Home

Epidemiology Version 2.5.1 User`s Manual

image

Contents

1. Medium 25 000 High 50 000 Very High 200 000 Use the space below to summarize the findings of the class Be sure to compare the density independent and density dependent models and be sure to describe both the interaction between population size or density and probability of transmission and the Epidemiology User s Manual 51 interaction between population size and virulence How did the results compare with your predictions What general conclusions can we draw from our results 52 Epidemiology User s Manual Discussion Questions Based on our explorations with Epidemiology here are some questions to consider 1 Does Ebola pose a serious threat to human civilization How do the lessons learned from our simulation modeling relate to this question 2 Some biologists and historians argue that many infectious diseases such as the bubonic plague measles malaria were only able to become epidemic after the human congregations in villages and cities reached large enough numbers Based on your experimental results do you see any theoretical validity to this view If so rank malaria measles and plague with regard to the threshold sizes you think would be necessary to sustain them Explain your rankings i e what characteristics of these diseases did you use to distinguish them Look up the timings of the origins of these diseases to see if they are consistent with your predictions 3 How do the lessons learned fro
2. recovered implies immune to further infection 8 Epidemiology User s Manual The simulation model keeps track of the number of individuals in each category and describes the rate individuals enter and leave each category For example new individuals enter the Susceptible category via birth Individuals may also move from the Recovered category into the Susceptible category This would represent individuals who had the disease but are now losing their immunity and hence becoming susceptible to infection again Individuals can leave the susceptible category in two ways through death or through infection In the latter case they enter the infected category Flow Chart Unintected Susceptible Infectious Recovered Hatural Disease Deaths Deaths Figure 1 The Flow Chart window for a simple epidemiological model Individuals in the population are categorized as Susceptible Infected Infectious and Recovered and the diagram shows the flows into and out of each category Clicking on the buttons on the flow chart brings up dialog boxes that allow the user to enter values for factors that influence the rates of flow Values for factors such as the birth rates death rates disease transmission rates rates of recovery etc can be viewed by clicking on the appropriate button on the flow chart For example clicking on the icon on the arrow next to birth rate brings up a dialog box ind
3. Rio UEST M BiogU IA S 7 Library VII Daniel Udovic University of Oregon Will Goodwin University of Oregon Epidemiology Version 2 5 1 User s Manual A BioQUEST Library VII Online module published by the BioOQUEST Curriculum Consortium The BioQUEST Curriculum Consortium 1986 actively supports educators interested in the reform of undergraduate biology and engages in the collaborative development of curricula We encourage the use of simulations databases and tools to construct learning environments where students are able to engage in activities like those of practicing scientists Email bioquest beloit edu Website http bioquest org Editorial Staff Editor John R Jungck Managing Editor Ethel D Stanley Associate Editors Sam Donovan Stephen Everse Marion Fass Margaret Waterman Ethel D Stanley Online Editor Amanda Everse Editorial Assistant Sue Risseeuw Beloit College Beloit College BioOQUEST Curriculum Consortium University of Pittsburgh University of Vermont Beloit College Southeast Missouri State University Beloit College BioQUEST Curriculum Consortium Beloit College BioOQUEST Curriculum Consortium Beloit College BioQUEST Curriculum Consortium Editorial Board Ken Brown University of Technology Sydney AU Joyce Cadwallader St Mary of the Woods College Eloise Carter Oxford College Peter Lockhart Massey University NZ Ed Louis The University of Nottingham UK Claudia N
4. Figure 3 The Model Definition dialog box allows you to select from among various model types Some check boxes are always selected and are grayed out These are not under user control For example if you choose to have a vector population it will have at least two categories susceptible and infected Your only choice will be whether to have a latent category or not The Model Definition dialog box allows user to control the level of complexity that they will see in the flow chart and simulation runs The basic model divides the host population into only three categories Susceptible Infected and Recovered By choosing the appropriate settings the user may add categories for immunized individuals and may subdivide the infected population into the following categories 1 latent i e asymptomatic healthy and not yet infectious as in rabies before the onset of symptoms 2 asymptomatic and infectious e g HIV but not suffering from AIDS and 3 symptomatic and infectious e g individuals with AIDS influenza etc A fourth possibility not currently included as an option would be individuals who still show symptoms of the disease but are no longer infectious Epidemiology User s Manual 11 Demography 2 5 allows users to model the dynamics of vector populations and reservoir populations as well as the dynamics of the host population Figure 4 Vectors are species that carry the disease organism from one host to anot
5. 25 symptomatic 29 T table icon 13 tables switching to 26 27 threshold density 48 52 tool bar 13 26 27 U University of Oregon 1 2 32 33 V vector populations 11 29 vectors 10 12 virulence 48 W windows Deaths vs Time 13 27 Flow Chart 8 25 37 Notes 35 Population Size vs Time 12 14 22 26 27 39 Status 12 22 25 40 Tile Windows 24 Windows menu 24 Workshop Biology 1 3 World Wide Web 2 4 33
