, energy content, vitamins), the biological value of major protein sources of feed plants will be assessed, selected secondary metabolites including known anti-nutrients will be measured and other quality indicators will be assessed including biocrystallization. Based on these results, 3 feed mixtures will be prepared, either based on defined weight percentages of each material from each treatment, or, if large variation in biological value is found, one or two feed mixtures can be adjusted to provide the same availability of protein and energy as the reference treatment (model 1). Potato, mature peas and kale will be cooked and freeze-dried, wheat is ground and baked to biscuits, oil is produced from the rapeseed, and raw carrots and apples are shredded and freeze dried, before feed pellets with the desired composition are prepared from the material. Three groups of rats are each provided one of the dietary treatments during 2.5 generation, and reproductive characteristics and performance are recorded. Subgroups of the last generation are selected for an intensive study in which uptake and excretion of energy and protein and selected micronutrients are determined. Respiration trials are performed to assess the energy metabolism, and simultaneous measurements of the activity levels of the rats are performed. In addition, blood and tissue samples of the rats will be obtained to study the effect of the dietary treatments on the immunological and antioxidant status of the rats. Data from the experiments are assembled and analysed using relevant statistical models, and the relationship to the nutritional characteristics of the plant material is described. Funding for the core project for a 4-year period is secured from the Danish Research Centre for Organic Farming (DARCOF). However, the intention is to provide a platform for international collaboration, since the well-documented material of plants and animals can provide multiple opportunities for associated projects. To investigate other aspects of plant composition or health than what is foreseen in the present project, or to follow up on it with additional experiments

A Guide to CoCo

CoCo is a program for estimation, test and model search among hierarchical interaction models for large complete contingency tables. The name CoCo is derivated of "Co"mplete "Co"ntingency tables, since the initial program could only handle complete tables, but the program has been enhanced to handle incomplete tables. CoCo works especially efficiently on graphical models, and some of the commands are designed to handle graphical models

DSC 2003 Working Papers (Draft Versions)

Draft: More complex graph computations for undirected graphical models by the CoCo bundle for

Efficient Methods for Estimation in Log-Linear Models

This paper is focusing on the computational aspects of using graphs in analysing log-linear models, but graphical models also have other advantages. By the graphs, the structure of a given model is visually represented. The conditional independences can be read directly of the graphs, and thus the graphs facilitate communication between statistician and researcher. Some textbooks on graphical models are Cox and Wermuth (1996), Edwards (1995), Lauritzen (1996) and Whittaker (1990)

Model Search in Contingency Tables by CoCo

CoCo 1 , a highly advanced program for analysis of complete and incomplete contingency tables, is presented. In the paper a short presentation of CoCo is given. Incremental search by backward elimination and forward selection and the global search procedure from Edwards & Havr'anek (1985) is considered. By incremental search a single minimal acceptable model is identified. By the principles of weak acceptance and weak rejection the class of minimal acceptable models are found in the global search procedure. In CoCo each of the model searches can be done by a single command, or CoCo can be guided through the search in a highly user controlled model selection. 1 CoCo CoCo works especially effectively on graphical models, and some of the commands in CoCo are designed to handle graphical models. Graphical models are for contingency tables log-linear interaction models that can be represented by a simple undirected graph with as many vertices as the table has dimension (Darroch, Lauritz..