MetaModel Manager Manual
Contents
1. MetaModel Manager Version 0 9 1 User s Manual NOTE if you choose Open an Existing Project at the start up screen MMM will import the specification files which the user had previously uploaded and saved to a mmmn file You will automatically be advanced the Dataset Definition screen MetaModel Manager Version 0 9 1 User s Manual Dataset Definition screen a9 DataSet Definition gt z Populations Defined by Vortex VPJ file Global variables will be shared across all applications Population and Individual Variables will be shared within the System therefore included on this list 10 MetaModel Manager Version 0 9 1 User s Manual Order Model Steps screen ab Order Model Steps 7 Model El Vortex System 159 exper2Vort Baseline Spatial Do Vortex Functions Model on this page you can control for the ordetin which MMM runs the linked programs and also specif ps each program will run before e user must decide the best order Buttons f the page control for the overall design of linked programs i Juping data overrides duration and number of iterations Up Down Buttons allow the user to move linked programs up or down and help the user control the overall order of the metamodel Group Group Group is used for managing the time steps With this function it is possible to group two2. Biocomplexity Network January 2013 MetaModel Manager Version 0 9 1 User s Manual Chapter 1 Introduction 1 1 What is the MetaModel Manager The MetaModel Manager is a new conservation biology software program designed to link population demographics of multiple interacting species with other processes such as emerging diseases habitat and climate change landscape dynamics and or animal movement patterns MetaModel Manager integrates computer simulation models such as Vortex Outbreak and Spatial in addition to other user created models to understand the influence of environmental demographic and genetic factors on the probability of extinction of threatened species Like the programs its works with MetaModel Manager s function is to serve as a predictive modeling tool used to determine likely outcomes for a given scenario or to compare outcomes across multiple scenarios The program runs iteratively and its results are generated in the form of means or probabilities within the linked program platforms Analysis and interpretation offesults can be used in the establishment of conservation goal and to direct or prioritiz conservation action MetaModel Manager can be used in ahinterdisciplinary workshop setting or by individual users The software wa srecently released as version 1 0 and further enhancements are planned for the near future 1 2 Philosophy Wildlife conservation problems are complex and must be looked at thr
3. You may use the up aad down arrows to specify at what stage in the MMM process the break shotild occur Once the program has paused the user must select th OKbutton for the simulations to resume The breaks always begin at year 0 By selecting Show Population a table will be generated that displays the entire popwlation with corresponding traits i e Name Index Age Sex Alive for Vortex andthe Disease state StatePermanant DaysInState and Is Vaccinated fofOutbreak The user can change any value in the table Reset changes will turn the values back into thos which had previously been generated in the model Write to a File makes a text file containing the information from the table Input Input The input function allows the user to import values to override those generatedyingthe modeling process This might be relevant in a situation where the user wants more control over the impact of temporally occurring events on population characteristics The text file must be set up according to the following rules 1 Any rows in the file that begin with are ignored so if you want file info a header etc start it with 2 Each row of the file represents a new year 3 Within each row separate the variables that you are changing order matters specified in the MMM interface by a semi colon 4 If the variable is an array separate the elements of the array with a comma 12 MetaModel Manager Version 0 9 1 User s Manual T
4. Macro is an extension of Evaluator allowing evaluation of short programs methods or macros that consist of assignments of variables using Evaluator functions within simple Basic language like program flow Both Evaluator and MMMacro can be used to transform state variables that describe the system populations or individuals See www vortex 10 org Evaluator doc for more information 13 MetaModel Manager Version 0 9 1 User s Manual Total Years is the length of time number of cycles you want full sequence of models to run for The default is 10 years Iterations is how many times you want MMM to generate a complete round of simulation modeling The default is one iteration When you select Next you will be given an option to save the MMM project It is not necessary to save your project in order to continue with the simulation but may be useful to you for future purposes 14 MetaModel Manager Version 0 9 1 User s Manual Simulate Options screen After selecting Next a screen comes up that looks like this N 159_exper2Vort Pop1 Population Landscape Height Population Landscape Width Show plot lines in real time Show plot lines at the end of each iteration D Show plot lines at the end of all iterations Do not show plot lines blob of ink that usually cannot be read it is faster to show the graph at the iteration and even faster to run it wi