6. and the prevalence of the disease through time Using modified SIR type models Susceptible Infected Recovered Epidemiology allows students to ask a variety of what if questions to design and perform their own investigations and to explore the implications of various public health policies The direct manipulation graphical interface encourages exploration and makes the program accessible to introductory students Nevertheless the simulation model is capable of addressing problems that even graduate students in population biology or public health should find interesting and challenging Epidemiology was developed by the Biology Software Lab at the University of Oregon as part of a curriculum project called Workshop Biology an innovative approach to teaching introductory biology to non majors As with our Workshop Biology course in general Epidemiology is designed to help accomplish three broad goals 1 to help students understand difficult concepts by inviting them to challenge misconceptions and preconceived notions 2 to get students involved in their own scientific investigations and 3 to help them make connections between important scientific ideas and methods and crucial issues of public policy and personal well being To accomplish these objectives we are developing a teaching module Appendix 4 that begins with very structured activities that address important concepts and moves toward open ended investigations that rela
7. and those that have recovered assuming that these individuals are now immune to infection This is the simplest view and is the basis for the so called SIR models Of course in more complex models each of these categories could be divided by gender age socioeconomic status etc But to start with lets keep it simple Other complications could include the size of reservoir populations intermediate host populations or vector populations Let s concentrate now on a simple disease like smallpox that is transmitted only from individual to individual and which seems to be an affirmative Epidemiology User s Manual 37 action disease showing no gender age or social preferences Once we understand aspects of this simple model we can consider how various complications might affect our results The computer program that we will be using Epidemiology allows you to control factors such as the probability of infection the death rate due to a disease the proportion of a population vaccinated and the average length of infection so that you can study the way these factors interact to influence the spread of a disease The next few pages introduce you to the computer program They are followed by some questions to help guide your explorations Using Epidemiology 2 1 The Flow Chart m aE Hatural Disease Deaths Deaths The flow chart describes the model of disease transmission in graphical form Individuals in the population
8. belong to one of four categories They are either susceptible to infection infected recovered and immune to further infection or they are immunized The arrows in the flow chart show how individuals enter and leave these categories For the disease graphed here all individuals are born susceptible They stay in that category unless they become infected or they die from causes other than the disease Recovered Clicking on the little icons buttons in the flow chart brings up dialog boxes that allow you to change the rates at which individuals enter or leave each of the four population categories For example clicking on the button on the arrow going from susceptible to recovered brings up the following dialog box 38 Epidemiology User s Manual Transmission Parameters Probability of transmission oo per contact Contact Rate Density Independent Average of contacts per interval Density Dependent Average of contacts per interval per 1000 pop Disease Introduction Introduce newly infected individuals every time intervals Increasing the value of either the probability of transmission or the contact rate average number of contacts per time interval will increase the rate at which susceptible individuals become infected Please ignore the rest of the dialog box for the time being Make sure that you understand what each of the icons represents The only ones that require special explanation are th
9. copy the contents of any window to the clipboard and then paste them into another document such as a draw program or a word processor see the Copy and Paste commands under the Edit menu After you have checked the page setup for your printer with the Page Setup command choose the Print command from the File menu to print a view of the windows from Epidemiology in their current state A dialog box will appear asking you to select the windows that you wish to print and how you want them arranged Once you have made your selections click OK The standard Macintosh print dialog box will appear Choose the appropriate settings and click OK to print your document 18 Epidemiology User s Manual Quit To quit Epidemiology choose the Quit command from the File menu If you have not saved the file a window will appear asking if you want to save the file All windows will disappear and the program will end Edit Menu Control Set Undo Cut 36H Copy 8C Paste U Clear Show Clipboard Undo Sorry The Undo option is not yet available To undo the most recent change to the model either a change in the shape of a graph or the running of a simulation choose the Undo command from the Edit menu You can only undo your last change see also Reset and Reset All under the Control menu Cut Use the Cut command from the Edit menu when you wi
10. of the Macintosh clipboard Control Menu Settings M Go Until gt Go For gt Go 6 Step E Stop 3 Reset 3R Reset All Hide Control Panel Go Until To run a simulation until a specified time period choose the Go Until command from the Control menu A hierarchical menu will appear giving you several choices for ending times If you wish to specify a number that doesn t appear in the menu choose Custom A dialog box will appear asking you to specify the ending time The simulation will run until it reaches the time period you specify and then stop automatically The Go Until command is inactive except when the simulation is stopped and will appear grayed out whenever the simulation is running 20 Epidemiology User s Manual Go For To run a simulation for a specified number of time intervals choose the Go For command from the Control menu A hierarchical menu will appear giving you several choices for the number of time intervals to run the simulation If you wish to specify a number that doesn t appear in the menu choose Custom A dialog box will appear asking you to enter the number of intervals The simulation will run for the number of intervals you specify and then stop automatically The Go For command is inactive except when the simulation is stopped and will appear grayed out whenever the simulation is running Go To
