DISPAS v.0.9 - User manual
Contents
1. is given from the RandomHelper class that belongs to RS it is the seed that is generated randomly by the compile to work with pseudo random numbers Is virgin stock Is a boolean variable where the user might decide the nature of the initial stock it means that if the user decide to put a period where the mortality probability by fishery it is egual to zero Hence the agents dies by the natural mortality probability Is the number of newborn variable It was a boolean value by default value is false It means if we checked the box we want to simulate a random stock value from the tick zero Otherwise unchecked state the simulator is going to take the initial values from the survey file Survey data file path The file path where is the survey data real data Default Dispas misc input FISHPASS csv it should not be changed Or here you place your own file data input e World Height Default value 100 ms e World Weight Default value 100 ms As the user wish the world size could be changed making variety values of the Height Weight making it of the desirable size but for our purpose we are going to take as a default value the 100 100 L_inf Max fish length 39 6 cm is the default value A Factor length weight Default Value 0 007 B Factor length weight Default Value 3 0638 kVB length grow rate Default Value 0 44 t 0 VB Default Value 0 46 10 Parameters Of dB X Simulation Parameters2. Default Random Seed 784 884 590 Is Virgin Stock Is the number of new born variable 7 L_inf Max fish length 39 6 Survey data filepath input FISHPASS csv World Height 100 World Width 100 a factor length weight b factor length weight kVB Length growth rate LOVE Figure 17 Simulation parameters screen shot Besides in DISPAS we are going to study the growth rate of our population In order to performe this study we were using the von Bertalanffy growth function where the body length is a function of age This four parameters are outcome from the SoleMon project and default value for this L inf A B kVB t_0 3 3 A Simulation Execution At the first time when the start button is pressed the class context builder is lunched this activity triggers a series of action that are going to be described as following e In the previous explanation we saw all the parameters that the user could change for each simulation Firstly the simulator allocates each agent in a random position in our simulated world as we saw each agent in the 2D world is represented by a circle of different colors It s given by the agent age class bellowing from class 0 to class 5 then we can see the list of colors Color Red Agent class 0 Color Blue Agent class 1 Color Green Agent class 2 Color Cyan Agent class 3 Color Orange Agent class 4 Color Black Agent class 5 The user should remember that fish class agent age c
3. Parameters before the simulation gets start Simulation Parameters on the RS framework In the Figure 14 is showed the upper part of the framework with it the user can start stop restart and pause the executior Above was mentioned the current simulation space is a km of area intending to be a km of the Adriatic Sea It is represented by a grill of 100m x 100m in with the individuals are placed The simulator has the capability to display two different views 2D and 3D The 2D view is a plain grid where the individuals are represented with circles of different colors Im the other hand the 3D view is a three dimensional grid where each individual has it own characteristics one of it is the shape size It changes along the execution depending the age class that the agent belongs to The Figure 15 and Figure 16 are examples of the two different views lThe user may not be familiarized with the RS framework then for know more about can open this Link Page 23 J Dispas de groovylib de repast simphony d Uninstaller __ Anstallationinformation l start_model bat start_model command Figure 13 DISPASim Directory File Run Tools Window T OIT o Figure 14 DISPASim Directory Figure 15 2D view example Figure 16 3D view example 3 2 1 The Simulation Parameters In this subsection we are going to explain the simulation parameters a screen shot is the following Figure 17 Default random seed
4. html Best Regards Made with IzPack http izpack org Step 2 of 8 Figure 5 Brief information page about DISPASim FT IzPack Installation of DISPASi Bca jc E Please read the following license agreement carefully The Dispas model is licensed as provided for by the authors Please contact them for details I accept the terms of this license agreement I do not accept the terms of this license agreement Made with IzPack http izpack org D Figure 6 License agreement of DISPASim E Select the installation path E Program Fies x86 DISPASm Finished Figure 8 Screen shot of the installation finished Figure 10 Installation Complete d Dispas 31 08 2014 21 31 Carpeta de archivos a groovylib 31 08 2014 21 29 Carpeta de archivos do repast simphony 31 08 2014 21 31 Carpeta de archivos di Uninstaller 31 08 2014 21 31 Carpeta de archivos _ installationinformation 31 08 2014 21 31 Archivo INSTALLA DISPAS setup jar 31 08 2014 11 31 a Executable Jar File amp start_model bat 31 08 2014 21 31 Archivo por lotes _ start model command 31 08 2014 21 31 Archivo COMMA Figure 11 Installation Complete Figure 12 Installation Complete highlighted file start_model bat is the executable for DISPASim Double click on it and is going to lunch the simulator 3 2 The Simulator DISPASim allow to the user change