5. PD demonstrated in the earlier chapter The following is a more detailed description of how to set up that linkage 1 Creating the Operational Link A key to creating a link to share data between two Vortex models is to define the same or at least overlapping set of global or population state variables GSvars and PSvars that will be shared by both programs but in most cases modified only by one of the two models In this example GS1 is set to be the number of ferrets and GS2 is set to be the number of prairie dogs For BFFs in their own BFF model the number of individuals GS1 is set each year to N the number of individuals generated by the model For BFFs in the PD model the BFF population size GS1 is first set to 50 and then assigned to remain to be GS1 which 22 MetaModel Manager Version 0 9 1 User s Manual means that the PD model will not change this GS1 variable but will read the number of ferrets for use in specifying impacts predation on the prairie dogs GS2 the number of PDs is set in the PD model each year to N the number of individuals generated by the model In the BFF model the number of PDs GS2 is first set to 250 and then assigned to stay as GS2 which serves to read the information from the PD model but not try to change the number of prairie dogs from within the ferret model Global Label Trophic Level State Vars PD Prey BFF Predator Init In Transition In I
6. Variables or may have pre defined state variables that are shared through MMM or may r ad from MMM the variables created by other linked programs For example Outbreak does not provide a way for the user to create his or her own state vatiables but Outbreak always creates a population variable called Prevalence and individual variables called DiseaseState DaysInState StatePermanent and IsVaccinated In addition Outbreak can use any other population individual tate variables created by other programs and handed to it by MMM Any program linked to MMM can accessfthe state Variables defined by other linked programs or can create new variables and add them to the data set MData that is shared with all linked programs This allows each linkedjprogram to read and optionally change the population and individual dafayereated by other programs Just as writing your own model to be linked ito others via MMM is not something that can be explained quickly in this mantalgunderstanding how to make use of the data that do flow among linked programs is also not something that will be immediately obvious to a new user Laterwersions of this manual will provide more detailed explanations and examples but for now an example is very briefly described below Examples inking ortex Vortex In a tw0 species two VorteX metamodel information from each species may be coded into global state variables such as in the case of BFF
7. linked programs to run between themselves for a specified amount of time steps before they pass information back to a third program This is often necessary for inter functionality of metamodels that run more than two linked programs For example Spatial and Outbreak could be run 365 times each for every time Vortex is run Without such grouping the model would look like this 11 MetaModel Manager Version 0 9 1 User s Manual Vortex 1 Outbreak 365 Spatial 365 Meaning that you would run 100 V years for each of which you would run 365 daily time steps of Outbreak and Spatial But in this case Outbreak and Spatial wouldn t really be working together but rather Outbreak would run for its 365 days of the year and then Spatial would simulate its 365 days To get Outbreak and Spatial to alternate one day of Outbreak then one day of Spatial etc they would need to be grouped together so that they as they each fun once they pass data to the other then run again Therefore the model should b s t up as Vortex 1 Group 365 Outbreak 1 Spatial 1 Here within each of the Vortex timefSteps there would be 365 daily time steps of the pair of programs Outbreak afidhS patial Break Break The user may wish to impose breaks during the simulation process in order to see change and msave the interim fesults The breaks can occur by years or multiple of years The breakstean also occur according to rules regarding a global variable
8. of the advantages of using MMM is that the user may model particular components of one program that are known or thought to influence the outcome of another system component For example the disease state of an individual obtained from an epidemiological modeling program may influence the likelihood of reproducing in a Population Viability Analysis PVA model Preparatory work to facilitate inter program information exchange is critical for the linkage between any two programs to carry biological meaning The coding for the linkage can be done directly within the independent specification files through a data translator Evaluator that is provided within MMM and or by using the utility program MMMacro installed with MMM that MetaModel Manager Version 0 9 1 User s Manual allows more complex multi step macros or scripts for manipulating data In many cases especially so for Vortex state variables will need to be set up Evaluator and MMM acro provide the user platforms to manipulate variables passing through MMM to from other programs Evaluator provides the user with a way to write one line transformations of variables describing individuals or the population MMMacro provides a simple way for a user to write on the fly short BASIC like programs often sequences of transformations each handled by Evaluator to process the shared variables in MMM Using MMMacro is not required to establish linkage in cases where specific linkage funct
