http://wiki.merlin-expo.eu/ 2026-04-29T19:12:06+00:00 http://wiki.merlin-expo.eu/ http://wiki.merlin-expo.eu/lib/exe/fetch.php?media=wiki:logo.png text/html 2025-01-16T15:23:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=afry_intelligent_scenario_modelling&rev=1737040996&do=diff AFRY Intelligent Scenario Modelling is a proprietary software developed by AFRY for modelling and simulation of dynamic systems on which MERLIN-Expo is based. See also * 4FUN text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=aggregate&rev=1402308074&do=diff The aggregate sums or multiplies a selection of blocks. It can also calculate their mean, min or maximum value. It is sometimes used to combine blocks with similar dependencies. See also * Block text/html 2015-03-09T13:58:02+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=archive&rev=1425909482&do=diff The results of a simulation are overwritten when a new simulation starts. If you want to retain results, for instance to be able to compare old and new results, you can create a simulation result archive. An archive is created from the result panel of either the text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=assessment&rev=1402308074&do=diff An assessment is the term used for a file which contains a project + all the simulation results for the project. The separation between project files and assessment files is made because simulation results typically takes up a lot of space. Thus the typical file size for a text/html 2025-01-16T15:27:32+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=block&rev=1737041252&do=diff A block is an AFRY Intelligent Scenario Modelling name for the components used in the construction of the mathematical model. Blocks can be visualized using the interaction matrix or box diagrams. These are the most common blocks used in MERLIN-Expo: * Compartment * Discrete event * Expression * General variable * Lookup table * Min/max * Parameter * Running mean * Snapshot * Source/Sink * Transfer See also * Mathematical model text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=category&rev=1402308076&do=diff Categories are used to group parameters (or other blocks) which are of similar type. The data input screens allow you to search for specific categories. See also * Tag text/html 2015-08-13T13:02:20+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=chart&rev=1439470940&do=diff Charts (plots/diagrams) can be created after a simulation has been run in the charts screen. The following types of charts are available. * Time chart - A chart where outputs are plotted against time. * Scatter chart - Scatter charts let you plot any output against another. * text/html 2015-03-09T13:58:34+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=charts_screen&rev=1425909514&do=diff Introduction The charts screen allows you to plot simulation results and has a lot in common with the tables screen. Depending on the type of simulation that has been run, different charts are available. A chart is created by first selecting outputs in the list. The will attempt to create a chart which suites the selected output, but if you want a specific chart you can select the chart type from the menu. text/html 2015-08-13T13:10:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=compartment&rev=1439471426&do=diff A compartment is a block that acts as an integrator of quantities of contaminants in a model. The quantity held within this block is calculated with a differential equation, where the input and output rates are defined by the transfer blocks. See also * Block text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=connector&rev=1402308074&do=diff A connector is used to connect two sub-systems. The connector allows you to pair one or more outputs of a sub-system with inputs in another sub-system. When a block which is marked as an input is connected to an output it will be replaced by the output block. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=contaminant&rev=1403687710&do=diff Contaminants in MERLIN-Expo are grouped into metals and organic compounds. For these compounds there are suggested parameter values by the model developers. You can add new contaminants in context screen, but you will then have to assign parameter values yourself. text/html 2025-01-16T15:32:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=context_screen&rev=1737041534&do=diff Context screen The context screen lets you select which contaminant(s) is relevant for your study. If your study includes modelling concentration in food items, or if you just need to enumerate food items that the local population consume, this is where you define them. If you are calculating exposure to more than a single individual, you can define which individuals to model here. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=conventions&rev=1402308074&do=diff The following conventions are used in this user guide: Link is used for cross-references and links to other pages. Bold is used for labels, buttons and other user interface controls. Examples: * Press the Generate button to generate a new report. text/html 2015-03-17T10:06:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=creating_an_aquatic_food_web_part_2&rev=1426586774&do=diff Introduction This is part 2 of the aquatic food web example. If you haven't finished part 1 of this tutorial, you can use [this] file. You will find that the pace quickens somewhat in this part, so be sure you have understood the basics of part 1 before you continue. In this part we first include a model for fish, and then define the three species of fish that inhabit the Glein river (Eel, Perch and Minnow). We examine the time series data for the fish model and reflect on how the fish and in… text/html 2015-03-19T07:58:58+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=creating_an_aquatic_food_web_part_3&rev=1426751938&do=diff Introduction This is part 3 of the silly tutorial creating an aquatic food web. In part 1 we started with a simple invertebrate model. In part 2 we added fish and river for them to live in. If you jumped straight into part 3, you can cheat by downloading [this] file. We can now estimate the lead concentration in the diet of the soldiers (dying on the beaches of the river Glein). This diet we can plug into a model for a human being. text/html 2022-06-30T18:20:48+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=creating_an_aquatic_food_web&rev=1656613248&do=diff Creating an aquatic food web - Tutorial Purpose The purpose of this tutorial is to get you acquainted with the MERLIN-Expo software. The situation is entirely fictitious, the data is fabricated. Introduction By using the aquatic food models you can design a full aquatic food web for a lake or river in the area you are studying. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=dealing_with_data_gaps&rev=1403687710&do=diff /* This page should be written by someone with experience in this field */ Bayesian updating of PDF's * BABAR QSAR models * ChemProp text/html 2015-08-13T13:08:08+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=default&rev=1439471288&do=diff The default index allows you to apply the same value for all indices of a non-scalar parameter, time series or option. For example, a parameter Initial_Age has different values for different people (it depends on individual). The study targets a hundred individuals, where all but one is 7 years old at the beginning of the investigated period. By entering the value 7 for the text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=dependency&rev=1402308076&do=diff The term dependency is used to identify different values for the same parameter (or any other block for that matter). Parameter values often have dependencies, such as dependency on atomic element (Iron, Methane, Oxygen), on media (concrete/clay/rock) or on location (Paris, Gothenburg, Kampala). text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=description&rev=1402308076&do=diff All objects (blocks, materials etc.) can be given a free text description. The description can contain hyperlinks to other objects, documents or web-pages. See also * Name * Block text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=deterministic_simulation&rev=1402308076&do=diff A deterministic simulation is a single simulation run with the best estimate value for all parameters (labelled Value in the parameters screen). The result is then one value for each output. See also * Probabilistic simulation * Sensitivity analysis * Simulation screen text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=dimension&rev=1402308076&do=diff The dimension of a block is determined by the total number of dependencies it has. A block with no dependencies is called “scalar”, one dependency a “vector” etc. See also * Dependency text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=discrete_event&rev=1402308076&do=diff Discrete events are used by various blocks in order to trig an action. The snapshot block uses a discrete event in order to trigger the snapshot, the transfer block can specify a discrete transfer by referencing a discrete event. The discrete event can also be used to notify the ODE text/html 2015-08-13T13:00:28+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=dopri45_solver&rev=1439470828&do=diff Dormand-Prince Explicit one-step solver based on Runge-Kutta (4,5) pair of Dormand and Prince. Applicable for non-stiff problems of medium accuracy. Applicable solver settings: * Absolute tolerance * Relative tolerance * Initial step size * Max step size text/html 2015-08-13T13:13:18+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=environment&rev=1439471598&do=diff There are (currently) three models that represent different parts of the environment; atmosphere, river and soil. These models only model the processes occurring in the media and not biota or fauna living therein. The concentrations calculated for media can be used by other models (eg. the food models). In the case where the user do not wish to dynamically model these concentrations, but use measurements instead, there are text/html 2015-08-13T13:06:02+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=error_messages&rev=1439471162&do=diff Introduction All error messages are presented in the simulation screen. Some are presented even before a simulation has been run, and some are presented in the simulation log if a simulation fails. Errors MessageSolutionNo materials enabledXXX is emptyValue/PDF is missing text/html 2015-08-13T13:04:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=excel_file_format&rev=1439471050&do=diff Introduction The Excel file format is designed in a way so that it is readable for both machines and people, and the same format is used for both parameters, time series and options. For