11. the Display command from the Settings menu you can select the appropriate subset to display Organizing Data and Reporting Results Marking The Mark feature allows you to set a mark at any particular time interval during the run of a simulation You can enter a meaningful name for the mark to help you understand remember why that particular time interval was important You can then enter notes to keep track of additional information in association with the mark When you set a mark Epidemiology saves all the values displayed in the windows as well as the position of the windows on the screen This allows you to come back to this point and even to start the simulation running again from that point if you wish Marks allow you to summarize a simulation run or a set of runs If you want to show someone what happens to a population at various times instead of running the simulation and stopping it whenever you want to point something out you can do the run beforehand and set a mark at each time interval of interest This can save a lot of time especially if the time intervals are far apart or you need to change fertility mortality and or age distribution settings along the way WARNING Because of a bug in Epidemiology 2 5 marks are lost whenever a new model type is defined If you have been working with one type of model for some time and wish to switch to a different type of model you should save your work close the file an
12. you will need if any check with your instructor to find out what they are called Find the icon for the Epidemiology application and double click on it The program will start up Opening a Problem You may simply start using the program directly or you may want to open a problem file with pre set values e g if your instructor has made one available or you have previously saved your work To open a problem file choose the Open command from the File menu If it is grayed out it means you already have a file open so you must close it before opening a new one To close the file choose the Close command from the File menu You will see a window with names of different files Find the problem file name and click on it to select it then click on the button marked Open or double click on the problem file name The program will begin opening the windows of the problem file Setting up a Simulation Interpreting the Flow Chart The population characteristics that influence population growth and the spread of a disease in the population are summarized in graphical form in the flow chart window The flow chart gives a graphical depiction of the way that the models underlying Epidemiology work The host population is broken down into several categories In the flow chart depicted in Figure 1 for example the categories are Susceptible Infected and Recovered In this case infected implies infectious and
13. 1 immunization rate 28 41 influenza 9 10 initial values 22 instructors 1 32 L Lassa Fever 43 latent 10 28 lyme disease 29 Macintosh operating system 30 Macintosh basics clicking 6 double clicking 6 dragging 6 Pointing 6 selecting 6 malaria 52 marks notes 18 19 24 35 setting 13 2 Epidemiology User s Manual Marks menu Go To 23 Notes 24 Remove 23 24 Set 23 measles 9 52 menu Settings 10 11 13 22 25 26 menus Control 11 12 18 19 20 21 Edit 18 19 File 7 14 16 17 18 35 Marks 18 19 23 24 Windows 24 25 27 microprocessor 68K 30 PowerPC 30 model settings 10 model types 10 22 models simple 32 mortality age specific 28 mosquitoes 11 29 O open ended investigation 1 34 Outbreak 1 P plague 11 29 popualtion categories latent 28 population categories 25 immunized 37 infected 1 7 10 22 25 32 36 37 recovered 1 7 8 10 22 26 32 36 37 susceptible 1 7 8 10 11 22 25 28 32 33 36 37 38 39 41 printing 14 probability of transmission 9 28 38 41 48 problems 31 public health policies 52 Q quitting 15 R rats 29 reservoir populations 10 11 12 29 S saving 14 scientific notation 26 Settings menu Current State 9 22 25 26 Define Model 10 22 Display Settings 25 Display 13 22 Fonts 23 Model 22 SIR models 1 32 36 smallpox 36 summary statistics definitions
14. ENDIX 4 MODELING THE SPREAD OF A DISEASE A SAMPLE LEARNING 36 MODULE Introduction 36 Using Epidemiology 2 1 37 Setting Up the Model 41 Posing a Question Making a Prediction 42 43 Exercise 1 Investigating Virulence and Ease of Transmission Exercise 2 How would immunization affect these results 47 Exercise 3 Initial Population Sizes 48 Discussion Questions 52 INDEX 53 Epidemiology User s Manual 1 Preface Ebola breaks out in Zaire The Hot Zone describes a close call with Ebola in Reston Virginia The movie Outbreak depicts a fictional hemorrhagic fever outbreak in the U S The AIDS pandemic is gaining steam in many parts of the world Given the threats from emerging diseases and concerns over the resurgence of older diseases exacerbated by the prospects for global climatic change and the evolution of drug resistant pathogens the threat of global pandemics seems to have replaced nuclear war as this generation s Armageddon One way to explore these issues in the classroom is to construct and explore models Epidemiology is a computer model that simulates the spread of an infectious disease through a population This program allows users to graphically enter population and disease characteristics e g the virulence of the pathogen the likelihood of transmission etc to set up an initial population and then observe the changes in population characteristics
15. Variable Settings By choosing the Current State command from the Settings menu users can modify the values for the initial time and for the current population size For example if you wanted to model bubonic plague in Medieval and Renaissance Europe you might want to set initial time to 1300 the susceptible population size to about 75 million the infected population to just a few individuals and the recovered population to 0 Running a Simulation m E ef fg Figure 5 The Control Panel buttons can be used to control the running of the simulation From left to right the buttons are Stop Go Step and Reset These commands are also available from the Control menu 12 Epidemiology User s Manual Once you have set up the simulation you can use the commands under the Control menu or the icons on the Control Panel Figure 5 to see how the population changes through time To advance the simulation just one time interval choose the Step command from the Control menu or the Step icon from the Control Panel To have the simulation run until a specified time or for a specified number of time intervals choose the Go Until or Go For commands from the Control menu To have the simulation continue advancing until you tell it to stop choose the Go command from the Control menu or the Go icon from the Control Panel Whenever you want the simulation to stop running choose the Stop command from the Control menu or the Sto