9. For multiple species models a system level program can be run for each species within a metamodel e Modifier programs these may modify characteristics of the individuals in the population s e Utility programs to provide data transformations these programs provide added functionality to the metamodel but are not n cessarily an attribute of the population being modeled or derived from individually based models Specification files As a first step the user must create specification fil s in each linked program see table below for existing programs adapted for MetaModel Manager The MetaModel Manager will not create these files for you it is something that must be done independent of the MetaModel Manager within the 1 terfaces provided by the linked programs see the introductory user statement at the Start ofthe manual Process order The programs executed via the MMM interface do not technically run synchronously rather they are ex cuted sequentially according to user defined order Switching the order in which the programsyrun may affect the final metamodel outcome and therefore it is important to determine the best ordering for your specific model Time teps Time steps can vary among programs A cycle in one linked program may run once a year whereas it runs daily for another thus occurring 365 times for each time the other runs Any amount of fime steps can be input by the user Inter program prep work One
10. MetaModel Manager Version 1 0 User s Manual METAMODEL m MANAGER one L users Manual version 1 MetaModel Manager Version 1 0 User s Manual MetaModel Manager User s Manual Software written by JP Pollak and Robert C Lacy Manual written by Becky E Raboy and Robert C Lacy Support for the development of the MetaModel Manager software and this manual was provided by the Chicago Zoological Society and a generous grant from Donna Myers and Aaron Leibovitz Thanks to the many colleagues of Metamodeling Network team and the IUCN SSC Conservation Breeding Specialist Group who helped in the conceptualization and development of the program A special thanks to Phil Miller Philip Nyhus and Sara Zeigler in addition to the developers and author of this manual for hours of brainstorming head scratching and testing of the program Cover design by Stephanie Raboy Bacteria photo credit upper right photo on cover Photo modified from Flickr contributor kaibara87 http www flickr com phtetos kaibaral2234750993 according to the creative commons Wolf tracks photo credit lower left photo on Cover NPS Photo wolf images 16190 Copyright 2013 Chicage Zoological Society JR Chicago Zoological Society Inspiring Conservation Leadership Citation of the software Pollak JP and Lacy R C 2013 MetaModel Manager Version 1 0 Brookfield IL Chicago Zoological Society Citation of this manual Raboy B E and Lac
11. ably best to install MMM in the default Program Files folder onthe computer e It is easiest and probably best to create a separate folder for holding your MMM projects The installation automatically creates a C MetaModelManager folder andja C MetaModelManager Projects subfolder for you e We recommend keeping Outbreak Spatial Vortex and other projects in a folder S other than the program file folder where the program is installed The installation creates C SpatialProjects and C OutbreakProjects folders for you The installation automatically creates program short cuts and puts them on your desktop Overview of program s mechanics The combination of making and choosing appropriate specification files that are all linked by unique identifiers with correct process order and time steps and structured with biologically meaningful inter program linkages enables MMM to run as intended to link multiple programs pseudo synchronously see discussion below on process order MetaModel Manager Version 0 9 1 User s Manual passing back and forth and modifying shared information The following sections in this chapter further explain some program technicalities Program Types There are three types of linked programs that MMM can incorporate e System level programs these initialize or define the individuals in the starting population s The system level program will often handle population demographics although this is not a requisite
12. added but not conveyed or modeled properly Sensitivity testing can indicate which variables are most critical to be modeled accurately and can be carried out within linked programs or at higher levels by adding and subtracting linked programs Arguably the success of the MetaModel Manager program for conservation biology is not in the accuracy results that are generated per se but in how well the results are interpreted when keeping in mind its aforementioned limitations 1 3 Implementation System Requirements MetaModel Manager was developed in the C NET programming languagehfor use on computers running MS Windows We believe that it will ran properly under Windows7 and all prior versions of Windows but we cannot guarafitee that it will work under all implementations of Windows It can be run on Apple Mac computers if they are running implementations or emulations of Windows MMM does not itself require much computer memory or processor speed to run However often the models linked with MMM will work best or only if the computer has ample RAM and a fast processor Installing MMM MetaModel Manager is available for fr e download online at www vortex10 org The installation for MMM MMMmInstallation msi pautomiatically configures necessary folders and includes the latest Outbreak Spatial PathHistory and the test version without yet a full GUD of Vortex 10 Some points adYic on folder locations e Itis easiest and prob