5. installation finished 7 Selection of the location path for the installation 9 Selection if the user want shortcuts of DISPASim 10 Installation Complete 11 Installation Complete 12 Installation Complete 13 DISPASim Directory 14 DISPASim Directory 15 2D view example 16 3D view example 17 Simulation parameters screen shot II 1 Introduction Overfishing in the Mediterranean Sea has gained an increasing considera tion in the last years In particular the potential damages in the recovery capacity of the commercial stocks Besides a lossy controlled fishing ac tivity could be a serious problem if it is not faced with appropriate infor mation and scientific support With this aim the Demersal flshing Stock Probabilistic Agent based Simulator DISPAS was developed With it is possible to gaining a better understanding of the marine exploitation performing the stock assessment Particularly this simulator was devel oped for a living species in the Adriatic Sea the common solea Solea solea Linnaeus 1758 Soleidae Witch main fish population is concentrated in the north and central part of the Adriatic Sea DISPAS has been developed following the Agent Based Methodology that is a growing approach with an increasing number of applications Scenarios where this methodology can be applied are from different and di verse contexts like ecosystem environment chemical r
6. pretty accurate with the first version In case of the user has any question not doubts to contact to the authors 12
7. DISPAS v 0 9 User manual Cesar Augusto Nieto Coria Luca Tesei School of Advanced Studies Computer Science Department University of Camerino 2nd September 2014 Camerino Italy Abstract The present document is an user manual and installing guide for DIS PAS It is going to explain how to install it as well as the uninstall process Further how to simulate with the tool Because of the simulator is fully developed under Java the process for installing is the same for all the Operative Systems available on the market In the first section we have an introduction to introduce to the reader on the research context In the second section is going to explain how to install and uninstall the simulator The third section is about the simulator their parameters and settings that user may tune with the aim to test different simulation scenarios Contents 2 Installation Guide 2 1 Installing DISPASim 2 2 Uninstalling DISPASim eee eee eo bee eee ew 32 The Similator ss segg de ve Ed PERE ES 3 2 1 The Simulation Parameters 3 3 A Simulation Executioni 08 4 List of Figures 1 The von Bertalanffy growth equation chart 2 DISPASim version 0 9 3 DISPASim Installer location example 4 Language selection screen shot 5 Brief information page about DISPASim 6 License agreement of DISPASim 8 Screen shot of the
8. e we need to download and run the next this is usually for MS Windows users In the other hand if you are a GNU Linux user is much easier just to open your shell console and download as usu ally for any program that you have installed before For e g in Ubuntu is sudo apt get install java Furthermore in the following Link the user can find the different Java distribution in order to download and install it Once that we have the JVM and downloaded the installer package we can proceed with the installation Go to the place that you have downloaded the installer in order to execute you have to make double click in the DISPAS setup jar As soon as we have downloaded the installation package make double click on it then is going to start the installing process The installation is a regular software installation process with windows environment The DISPAS installer can be executed in all platform The first screen shot Figure 4 that we have is where the user can select the installing language Once that we have choose it press Ok button Figure 4 Language selection screen shot The next installation step Figure 5 is a brief information about DIS PAS to continue press the button Next Following we have to agree with the License Agreement Fig 6 In the Figure 7 displays the next step where the user can select the folder installation location If the user wants to install it in the root directory might execute
9. eaction simulations financial markets simulations decisions support systems traffic control systems With regards to the purpose of the simulator e g simulating the marine ecosystem in the Adriatic Sea we need modeling techniques that can deal with the complexity of the task This led to the use of the agent based methodology for developing DISPAS The simulator is able to reproduce a good number of scenarios for example generating a random population or from a text file Also allows the user to change parameters for the simulation interactively within the Repast Symphony framework The simulated space represents a square km of the Adriatic Sea It is displayed by a grill of hundred meters per hundred meters 100m x 100m in which the individuals our specie of study common soles are living The current view is in two dimensions 2D but the simulator also has the capability to display a 3D view were the agent size and the difference between the different age classes can be appreciate As it was mentioned the individuals are classified in an age classes division It is performed applying the von Bertalanffy growth equation which is the most widely used growth curve and is specially important in fisheries studies The principal objective of the simulator is the common sole stock as sessment In order to accomplish it DISPAS uses input data coming from the SoleMon project which is based on an independent fishery study col lecting data di