16. above might change for different levels of immunization or for different durations of infection Use the space below to describe your predictions to show your results and to draw some conclusions NOTE To set up Epidemiology to allow for immunizations choose Define Model from the Settings menu In the Model Definition dialog box enable immunization by clicking the check box next to it Then click OK A new set of windows will appear with a new flow chart that includes a category for immunized individuals 48 Epidemiology User s Manual Exercise 3 Initial Population Sizes One of the more interesting results from epidemiological modeling has to do with the way the size of a population influences the ability of a disease to spread In the this exercise we will examine this relationship by exploring what happens when we start out with populations of different sizes In the previous exercise the model that we used assumed that the average number of contacts per individual did not change with population size For many diseases this will not be the case Contacts will increase with the density of the population Building a more realistic model that allows for this could have a dramatic impact on our results Can you explain why this might be We will divide the class into four different groups Each group will do a similar set of simulation runs mapping out an area of parameter space but the groups will differ slightly i
17. acts No one knows which students were infected originally so the problem is for the class to try to deduce the index case s from information that they collect about their contacts There are many variants of this exercise but a simple effective and fun lab exercise is described by Dickey 1989 American Biology Teacher 51 6 364 365 The whole exercise can be done in 30 40 minutes Once the exercise is complete the instructor can work with the class as a whole and develop a graph of the number of susceptible and infected individuals through time A second preparatory activity is to have students working in groups develop a flow chart or concept map describing the relationships between factors that influence the spread of a disease Butcher paper magic markers and post its can be provided as materials Finished diagrams can be presented to the whole class for discussion If students have worked on their diagrams individually e g as a homework assignment before class they will be prepared to make more rapid progress as a group Their diagrams can form the springboard for a discussion of various proximate and ultimate causes of disease outbreaks and for an introduction to the flow chart models used in Epidemiology The Epidemiology exercises move from simple and highly structured to more complex and open ended We encourage this approach since it eases students into the program building both confidence and understanding If your students
18. aracteristics that influence population growth and the spread of a disease in the population are summarized in graphical form in the flow chart window The flow chart gives a graphical depiction of the way that the models underlying Epidemiology work The host population is broken down into several categories In the flow chart depicted above for example the categories are Susceptible Infected l immunized 26 Epidemiology User s Manual and Recovered In this case infected implies infectious and recovered implies immune to further infection Values for factors such as the birth rates death rates disease transmission rates rates of recovery etc can be viewed and or changed by clicking on the appropriate button on the flow chart For example holding the mouse button down on the icon on the arrow next to birth rate brings up a pop up menu indicating the current setting of the birth rate and providing several other choices If you wish to enter a value other than those available from the menu select the custom option which will bring up a dialog box allowing you to type in a value You can change these values at any time even when the simulation is running Population Size vs Time oO Host Population B 60 000 48 000 36 000 24 000 30 TEE c oo T 12 000 0 This window displays the number or proportion of individuals in differ
19. ave made changes to the current file and have not saved them a window will appear asking whether you want to save the changes To save the changes to this file click on the Yes button To close the current file without saving the changes click on the No button To return to using the current file instead of closing it click on the Cancel button Save To save the file you are currently using choose the Save command from the File menu A window will appear asking you to choose a name and location for the new file Type in anew name and click on the OK button Caution if you have opened a file made changes to it and you want to save these changes to your own file but don t want to change the original file use the Save As command instead Save As To save the file you are currently using under a different name choose the Save As command from the File menu A window will appear asking you to choose a name and location for the new file Type in a new name and click on the OK button The old file will not be affected Page Setup Sorry The Page Setup option is not yet available The Page Setup command from the File menu displays a window which shows the current page setup for the printer Choose this command before you choose the Print command to ensure the page setup is the way you want it Print Sorry The Print option is not yet available To print out your results first