13. created to build interdisciplinary connections a an exchange of expertise among specialists concerne ion of biodiversity Westley 2003 An initiative was id odevelop tools and processes for securing the involvement collaborati and responsibility of a wider range of local stakeholders in conserving species in d the ecosystem management required to achieve i enhancing interdisciplinary information exchange gave rise odiv rsity Research Network to the Biocomplexity Network same participants and new members as well The Biocomplexity 2 creating new software Spatial Vaccinator 3 identifying other complementary software HexSim RAMAS the ARC GIS platform 4 identifying potential new programs for development Sim Social 5 and by creating the MetaModel Manager to serve as an interface between these and other user created programs Metamodel Manager is a significant step towards developing truly integrated solutions for species conservation by working across disciplines and by considering the larger picture of interacting and often spatially and temporally explicit phenomena that affect a species outcome The issue of how accurate such complex modeling can be remains a concern Program users and those interpreting results may expect that as model MetaModel Manager Version 0 9 1 User s Manual complexity increases the overall predictive accuracy should increase However the opposite could also occur when complexity is
14. delManager Projeets Samples folder or wherever you may have stored it afterfthe MMM installation 3 Next choose PD MM ReproEffect scenario from the dropdown box 4 Click on Adda Modifier Model and then choose Outbreak from the drop down box 5 Under Project File lick on the icon to open a file dialog and select the PDPlague xmbhOutbreakSpecification from the MetaModelManager Projects Samples folder 6 Now click on Add a System Model and then select Vortex from the Model drop down box 7 Set your Vortex vpj project by opening the choose link and selecting MMM BFFerrets vpj 8 Next choose BFF MM Worse scenario from the dropdown box 9 There is no other linked model to set for Black Footed Ferrets so now select Next to move to the next screen DataSet Definition screen 1 Everything should come up by default showing the GSvars and PSvars used by the Vortex and Outbreak projects Select Next Order Model Steps screen 1 Change Outbreak to have 365 time steps so that it will run a daily simulation Vortex should remain at the default timestep 1 for 1 year 18 MetaModel Manager Version 0 9 1 User s Manual 2 Change total years to 100 and Iterations to 50 Note that you will want to run more iterations for actual scientific analyses here we suggest a small amount just for the sake of time since running more iterations takes significa
15. erein in bold lettering with descriptions following MMM Opening screen Modify Creating and managing loaded applications will usually be a process for prorgamn developers not users of existing programs See chapter 4 for more details on using additional applications Quit select to leave the program Setting System Level and Modifier Programs screen 7 MetaModel Manager Version 0 9 1 User s Manual ription Project File Stochastic Population Viability Assessment Model Choose a Vortex project file r infectious di Choose a Outbreak project file Add System Model Add Modifier Model _ Remove Model modifier files for your model You age fi noose a model Select your system level linked progra choose your specification file from the browser at opens If a Vortex vpj file has multiple scenarios you will need to choose which scenario from a dropdown list Next you can add a modifie Model button Add Modifier Model Selecting this on adds a modifier program Choose the modifier program from the dro for each system level model In some Note that Outbr ak can be run as either a system model doing its own demography or as a modifier model with Vortex or SimSimba or something as the system model If the specification files are not set you will see the message reminding you to do so before you can advance to the next page When user has completed this page select Next
16. esfunctions necessary to have programs developed in these languages access data in MMM However even if you have no expertise programming insuch languages yow an write simple macros or scripts as you might in Excel or forg statistical package to carry out relatively simple data manipulations using the MM Macer or Evaluator utilities that are included with MMM MMMacro handles all the data exchange with MMM for you To add your own Modifier models to the toolbox available to MetaModelManager you will need to create a NET compatible dyfamic linklibrary dll with functions that provide the interface through which to access the Global Population and Individual data contained within class MData The standard funetion calls that MetaModelManager uses to communicate with any linked model are Initialize Simulate and Close although these three functions can be given different names if the synonymous names are specified to MetaModelManager in the modehspecifications The structure of the metamodel data in MData is defined in the small library MMMCore The C code for the MMMCore dll is provided in the MetaModelManager installation file Another small code file MMLinkTemplate cs is included to provide a template for the three k y functions for passinggdata between MetaModelManager and a user provided model In addition the code for the MMMacro modifier program which provides a means to modify variables in MMData via macro