10. lass depends on the length and growth It means that meanwhile the time is passing the individuals are evolving this evolution is reflexed in the agent age class change 11 e The quantity of the initial stock could comes from two different sources One that we should decide initialize our virgin stock in a random way Is virgin stock equals true The second one is taken the data from our own survey file e When the user press the play button the simulation is going to start is essential remember that in the temporal aspect RS tool kit use the sense of tick a single tick could take any representation that we would want hours minutes seconds milliseconds and so on in our simulator each tick is equivalent of a month for example in the tick number 1230 and taken as point of start the 2 005 year we are in June of 2 107 year e The newborns agents are added respecting the amount indicated on the survey file in the current version of the simulator the newborns are added in June of each year Due to a biological conditions of the common sole However where are not more data available the newborns are added in a random quantity depending on the last year data and making it change depending on a calculated standard deviation e Finally the simulated population generated with DISPASim is stored in an external text file in the following address Dispas output Note The current document is not the final version of the user manual but is
11. rectly from independent surveys in the Adriatic Sea For this work we have been provided with the data from the National Council of Research CNR We used data that is the number of soles per each age class found in the same square km every year in November from 2005 to 2011 After processing the data we have derived the fishing probabil ity and the natural mortality probability for soles divided into five age classes We obtain the probabilities and quantities monthly for each agent age classes It was mentioned above the agents are classified in five age classes the classification is made using the von Bertalanffy growth equation The simulator calculates sole s length in function of its age in a particular time using the von Bertanlanffy growth equation t L length Graph n AS SET nf Equation B LOL 1 6404 a E Li 0 A Fyn 0 age Figure 1 The von Bertalanffy growth eguation chart Fe Fan Tas inda JB OVO Vy BCOVAGSERE R Tie Count 20 haipad arab Sees Tree Ueber Parsel Baneri rekriduih See cais Eigra Toei Mode DD Degli ena Mode Wb Value Laver Passed o Figure 2 DISPASim version 0 9 The time is an important characteristic because it provides the indi vidual s notion of evolution In DISPAS at each time step tick in Repast Simphony represents a month of the year The simulator uses the data derived by the SoleMon Project
12. that it consist in scientific independent surveys as input The data encompass the fish quantity belonging to each fish classes as well as the indexes for the natural mortality probability and fishing probability After execute the simulation DISPAS saves in an ex ternal text file the results of simulation with the following information Total Biomass and Number of individuals per Class gt Oo Download X Buscar Download Organizar v Incluir en biblioteca v Compartir con w Grabar Nueva carpeta Hss Fill A E Nombre Fecha de modifica Tipo Tamano Ft Favoritos Je Descargas DISPAS setup jar 29 08 2014 07 17 a Executable Jar File 94 786 KB 2 Dropbox WE Escritorio Bibliotecas Sitios recientes di workspace A Bibliotecas Documentos amp Im genes a M sica Subversion BJ Videos iM Equipo amp Disco local C ca Disco local D 1 elemento Figure 3 DISPASim Installer location example 2 Installation Guide 2 1 Installing DISPASim The starting point of this guide is download the DISPAS installation pack age that can be found in the following Link DISPAS was developed using the Repast Simphony RS framework in RS the modeler can develop in which language he she prefer e g Java Python Netlogo Groovy etc The RS suite runs under Java it means that to be able to run our model we need to have installed the Java Virtual Machine if the computer does not has it befor
13. the installation package with the those privileges After that the installation will proceed And the successive step will as if the user want to create the DISPASim shortcuts The installation is pretty intuitive if you have any problem with it please contact us 2 2 Uninstalling DISPASim The uninstall process is going to delete the DISPASim from your hard disk as is displayed in the Figure 11 the highlighted folder in the where is it the Uninstaller package In order to execute it the user just have to make double click in it So the uninstall process will start as it is displayed in the Figure 12 Finally when it is complete the user can close the window Note after the uninstallation some directories are going to remain in your installation location those are where the simulator output files were stored 3 DISPASim 3 1 The Simulator Execution In the section below we are going to explain how to execute and tune the simulator First we are going to see how to execute in your DISPASim location folder you might have something like in the Figure The 14 Please read the following information The present is the DISPASim installer THe software has the purpose to perform the stock assessment for the Demersal Fishery in the Adriatic Sea It was developed under the Repast Symphony suite for the staff of the University of Camerino For further information you can go to http giano cs unicam it documentation
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