20. change in doubling time Duration of infection This is the average number of time units that an individual remains infected before moving into the recovered category provided of course that he she doesn t die Immunity Loss A measure of the rate at which individuals who have recovered from the disease or who have been immunized lose their immunity and become susceptible to infection again In age structured models this rate can depend on age Immunization rate This is the proportion of newborns that are vaccinated Right now the program makes the unrealistic assumption that vaccinated individuals remain immune for life To start out set this to 0 Latent Individuals are in a latent state when they have been infected but are not yet showing symptoms and are not yet infectious Natural or Background Death Rate The fraction of the population that dies during a specified time interval due to causes other than the disease Probability of transmission The probability that a susceptible individual will become infected in a particular contact with an infectious individual This value must be between zero and one Epidemiology User s Manual 29 Recovery Rate The rate at which infected individuals recover from the infection and become immune In age structured models this rate can depend on age Reservoir Populations Populations of species other than the host can harbor the disease causing organism e g rats harbor plag
21. convenient way to run simulations It always appears in front of other Epidemiology windows Occasionally you might find it useful to hide the control panel You may do this either by clicking in the panel s close box or by choosing Hide Control Panel from the Control menu When the panel is hidden you may choose Show Control Panel from the Control menu to bring it back into view 22 Epidemiology User s Manual Settings Menu Marks Current State Display Model gt Define Model Font Size Current State Choose Current State from the Settings menu to set the starting time of a simulation or to alter the current size for any population category A dialog box will appear with boxes to enter the appropriate numbers The starting time can only be changed at the beginning of a simulation Display Choose the Display command from the Settings menu to select the values to be displayed in the Status window and in the Population Size vs Time window Model Choosing Model from the Settings menu brings up a hierarchical menu with options to bring up dialog boxes or windows for the various factors that influence the model These options can also be selected by clicking on the appropriate buttons in the Flow Chart window see pages 7 and 25 for more details on the Flow Chart window Define Model Choose the Define Model command from the Settings menu to choose the
22. d open a new file before defining your model type 14 Epidemiology User s Manual Exporting In preparing reports or handouts it is often useful to export data or graphs In Epidemiology 2 0 the contents of any window with the exception of the summary statistics window can be copied into the clipboard and pasted into other documents For example by choosing Copy when the Population Size vs Time window is the active window either the graph or the table whichever is showing will be copied onto the clipboard The table could be pasted into a spreadsheet or into a word processing document Or the picture of the graph could be pasted into word processing documents or into documents from drawing programs The contents of the notes windows associated with marks can also be copied and pasted into word processing documents Printing Sorry The Print option is not yet available To print out your results first copy the contents of any window to the clipboard and then paste them into another document such as a draw program or a word processor see the section on Exporting above You can print out a view of all the data in the windows as they are shown at any time during the run of a simulation Choose the Print Setup command from the File menu to make sure that the printing settings are okay for your printer Choose the Print command from the File menu to begin printing A dialog box will appear allowing you to ch
23. density independent model the average number of contacts in a time interval does not depend on the density or size of the population This might be the case for sexually transmitted diseases in populations where the average number of sexual partners is not influenced by the size of the population In the density dependent model the average number of contacts made by an individual during a time interval depends in a linear way on population size This might be the case for example for airborne diseases like colds flu or measles Transmission Parameters Probability of transmission oo M per contact Contact Rate Density Independent Average of contacts per interval Density Dependent Average of contacts per interval per 1000 pop Disease Introduction Introduce newly infected individuals every time intervals Figure 2 The Transmission Parameters dialog box allows you to change factors that influence the rate at which susceptible individuals become infected You may change the probability of transmission given contact and you can choose between two models of how the rate of contact changes with density The disease introduction feature allows users allows immigration of infected individuals into the population The size of the population in each of the model categories may be altered by choosing Current State from the Settings menu This may be done at the beginning of a simulation or at any
24. e and type ina new name When you are finished entering the name of the mark click on the OK button or press the return or enter key on your keyboard If you decide you don t want to set the mark use your mouse to click on the Cancel button in the dialog box Go To After you have set a mark in a run of the simulation you can restore the run of the simulation to the state it was in when you set the mark Move the cursor over the Marks menu press the mouse button and drag the cursor down until Go To is highlighted but don t release it yet Now drag the cursor to the right until you can see the names of the marks Drag down until the mark name you want is highlighted then release the mouse button Before the program goes to the mark it will ask you whether you want to save the current state of the simulation the state before you go to the mark If you click on the Save button it is the same as placing a mark at the current state of the simulation before going to the mark In fact the mark it places is called Current state at n where n is the number of the current time before the simulation goes to the mark The current state mark will show up in the Go to and Remove lists so you can treat it like any other mark Type a new name for this current state mark if you want Click on the OK button The program will go to the mark you requested 24 Epidemiology User s Manual Remove If you decide you no lon