17. gnificantly in numbers on some iterations To learn more about the options available in MMM select Quit MMM and start over again this time callingthe saved MyFirstTutorial MMM project Opening Sereen 1 SeleetsOpen an Exisiting Project from the opening screen 2 Select MyFirstTutorial Order Model Steps 1 Create a break at the end of the second system level run by selecting Break and making sure it is the last item on the model list Choose for the break to occur every 10 years 2 Also change Total Years to 50 and iterations to 1 so the metamodel will run faster Simulate Screen 1 Rather than launching into the summary graph a screen will pop up showing statistics of the populations at the desired intervals 19 2 3 4 MetaModel Manager Version 0 9 1 User s Manual With Vortex 1 Population 1 highlighted Select Show Population and the population at time step O will appear for PDs including their Outbreak disease state characterisitics With Vortex 2 Population 1 highlighted Select Show Population and the population at time step O will appear for BFFs There is no disease state information to show because Vortex was run alone for this population without Outbreak as a modifier Let save the statistics of BFFs to a file Slect Write to File MyFirstTutorial_BFFBreakO I MyFirstTutorial_BFFBreak0 Notepad BAX Fie Edit Format view Help Population File Globalva
18. he following are examples of simple input files The first represents a file setting two variables for 5 years First Example 2 variables for 5yrs 0 1 0 9 0 2 0 8 0 3 0 7 0 4 0 6 0 5 0 5 The second an array with 4 elements for 5 years Second example array 4 elements for 5yrs 0 1 0 2 0 3 0 4 0 2 0 3 0 4 0 5 0 3 0 4 0 5 0 6 0 4 0 5 0 6 0 7 0 5 0 6 0 7 0 8 And finally a regular variable then amarray of 4 elements Third example 1 normaljyariable 1 array elements Syrs 0 9 0 1 0 2 0 3 0 4 0 8 0 2 0 3 0 4 0 5 0 7 0 3 0 4 0 5 0 6 0 6 0 4 0 5 0 6 0 7 0 5 0 5 046 0 7 0 8 The Input Step Setup will allow user to choose the text file Below that the user must specify whichwvariables will be input If more than one variable is being input order Matters The order must follow the order that is indicated in the text file that was created Thus the up and down buttons can be used to regulate order Output This option lets you output the population data as stored in MMM rather than any data output specific to a component model This will create a dump of all data on the population and individuals each time step which can be a very useful way to see just what is happening in your simulation Evaluator Evaluator was developed as a utility to provide to MMM and other software the ability to evaluate user defined functions to which are passed the sets of parameter values
19. ions are instead created within the original specification files Existing Program Suite Pre Adapted for compatibility with MMM Program Type Developer Web Address for download Vortex System R Lacyand http www voxfex10 org VortexTOhtml level J P Pollak Outbreak System J P Pollak http www vortex10 org Outbreak html levelor R Lacy and modifier others Spatial Modifier J P Pollak http www vortex10 0ng Spatial html MMMacro Utility R Lacy Included inthe MMM installation Path Utility J P Pollak Included in the MMM installation History A B cv rcCcCC0 gt C CECE nrQgEQE See Chapter 4 to learn how to adapt user reatedim dels to run within MMM Processing speed Depending on your input programs MetaModel Manager may run slowly We suggest that you run test models firstwithJess iteration over less time and with fewer metamodeLeomplexiti s before attempting longer and more intricate runs For example you maylimit then mber oftiterations time steps cycles or even the numbers of programs interacting at first to make sure you are satisfied with your model construction MetaModel Manager Version 0 9 1 User s Manual Chapter 2 Getting Started with MMM This chapter explains the choices available on each screen of the MetaModel Manager An examples showing some of the functionality of the MMM program will be presented in Chapter 3 The choices that a user has per screen are indicated h
20. nit In Transition In GS1 BFF 50 GS1 N N GS2 PD N N 250 GS2 2 Creating the Ecological Link The ultimate ecological link between the 4wo Vort x models occur when the global state variables are later used in equations to parameterize the demographics of each of the two populations In our example the mortality of PDs in the PD model for females from age 0 to 1 equals 45 15 GS1 N The fewer PDs present in the population relative to BFFs the more young PD mortality goes up ln the BFF model first year mortality is specified as 46 6 20 N 1 GS2 so that higher ratio of predators to prey reduces the survival of young ferrets Links between models may also be made through using individual state parameters whereby specifi information is tied to specific individuals in the population In the BFF PD Plague metamodel IS tracksithesiseaseState of each prairie dog DiseaseState is determinedfwithin the Outbreak model of plague and transferred to the Vortex model by MMM Vortex then uses this IS variable to modify the reproductive rate of prairie dogs with function that specifies that currently sick DiseaseState I IS1 3 females cannot reproduce Vortex ignores the disease status of each individual when setting mortality rates because the death of prairie dogs from plague occurs within the Outbreak model with 50 mottality40f diseased PDs We do not want to imply that these few simple relationship