simplicity this page will refer to them all as parameters. To make things easier when importing values, it is highly recommended to create a template file by exporting the values from MERLIN-Expo. The values in the template are then replaced with real values and the file can then be imported back into MERLIN-E… text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=exporting_charts&rev=1402308076&do=diff A chart can be saved as an image. The data presented in the chart can also be exported to Excel. Note that exporting chart data exports only the numbers displayed in the chart. That is, if you need all the underlying data you need to export simulation results directly. To save the chart as an image: text/html 2015-08-13T13:26:20+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=exporting_parameters_time_series_and_options&rev=1439472380&do=diff Introduction By exporting parameter and lookup table values to Excel, data can be separated from the model structure. In larger projects this separation is common, as model development usually is the responsibility of a different group of experts compared to the gathering of input data. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=exporting_tables&rev=1402308074&do=diff Data for a table can be exported either to Excel or as Tab-separated_values. For large tables, a tab-separated values file is generated much faster than an Excel file. Note that exporting table data exports only the numbers as displayed in the table. That is, if you need all the underlying data you need to text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=expression&rev=1402308076&do=diff The expression block can be used to specify an arbitrary function of the model parameters and /or the quantity in other blocks (such as compartments and lookup tables. In short, the expression block represents an algebraich expression in the model. See also * Block text/html 2015-03-05T14:48:50+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=food&rev=1425566930&do=diff Concentrations in food is used by the human intake model. Food are separated into the following categories: * Fish - Bass, Perch, Salmon etc. Given by the Fish model * Fruits - Apple, Peach etc. grown locally. Given by the Fruit tree model * Grain - Wheat, Rye etc. Given by the Grain model text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=full_name&rev=1402308074&do=diff The full name is a descriptive name of a block, material or other object. As the name of a block or material is used in equations it is typically being an abbreviation of the full name or a symbol. The full name thus serves as an explanation of the name. If a full name is given to a block, it is used in favour of the text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=general_problems&rev=1403687710&do=diff a text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=general_variable&rev=1402308074&do=diff A general variable acts as substitute for another object and is used when the model creator wants to present users with different options for a certain calculation. In MERLIN-Expo, general variables are listed in the options screen. See also * Options screen * Block text/html 2015-08-13T13:24:52+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=glossary&rev=1439472292&do=diff * Aggregate * Assessment * Block * Chart * Compartment * Connector * Contaminant * Default * Dependency * Description * Deterministic simulation * Discrete event * Expression * Food * Full name * General variable * Group * Graph * ID * Index-list * Interaction matrix * Iteration * Lookup table * Material * Matrix - see Interaction matrix * Measurement model * Model * Model input * Model output * Name * ODE * Ordinary d… text/html 2015-08-13T08:15:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=graph&rev=1439453726&do=diff The graph is a box and arrow diagram which is used to visualize a model in the model screen. text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=group&rev=1402308076&do=diff A group is a light-weight sub-system, which is used only to group or package blocks graphically. * Groups are represented containers in the interaction matrix and graph, and can be expanded or collapsed by pressing the + symbol. * A group will _not_ affect the ID of a block. * Groups cannot be connected using text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=guid&rev=1402308076&do=diff Globally unique identifier A 16 letter code which is used to identify a value or object. See also * Excel file format text/html 2015-08-13T13:03:20+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=how_to_read_this_guide&rev=1439471000&do=diff This guide is written as a wiki, which is a popular format for user manuals as it allows many collaborating authors to work together on the same document. It is available from within the MERLIN-Expo software and also from the MERLIN-Expo homepage. On the homepage you will also find many other resources such as videos and training tutorials. text/html 2015-08-12T11:29:40+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=human_intake&rev=1439378980&do=diff For estimating the exposure to man there are two models; * Human intake will assemble the total exposure to one person (concentration inhaled and total quantity ingested) from different sources (internal and external to the investigated area). * Man will calculate the final concentrations in organs of a human body using the concentration/quantity) of the human intake model as input. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=id&rev=1402308074&do=diff The ID gives the full path to a block through the hierarchy of sub-systems that contain it. The ID consists of the name of the block and the ID of its parent sub-system. For example, with a hierarchy where the sub-system _France_ contains the sub-system _Paris_ which in turn contains the expression _Price_ their ID's are: text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=importing_and_exporting_data&rev=1402308076&do=diff Introduction Import and export of data is a useful feature for modelling software. It allows decoupling of user roles, so that people dealing with data collection can work independently (more or less) of people running simulations and of people concerned with analysis of results. text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=importing_and_exporting_simulation_results&rev=1402308076&do=diff Overview Simulation results are necessary to create charts and tables. You can mix results from different simulations in the same chart or table. By exporting (and importing) results, you can include results from other simulations in your project in order to compare or benchmark results. text/html 2015-08-13T12:48:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=importing_parameters_time_series_and_options&rev=1439470126&do=diff In order to import values, the data must be organised according to the Excel file format. The easiest way to achieve a correct syntax is to first export the parameters to * Click the Import button in the toolbar of the data input screens. * Select the Excel file(s) that contain the values to import. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=index-list&rev=1402308074&do=diff An index-list is used to describe a dependency. It has a name, full name etc, and also a listing of indices. For example, the material index-list lists all materials being studied. See also * Dependency * Index text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=index&rev=1402308076&do=diff An index is the atomic part of an index-list. Rather than using numbers for indices, MERLIN-Expo uses string values which are enumerated using index-lists. Examples of indices are “Arsenic”, “Clay” or “Adult”. See also * Index-list text/html 2022-06-30T18:12:00+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=info_screen&rev=1656612720&do=diff Information screen The information screen is displayed when MERLIN-Expo is launched. It is used to , and save projects. It also lets you describe the study being made and attach files related to the study. Tool bar New Starts a new project. See Open text/html 2022-06-30T18:24:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=installation_instructions&rev=1656613466&do=diff Windows Download installer * Log in as administrator. * Check if your operating system is 32-bit or 64-bit (instructions). * Download the setup program from the Download section of the MERLIN-Expo homepage. * Run the MERLIN-expo_setup_XXX.exe file. * Read the license agreement * Select a destination folder for MERLIN-Expo. The todefault is text/html 2015-08-13T08:19:04+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=interaction_matrix&rev=1439453944&do=diff An interaction matrix is an alternative way to visualize a model. The model components are placed on the diagonal of the matrix and the interactions (processes) are placed clockwise on the off-diagonal elements. MERLIN-Expo lets you see the model either as a box-and-arrow diagram ( text/html 2026-04-21T12:30:25+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=introduction&rev=1776774625&do=diff Welcome to MERLIN-Expo. About The MERLIN acronym derives from this description of the tool: Modelling Exposure to chemicals for Risk assessment: a comprehensive Library of multimedia and PBPK models for Integration, Prediction, uNcertainty and Sensitivity analysis. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=iteration&rev=1403687710&do=diff In an iteration the equations of the mathematical model are solved from the start to the end time. A deterministic simulation only requires one iteration, whereas a probabilistic simulation or a sensitivity analysis require many iterations. See also * Simulation text/html 2022-06-30T18:22:20+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=library&rev=1656613340&do=diff Models library The MERLIN-Expo models library is a collection of models that can be used individually, or together, to form the mathematical model for the study. These models are referred to as sub-systems. Sub-systems can be connected, so that one sub-system provides input data for another sub-system. Contents text/html 2015-08-13T13:09:22+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=link&rev=1439471362&do=diff A link lets you teleport from one point in cyberspace to another text/html 2015-03-13T05:40:50+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=log_file&rev=1426225250&do=diff To access the log file for MERLIN-Expo, follow these steps: 1. Open Windows explorer (the file manager). 2. In the address field, write %appdata% and press ENTER 3. Go into the 4FUN folder, then into the log folder. 