25. e death rate icons One represents the background death rate due to causes other than the disease This rate is the same for individuals in all four categories The other represents the death rate resulting specifically from the disease It applies only to individuals in the infected category Epidemiology User s Manual 39 The Population Window 200 000 U 160 000 120 000 80 000 3 0O me St OS a OO 40 000 0 The population window tracks the number of individuals in a population through time in each of the three categories susceptible infected and recovered Describe in words what happened to this population from time 0 to time 50 Two buttons at the top of the population window provide viewing options allows you to toggle back and forth from looking at population sizes to looking at percentages allows you to switch back and forth from a graphical to tabular view Graphs give you a good overview of trends but if you want to know the actual values at specific times then choose the table view 256 0 72 Another box at the top of the window shows the current x y coordinates of the cursor when it is within the region of the graph You can use this feature to find a close approximation of a given variable without switching to a tabular view 40 Epidemiology User s Manual The Status Window Current Time 50 Status Stopped Susceptible 24 796 26 Infectious 3 820 40 Recovered 25 139 56 To
26. emiology choose the Quit command from the File If you have made any changes a dialog box will appear giving you the opportunity to save your work before exiting the program 16 Epidemiology User s Manual Menus and Commands This section will describe the menu structure of Epidemiology and show you how to use the menus to choose commands to open files change parameters set marks run the simulation and print results File Menu PGgRRE HEN PPEP HEE Close Ww Sapa HES Save As Beuert in Saved Page Setup Print PF Quit 0 New Use the New command if you don t have a file open and you want to start a new file from scratch Choose the New command from the File menu All seven Epidemiology windows will appear with default parameter values You are now ready to start making changes to this new file Open To open a file choose the Open command from the File menu A window will appear asking you the name of the file you want to open and where on the disk this file is Click on the file name to select it then click on the Open button The Open command is inactive whenever there is already a file open and will appear grayed out Close the current file before opening a new one see Close command below Close Before you open a new file you must close the file that you currently are using by choosing the Close command from the File menu Epidemiology User s Manual 17 If you h
27. ent population categories through time When the population gets large the population values on the y axis will be expressed in scientific notation for example 5 00 e 07 which represents 5 times 10 to the 7th power or 50 000 000 To change from total numbers to proportions or back again click on the icon on the tool bar at the top of the window The display can either be in a graphical form or in tabular form To switch from one to the other click on the table or graph icon in the tool bar above the graph The values displayed are calculated from other population values you cannot change this window directly You may alter the current population sizes by choosing Current State from the Settings menu and entering the value that you want into the appropriate field of the dialog box Epidemiology User s Manual 27 To see this window if it is not already shown choose the Host Pop Size vs Time command from the Windows menu Deaths vs Time This window displays the number or proportion of individuals in the population that died during each time interval It displays both the number of natural deaths and the number dying from the disease When populations are very large these values will be expressed in scientific notation for example 5 00 e 07 which represents 5 times 10 to the 7th power or 50 000 000 Mortalitt To change from total numbers to proporti
28. euhauser University of Minnesota Angelo Collins Knowles Science Teaching Foundation Patti Soderberg Conserve School Terry L Derting Murray State University Roscoe Giles Boston University Louis Gross University of Tennessee Knoxville Yaffa Grossman Beloit College Raquel Holmes Boston University Stacey Kiser Lane Community College Daniel Udovic University of Oregon Rama Viswanathan Beloit College Linda Weinland Edison College Anton Weisstein Truman University Richard Wilson Emeritus Rockhurst College William Wimsatt University of Chicago Copyright 1993 2006 by Daniel Udovic and Will Goodwin All rights reserved Copyright Trademark and License Acknowledgments Portions of the BioOQUEST Library are copyrighted by Annenberg CPB Apple Computer Inc Beloit College Claris Corporation Microsoft Corporation and the authors of individually titled modules All rights reserved System 6 System 7 System 8 Mac OS 8 Finder and SimpleText are trademarks of Apple Computer Incorporated HyperCard and HyperTalk MultiFinder QuickTime Apple Mac Macintosh Power Macintosh LaserWriter ImageWriter and the Apple logo are registered trademarks of Apple Computer Incorporated Claris and HyperCard Player 2 1 are registered trademarks of Claris Corporation Extend is a trademark of Imagine That Incorporated Adobe Acrobat and PageMaker are trademarks of Adobe Systems Incorporated Microsoft Windows MS DOS and Windows NT are either