21. ntly longer time to execute Hit Next 3 At the Save this project before continuing prompt select Yes and name it MyFirstTutorial Simulate Options screen 1 Note that the population sizes will be displayed the default Select Show plot lines in real time Hit OK Simulate screen 1 Select Simulate The simulation will start Do not betsurprised if the screen fails to show the graph correctly The graphics in some cas s are not able to keep up with the simulation processing Also if you click off the sere n to move control to a different window the simulation screen will probably Stop bemgupdated during the iterations and may display a message that Mortex is notr sponding Do not worry as the simulations are continuing to work away in the background The final graph will be displayed correctly when the simulationyis finished 2 When the processing is finished you will See a Complete box pop up You can select okay to make it go away and see your graph again Congratulations You have completed your first metamodel analysis of a dynamic two species system in which the prey species Is subject t epidemics of disease The final figure generated should show prairie dog population size fluctuating quite a bit because of disease sometimeg leading to the decline or local extinction of the black footed ferrets The prairie dogs themselv s rarely go extinct although drop si
22. ough the perspectives of many different disciplines MetaModel Manager offers a way to achieve transdisciplinary modeling with general facility and creates a central convening point for people to come together to make critical conservation decisions using a wider variety of information The principle b hind the development of MetaModel Manager was to create a robust interface that calls in existing programs to work synergistically In so doing the user can tap into th unique capabilities of each program without the need to create new potentially cumbersome mega models Figure 1 The program provides an interface for she transfer of information across individually based models that carry biological information attributable to specific indexed individuals in a population The information that is sentback and forth between programs is considered open data and can be modified by anyjof the linked programs operating within the MetaModel Manager framework MetaModel Manager Version 0 9 1 User s Manual Species biology Habitat Climate limate ecology change Resource Land economics development Human Disease population growth Ethics Government MEGAMODEL METAMODEL Figure 1 Conceptual comparison of a megamodel versus a metamodel of interacting factors influencing species biology 7 The roots of the MetaModel Manas informal grouping of people known as the Bi diversity Research Network
23. riables NumGsvars 3 BFF PD ABFF 62 000000 250 000000 62 000000 Populationvariables NumPsvars 0 Name Index Age Sex Alive 2 0 730 0 1 3 1 730 0 1 Si N N w a HoOoHHOHOHHOOHHO BREBEBBBBBBBEBBBEE w a o w a a pir PRERBEBEBREBEBR 146 44 365 0 Select OK andjthe simulation will proceed but pause again at year 10 Show population of BFFs and save to file again this time as MyFirstTutorial BFEBreak10 Keep doing this through the first iteration 20 MetaModel Manager Version 0 9 1 User s Manual Chapter 4 Template for open data exchange via MetaModel Manager We hope that in addition to the demographic animal movement and disease spread program suite built by various members of the Biocomplexity Network you will find opportunities to build your own programs in conjunction with MMM If you choose to do so your program must be developed in a way that is compatible with the MMM You can use the information and template described below to help set up the coding for your own programs so that they are compatible with the MetaModel Manager and can share system population and individual data with other linked programs We won t pretend that those who are new to programming will be able to write computer code for a model that is then linked to others via MetaModel Manager You need to be experiencedhin a computer language such as C Visual Basic Delphi or Java to be able to write th