4. The log file is named log.txt text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=lookup_table&rev=1402308074&do=diff The lookup table block computes an approximation to some function y=f(t) given data vector y. By default t is the current time point of the simulation, but can also be sent as an argument when calling the lookup table. A lookup table can be cyclic, meaning that it repeats itself when asked for data outside of the time frame given. It can also be set to either interpolate/extrapolate values or to return values as a step function. text/html 2015-08-13T13:23:22+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=material&rev=1439472202&do=diff “Material” is the term used in MERLIN-Expo to identify the modelled items, for example contaminants like Lead or Arsenic. In other software and literature, material is sometimes referred to as species. See also * Contaminant text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=mathematical_model&rev=1402308076&do=diff A (mathematical) model is the representation of a process or system. It contains a set of parameters and mathematical equations related to each other, in order to describe the behavior of such process or system. A model consisting of several interconnected compartments is equivalent to a system of coupled ordinary differential equations (ODE). text/html 2015-08-13T08:56:52+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=measurement_model&rev=1439456212&do=diff When the user wants to use measurements or pre-calculated data, rather than using MERLIN-Expo to calculate it dynamically, the measurement versions of the environmental models can be used to avoid having to enter the same data in many places. For example: The user wants to calculate the resulting concentrations of different types of crop, given soil concentrations that have been measured. The user thus adds one model for each category of crops. Each category will ask for soil concentrations (i… text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=min_max&rev=1402308076&do=diff The min/max block will store the minimum or maximum value of a given expression during the simulation. It can be set to “reset” at a specific time point or event. See also * Block text/html 2015-03-05T14:48:50+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=model_input&rev=1425566930&do=diff A sub-system often needs input data from you. A soil model might need precipitation data, a fruit model might need soil concentration data, etc. Sometimes this data can instead be provided by another sub-system. A block whose data can be provided by another sub-system is referred to as a model input. text/html 2015-03-05T14:48:50+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=model_output&rev=1425566930&do=diff The data computed by a sub-system can sometimes be used as input data to other sub-systems. A block which can be used as an input for another sub-system is referred to as a model output. See also * Connector * Model input * Sub-system text/html 2022-06-30T18:17:02+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=model_screen&rev=1656613022&do=diff Model screen The Model screen displays the mathematical model for the study and is in a sense the heart of the MERLIN-Expo software. It allows you to review all equations, parameters and variables of the model and to see how different parts of the model are related. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=model&rev=1403687710&do=diff See mathematical model text/html 2015-08-13T10:00:22+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=models&rev=1439460022&do=diff MERLIN-Expo has a rich and growing library of (mostly) dynamic models which can be combined to form a web of models that together calculate the exposure pathways from one or more sources to the end-point(s) of your scenario. The models are accessed from the text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=name&rev=1402308074&do=diff The name of an object is used in equations to identify the object. The name of a block must be unique within its sub-system. See also * Full name * Symbol * ID * Sub-system text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=ndf_solver&rev=1403687710&do=diff Implicit multistep-solver of variable order (1-5) based on the Numerical Differentiation Formulas (NDFs). Applicable for stiff problems of low to medium accuracy. Applicable solver settings: * Absolute tolerance * Relative tolerance * Initial step size * text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=ode&rev=1403687710&do=diff The mathematical model consists of a system of ordinary differential equations which are solved using a numerical solver. See also * Solver text/html 2022-06-30T18:18:20+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=options_screen&rev=1656613100&do=diff Option screen The option screen lists all options offered by the sub-systems that you have selected for you model. Tool bar Help Shows this page Changing options Select an option in the list to the left to change it. Information about the selected option appear in the panel on the right. text/html 2015-03-09T11:58:28+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=options&rev=1425902308&do=diff Model components can offer different options. For instance, the user can select to insert either time dependent or constant data for a specific input. Another example could be different choices to calculate a partition coefficient or selection of a QSAR model. text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=parameter&rev=1402308076&do=diff