29. ger need a mark that you have previously set you can remove the mark Move the cursor over the Marks menu press the mouse button and drag the cursor down until Remove is highlighted but don t release it yet Now drag the cursor to the right until you can see the names of the marks Drag down until the mark name you want is highlighted then release the mouse button A window will appear asking you to confirm that you want to remove the mark If not click on the Cancel button Otherwise click on the Remove button The mark you selected will be removed Notes After you have set a mark in a run of the simulation you can enter a note to keep track of some information about the mark Move the cursor over the Marks menu press the mouse button and drag the cursor down until Notes is highlighted but don t release it yet Now drag the cursor to the right until you can see the names of the marks Drag down until the name of the mark you want is highlighted then release the mouse button A text window will appear The window will contain any previously entered notes for this particular mark It will be empty if no notes have were previously entered You may use the standard Macintosh methods for typing and editing text including cut copy and paste Windows Menu Windows Host Status Host Flow Chart Host Pop Size vs Time v Host Deaths vs Time Tile Windows All the commands under the Windows menu with the e
30. have had little experience using computers in your class even our simple initial exercise is likely to cause some frustrations In such circumstances we would recommend that you construct a few brief preliminary and highly directed exercises that will insure that all students feel comfortable with the program and the material As we help students through the structured exercises we try to avoid leading students to the right answer Rather we try to help them understand their 34 Epidemiology User s Manual observations clarify their thinking and design good experiments Furthermore whenever possible we have students take the time to think about what they expect to happen usually in small groups to write down predictions and to explain the basis for their predictions Often comparing the results that they obtain with their predictions leads to cognitive dissonance which can be very useful in the learning process Initially some students may feel that this is a glorified game of hide and seek in a sense it is In addition though it is essential practice for open ended investigations and the interaction between faculty and student is much more rewarding than when guiding students through prescribed steps that lead to the correct answer Students develop a deeper understanding of the concepts and gain important skills in designing and performing experiments and faculty gain important insights regarding studen
31. her Often these are biting insects or other ectoparasites e g mosquitoes or fleas Reservoirs are species that are also affected by the disease organism They are called reservoirs because they are a source for the disease even when it is rare or absent from the host population For example rats are a reservoir for plague and many birds and mammals serve as reservoirs for lyme disease Some diseases e g plague involve both reservoir and host populations E ector Flow Chart 3 Uninfected Infected Susceptible P Infectious Figure 4 The flow chart for a vector population Individuals are either susceptible non transmitters or infectious transmitters When vectors and or reservoir populations are included in a model the parameters involved in disease transmission become more complex Parameters determining transmission from vector or reservoir to the host population can be accessed from the vector or reservoir flow charts respectively by clicking on the button near the arrows going from susceptible to infectious Keep in mind that direct transmission from host to host can be occurring at the same time Parameters controlling direct transmission are still available from the host flow chart If you are modelling a disease in which direct transmission does not occur e g malaria at least before blood transfusions then you can set the probability of direct transmission to zero
32. icating the current setting of the birth rate Figure 1 The user can change these values at any time even when the simulation is running Epidemiology assumes that individuals can die from the disease disease death rate or from other causes natural or background death rate Individuals in all categories including those showing symptoms of the disease may die from other causes but only individuals showing symptoms will die from the disease Epidemiology User s Manual 9 Manipulating Population Characteristics The values for factors that influence population growth and the spread of the disease may be changed by clicking on the appropriate buttons or pop up menus on the flow chart This may be done even when the simulation is running if running the simulation will temporarily stop while you make changes and then start up again Disease transmission is the most difficult aspect of the model Clicking on the button near the arrow going from susceptible to infected brings up a dialog box that allows the user to view or alter the parameters determining disease transmission Figure 2 The rate at which susceptible individuals become infected depends on the probability of transmission given contact between a susceptible individual and an infected individual and on the rate at which individuals come into contact Epidemiology 2 5 allows users to choose between density independent and density dependent models of contact rate In the
33. iology 2 5 is accelerated for running on computers with PowerPC microprocessors Three versions of the program are available a 68K version which will run in emulation mode on PowerPC computers a PowerPC only version and a fat binary version which automatically run the version of the application best suited to your computer e Epidemiology application installed on the hard disk e On a color monitor the graphs will be displayed in color On a monochrome monitor the graphs will be displayed with different patterns Epidemiology User s Manual 31 Appendix 2 It Doesn t Work Even the best program has some bugs in it However there are many situations in which there is some other problem something that is not an error at all I can t open the program If Epidemiology reports an insufficient memory error during startup the problem may be that there is not enough memory Are you sure the machine has at least 1 megabyte of free RAM memory Are you running other applications under MultiFinder which can be closed First find out how much memory you have Under the Apple menu select About Finder In System 7 this is called About This Macintosh You will see a dialog box detailing the current memory usage in your system The crucial figure is the Largest Unused Block This value must be over 1000K in order for the system to run If it is not and there are no other applications currently running then Epide