24. rsion 0 9 1 User s Manual Chapter 3 Example This chapter reviews an example using the MetaModel Manager to model black footed ferrets and prairie dogs with sylvatic plague The data files for this example are included in the installation of MetaModel Manager placed into a C MetaModelManager Projects Samples folder Additional sample MMM projects are available on the MMM website at www vortex10 org MetapopDzDemo zip and www vortex 10 org PredatorPreyDemo zip Background This example models the demographic responses to dynamic predator prey relationships in the presence of disease Black footed ferrets are perhaps one of the most endangered species in the United States They are specialized on eating prairie dogs which make up over 90 of the food ingested by the ferrets The prairie dogs are subject to the sylvatic plague which can reduce population size dramatically Please n te that in many cases parameters are based on fictional information The example presented below should be interpreted for educational experience only and not cited as factual BFF PD TUTORIAL Opening screen 1 Select Begin a New Project from thetop nin screen Setting System Level and Modifier Programs s reen 1 From the Population System Models first drop down box select Vortex 2 Set you Vortex vpj project by opening the choose link and selecting MMM PDog vpj You will need to navigate to this file in the C MetaMo
25. s describe accurately the functional response of predator to prey and the reverse we just inserted some simple functions to show how such relationships can be specified and modeled within a 2 species metamodel with disease impacting one of the species A more complete and realistic metamodel for ferrets and prairie dogs might include reciprocal effects on adult survival of both species effects on reproduction of ferrets and possibly other functions defining the interactions between the species 23
26. s or scripts is provided to show a more complete andicomplex example Your program will appear on the program list on your computer if you set it up to do so It will only be resident on your computer This is done via the Manage Loaded Apps option on the opening screen of MMM If you think your program may have broader utility to the conservation community then we encourage you to make your program available for others to use The metamodeling tools website www vortex10 org will provide downloads for relevant software that developers are willing to distribute freely and will provide links to other sites for programs that charge a fee or are otherwise restricted in their use 21 MetaModel Manager Version 0 9 1 User s Manual Chapter 5 Understanding the use of State Variables to model biological links Vortex offers the infrastructure to set up state variables in order to provide extra information regarding an individual population or metapopulations Defining and using these variables is key to creating successful linkages between programs in order to express how the parameters of one population may be influenced by outcomes from other programs Vortex has three levels of state variables global population and individual These state variables must be numerical can change over time See the Vortex manual for more information on how it creates and uses state variables Other modeling programs may also provide the means to set up state
27. thout showing the graph at all 15 MetaModel Manager Version 0 9 1 User s Manual a Simulate O Displaying population size over time for each iteration R KA STON WETAN I Peed do Waser Lh Crau a A H ii PH a JN Aa ast 3 5 40 45 50 55 60 65 70 gt Bf 5 75 The graphic shows the changes in population size or whatever variable you asked to be shown on the previous specificati een e populations associated with the linked models Tip Colors repfesei the legend below the graph can close the simtulate box to go back to the previous screen change options and then re run Sometimes backing up in screens causes MMM to get confused If that seems to be happening close MMM restart the program load your project if you saved it before and resume your analyses Quit MMM This button provides a way to exit the program after the simulation has completed To see output you need to quit MMM and open up the individual programs and refer to their normal protocol for viewing output 16 MetaModel Manager Version 0 9 1 User s Manual Running the MMM program will generate a set of output files The files that are created will depend on the programs that are invoked in the metamodel Unless the user specifies an Output step in the Order Model Steps screen MMM itself won t produce any output files That is left entirely to the programs running within the MM 17 MetaModel Manager Ve
28. y R C 2013 Metamodel Manager User s Manual Brookfield IL Chicago Zoological Society MetaModel Manager Version 1 0 User s Manual Contents Statement of I S L ey vet koy n a ii boo pete ge a RAAR meus 1 Chapter I Introduction arrena ay e ate a ate R a e ER e ar an O OE 2 What is the MetaModel Manager was csccccacasecsacessseccadsacassaceasdaccetualdegarasessceecaccasanes 2 PHUOSOpDY osere Ge e n es gere a e E PO SONYA A seb eee eR De 2 Implementation eee AE AEE A AEA E 2527 4 Chapter 2 Getting Started with MMM X Chapter 3 Tutorial vives os ati ieee ea ass X Chapter 4 Template for Open Data Exchange X Chapter 5 Understanding State Variables X Appendix I Literature Cited E SE wc eere X Appendix II Nyhus et al 2007 b heee SJE cece cece ence ence cece eeneeeneeeeneees X Appendix III Ev 2 Saas Yo ab Bassai See ki ke anba kaponnen Appendix IV MM M eases MetaModel Manager Version 1 0 User s Manual Statement of Use On behalf of the team of collaborating scientists d veloping this Software we wish to convey an important cautionary note This ma does not explain to users how to set up scenarios in the individual modu i ed to as linked programs brought S iS manual is metamodeling approach and how the gerprogram works ug reports suggestions and any requests for additional information We cannot guarantee that all comments and requests will be feedback
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