Parameters are objects that hold values and that are used in other objects of the model, for instance in transfers and expressions. The value of a parameter must remain constant through a simulation, and is given either as a number or a probability density function. See also * Block * Parameters screen text/html 2025-01-16T15:19:12+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=parameters_screen&rev=1737040752&do=diff Introduction This screen lists all parameters that can be changed by the user. For a normal deterministic simulation, you need to enter a nominal value for each parameter. For a probabilistic simulation, you need also to assign probability density functions to the uncertain parameters that you wish to include in the analysis. Tool bar text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=parent&rev=1402308076&do=diff The term parent (node) is often used in computer science when talking about tree data structures. In MERLIN-Expo, a common tree is the hierarchies of sub-system, where a block resides in a parent sub-system. See also * Sub-system text/html 2025-01-16T15:17:30+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=pdf&rev=1737040650&do=diff A probability density function describes the (lack of) knowledge for a parameter. Uncertain parameters can be assigned PDF’s and be included in a probabilistic simulation. Common probability density functions are * exponential distribution * normal distribution and log-normal distribution * triangular distribution * uniform distribution PDF's are assigned to parameters in the parameters screen using the PDF editor. See probability density functions for a list of all PDF's. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=performing_a_sensitivity_analysis&rev=1403687710&do=diff Introduction There are several methods and algorithms used in sensitivity analysis: * - are used to discover non-linearity. * - are used to find which parameters are relevant to study. * - for linear models. * - for monotonic functions. * - model free but computational expensive. Charts and tables text/html 2025-01-16T11:54:02+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=performing_an_uncertainty_analysis&rev=1737028442&do=diff Introduction Uncertainty analysis involve the propagation of uncertainty in model inputs (parameters) to estimate their impact on model outputs. From uncertainty analysis one can also learn of the importance of specific parameters (and other model components) to an end result. It is recommended that uncertainty analysis is performed iteratively. It is time consuming (and therefore costly) to collect detailed data for parameters. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=preferences&rev=1403687710&do=diff Introduction Preferences let you customize the visual appearance of MERLIN-Expo and to give settings for databases and simulation engines. The preference window is opened from the menu File | Preferences. Charts and tables * Log axes - Set log scale axes for new charts text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=probabilistic_simulation&rev=1402308076&do=diff A probablistic simulation, or Monte Carlo simulation is used to calculate the risk or uncertainty in simulation results from uncertainty/variability in the simulation inputs (parameters)). Instead of running one simulation, many simulations are run where the parameter values are randomized to cover as many combinations of parameter values as possible. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=probability_density_function&rev=1403687710&do=diff See PDF text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=project&rev=1402308076&do=diff A project contains all the information related to your study; the model with its equations and structure, the default data and the data provided by the user, plots and tables of simulation results and the report. When saved to disk, a project file is given the extension .eco. text/html 2015-03-19T12:09:58+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=report_screen&rev=1426766998&do=diff Introduction The report page lets you generate a report for the study. You can control what to include in the report by editing the report settings. Once a report is generated, you can save it as an html file (which can be opened in Microsoft Word or OpenOffice), or as an Adobe PDF file. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=running_mean&rev=1402308074&do=diff The running mean will integrate a given expression over time and return the mean value. The running mean can be set to start or stop the integration at specific events or to reset the integrated value. See also * Block text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=scenario&rev=1402308074&do=diff Scenarios are used for running a sequence of simulations, typically when you want to use the same model for different sets of input data - perhaps for different geographical locations. You can also use scenarios to experiment with solver settings or to run a sequence of different sensitivity analyses. text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=sensitivity_analysis&rev=1403687710&do=diff Sensitivity analysis studies how input factors (parameters) impact a model output, typically how variability in the parameters contribute to the total variability of a simulation end-point. See also * Performing a sensitivity analysis text/html 2015-08-13T12:45:24+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=simulation_issues&rev=1439469924&do=diff Introduction The dynamic nature of the environmental models make them very sensitive to input data. This means that with inconsistent parameter and time-series input data, the numerical solver might not be able to solve the equations or might end up with crazy results. With the risk of annoying the reader, it must be re-iterated that the most common source of problems is that the user has started too big. By working in smaller increments many problems can be avoided. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=simulation_output&rev=1402308074&do=diff A simulation output is the value(s) of a block that have been calculated during a simulation. A simulation output can be constant or a time series, and have several dependencies. The list of outputs to present after a simulation is available in the Outputs tab in the simulation settings window, and you can choose to include as many or as few outputs as you wish. Note however, for text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=simulation_screen&rev=1403687710&do=diff Introduction The simulation page lets you run deterministic, probabilistic (Monte Carlo) or sensitivity analysis simulations. The error section lists problems that must be solved before a simulation can be performed. Toolbar RunStarts a simulation.Simulation settings...Displays the window.Probabilistic settings text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=simulation&rev=1403687710&do=diff During a simulation, the simulation outputs are calculated for the inputs as provided by the user. The simulation is started in the simulation screen. A simulation will return a folder in the result panel which contains all the simulation outputs. A simulation consists of one (deterministic or more (probabilistic) iterations. In each iteration all the equations of the text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=snapshot&rev=1402308074&do=diff The snapshot block takes a snapshot of a given expression when a discrete event is triggered. See also * Discrete event text/html 2015-08-13T13:11:32+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=solver_settings&rev=1439471492&do=diff The solver tab lets you choose which Ordinary Differential Equation (ODE) solver is to be used in the simulation. Absolute tolerance Absolute error tolerances that apply to the individual components of the solution vector. Absolute tolerance is a threshold value below which the value of the solution component is unimportant. The absolute error tolerances determine the accuracy when the solution approaches zero. The setting is globally defined in the solver tab but can be overridden if defined… text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=solver&rev=1403687710&do=diff A solver is a software algorithm that solves a system of ordinary differential equations. The choice of solver is crucial for complex models. Below we describe some of the terms defining the different solvers implemented in MERLIN-Expo. The solver is selected in the solver tab of the simulation settings window. This tab also let you configure parameters for the solver. text/html 2014-06-09T10:01:16+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=source_sink&rev=1402308076&do=diff Source/sink blocks represent objects outside of the model who either feed or pulls materials from compartments. See also * Compartment * Transfer * Block text/html 2022-06-30T18:13:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=start&rev=1656612794&do=diff The MERLIN-Expo user guide * Introduction * How to read this guide * Conventions * Glossary Examples and tutorials * Getting started * Creating an aquatic food web * Uncertainty analysis * VERMEER Tools Reference * User interface * Information screen * Model screen * Context screen * Options screen * Time series screen * Parameters screen * Simulation screen * Charts screen * Tables screen * Report screen * Models * Environment * … text/html 2015-08-13T13:22:44+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=sub-system&rev=1439472164&do=diff Sub-systems are containers for blocks and are used to make large models more manageable and understandable. The sub-system also acts as a name space for the blocks that it contains, which means that it will determine the ID of the blocks and guarantee that there are never two blocks inside the same sub-system with the same name. Finally, sub-systems can communicate with other sub-systems through the use of text/html 2015-08-13T12:43:24+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=symbol&rev=1439469804&do=diff In mathematical expressions it is common to use symbols for variables and parameters - greek letters are popular. This makes equations more compact and also international - ρ is understood by French and English phycisists to be density. MERLIN-Expo uses symbols in the text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=system_requirements&rev=1402308074&do=diff MERLIN-Expo is designed for Microsoft Windows, but can also run on OSX, Linux and Unix. Minimum System Requirements * OS * Windows - Windows XP (32-bit) * Linux * Red Hat Enterprise Linux 5.5+, 6.x (32-bit), 6.x (64-bit)* * Ubuntu Linux 10.04 and above text/html 2015-08-13T12:39:08+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=table&rev=1439469548&do=diff Tables present simulation output data in tabular form. Depending on which view of the output data you seek there are different tables to choose from: * Time table - Displays data for each time point. Useful for time dependent simulation outputs, like those from compartments. * Index table - Displays data for each index. Useful for one or two dimensional outputs. text/html 2015-08-13T12:42:30+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=tables_screen&rev=1439469750&do=diff Introduction The tables screen lets you create tables with data from simulation outputs. It is very similar to the charts screen. When you run a probabilistic simulation there are several types of tables that are dedicated to probabilistic results and sensitivity analysis. A table is created by selecting outputs in the list. MERLIN-Expo will attempt to create a table which suites the selected output, but if you want a specific table you can select the table type from the menu. text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=tag&rev=1402308074&do=diff A tag is a label assigned to a parameter (or other block) and is used as a search keyword. Any number of tags can be assigned to a block. Tags can be seen as “light” categories. See also * Category * Sub-system text/html 2014-06-25T09:15:10+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=tasks&rev=1403687710&do=diff This chapter deals with common tasks performed with the MERLIN-Expo software. * Importing and exporting data * Performing an uncertainty analysis * Performing a sensitivity analysis * Dealing with data gaps text/html 2015-03-09T14:03:30+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=time_series_screen&rev=1425909810&do=diff Introduction Time series are used for temporal measurements and data such as wind speeds, precipitation, concentrations in water etc. The data you need to provide for your study depends on which sub-systems you have selected for your model. Tool bar Export to Excel See text/html 2015-03-09T14:03:54+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=time_series&rev=1425909834&do=diff Time series data is implemented in models using a lookup table. You enter time series data in the time series screen. See also * Glossary * Lookup table text/html 2014-06-09T10:01:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=transfer&rev=1402308074&do=diff Represents the transfer of quantities of materials between compartments. It defines the quantity of the materials that is subtracted from a source/sink or compartment block and added to a destination compartment or source/sink block. Transfers can be made discrete (instantaneous) by assigning a discrete event. See also * Compartment text/html 2015-08-11T08:07:14+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=troubleshooting&rev=1439280434&do=diff MERLIN-Expo is a flexible tool which allows you to do things in the order you prefer. It has powerful features such as probabilistic simulations and sensitivity analysis. The models are dynamic and often sensitive to input provided by the user. All of these things make it more or less inevitable that you will sooner or later run into trouble. text/html 2022-06-30T18:19:02+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=tutorial_getting_started&rev=1656613142&do=diff Getting started This brief tutorial will get you acquainted with the MERLIN-Expo user interface and philosophy. We will cover the different steps taken when using MERLIN-Expo for a study, from setting up the model to entering data to running simulations to inspecting results. text/html 2022-06-30T18:15:54+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=tutorial_uncertainty_analysis&rev=1656612954&do=diff Uncertainty analysis - Tutorial (Work in progress) In this tutorial you will perform an uncertainty study on the fruit tree model. The goal is to find out how PCP101 is taken up via root uptake by apple trees. You will learn * How to describe the uncertainty in parameters by assigning text/html 2015-08-13T13:14:28+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=unit&rev=1439471668&do=diff Notation Units are written using superscript, eg. kg m-3. Subscript is used for annotated units, eg. kgFW (kilogram fresh weight) Units in MERLIN-Expo Data is entered and delivered by MERLIN-Expo in SI-units. Contaminant masses in MERLIN-Expo is entered in text/html 2015-03-05T14:08:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=user_interface&rev=1425564506&do=diff Overview The user interface of MERLIN-Expo is organised as ten screens which are accessed through tabs (coloured blue in the picture above). The tabs are ordered as the screens are intended to be used: * Info screen - for opening and saving projects and for describing your study. text/html 2015-08-13T08:20:58+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=value&rev=1439454058&do=diff The word Value typically refers to the nominal value/best estimate of a parameter. text/html 2022-07-13T09:19:52+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.merlin-expo.eu/doku.php?id=vermeer_tools&rev=1657703992&do=diff VERMEER Tools As a result of the work done within the LIFE VERMEER project, new models (VERMEER tools) were added to the MERLIN-Expo software. The VERMEER tools are embedded in the tool as model templates in the form of predefined scenarios that correspond to the specifications that were identified for the case studies in VERMEER project.