34. kind of model that you wish to explore and to set values for certain settings that cannot be changed in the middle of a simulation A dialog box will appear allowing you to choose The Model Definition dialog box allows user to control the level of complexity that they will see in the flow chart and simulation runs The basic model divides the host population into only three categories Susceptible Infected and Recovered By choosing the appropriate settings the user may add categories for immunized individuals and may subdivide the infected population into several categories see page 10 Defining a Model for more details Epidemiology User s Manual 23 Fonts Sorry The Fonts option is not yet available Choose the Fonts command if you wish to change font sizes e g for presentations It is a good idea to size the window you re looking at to take up the whole screen if you increase font size Otherwise the graph may appear crowded and hard to read Marks Menu Marks Set Go To Remove gt Set To set a mark place the cursor over the Marks menu press the mouse button and drag down until the Set command is highlighted then release the mouse button A dialog box will appear with the text Please enter a name for the mark A name will already be there Mark at time 5 for example where 5 would be the 5th year in the run of the simulation You may move your mouse to click on this spac
35. l remains infected before moving into the recovered category provided of course that he she doesn t die Try a value of 3 to start out with Immunity loss This is the average length of time that a recovered individual remains immune to further infection When individuals lose their immunity the move from the recovered category to the susceptible category Immunization rate This is the proportion of newborns that are vaccinated Right now the program makes the unrealistic assumption that vaccinated individuals remain immune for life To start out set this to 0 Now that you have entered these settings go ahead and run the simulation Let it run for about 50 time intervals Examine and interpret the resulting population graphs Did anything unexpected happen 42 Epidemiology User s Manual Posing a Question Making a Prediction Working with your partner choose one of the factors from the previous page and make a prediction about how you expect the outcome of the simulation to change if you change that factor Which factor did you pick What is your prediction If I increase decrease the value of I expect Now make the change and run the simulation Describe the outcome of the simulation and how it compares with your predictions What hypotheses can you come up with that might explain the differences between the expected and the actual outcomes Epidemiology User s Manual 43 Exercise 1 Investigating Vir
36. ld be looking at diseases of humans or of other animals or even plants Based on their findings they could be asked to prepare a report for the class Combining these modeling activities with a more complete study of a disease including elements such as the impact of a disease in human history related scientific discoveries such as treatments or vaccines and their associated controversies could make an excellent term long project In the terminology of the Bio QUEST Consortium students would be posing their own problems investigating possible solutions and in their classroom presentations persuading their peers Epidemiology User s Manual 35 Using Epidemiology s Features to Prepare Learning Materials Epidemiology can be used to create custom files for problem sets exams or classroom demonstrations The steps involved in creating custom files changing parameters and settings marking saving files are no different than those to use the program and hence all of the relevant program features are described in the manual Here we provide a few pointers that you might find useful Setting marks can be a powerful tool in creating presentations and problem sets Marks allow you to set parameter values exactly the way that you want them position and size windows to suit your needs give those settings an appropriate name and add comments in the associated Notes window By setting up several marks in the same file you can quickly
37. m these simulation exercises relate to the co evolution between hosts and disease causing organisms 4 Public Health experts often claim that immunization rates much less than 100 can be satisfactory to cause a disease to die out in a given area Do our results lend any theoretical validity to these arguments A Acknowledgments 3 AIDS 10 36 Asymptomatic 28 Biology Software Lab 1 4 birth rate 28 41 bubonic plague 52 C concept map 33 contact rate 28 38 41 density dependent 48 Control menu Go 12 20 21 40 Go For 12 20 Go Until 12 19 Reset 18 21 40 Reset All 18 21 Show Hide Control Panel 12 21 Step 12 20 21 40 Stop 12 21 40 Control Panel 11 12 21 40 D death rate 28 41 disease 8 28 41 natural 8 28 density dependent 9 28 density independent 9 28 disease introduction 9 diseases airborne 9 sexually transmitted 9 doubling time 28 duration of infection 28 41 E Ebola 1 4 36 43 52 Edit menu Clear 19 Copy 18 Cut 18 Paste 19 Show Hide Clipboard 19 Undo 18 exporting 14 Epidemiology User s Manual 53 Index F File menu Close 16 New 16 Open 7 14 16 Page Setup 17 Print 14 17 Print Setup 14 Quit 15 18 Save 14 17 Save As 14 17 fleas 11 29 G goals 1 graph icon 13 graphs switching from tables 13 switching to 26 27 H hardware requirements 30 Hot Zone The 1 immunity loss 28 4
38. miology can not be run on that machine If there are other applications currently running try quitting those applications in order to free up memory can t open a Epidemiology document Was the document created with an early version 1 x 2 1 of Epidemiology Epidemiology 2 5 will not open documents created with earlier versions get an error message when try to set a mark If Epidemiology reports an insufficient memory error when you are attempting to create a new mark the problem may be that there is not enough memory for the requested operation Try removing unused marks then save the file If there are other applications currently running try quitting those applications in order to free up memory I m having trouble setting my graphs Make sure you click on the window first to make it the active window Check to see that the cursor turns from an arrow to a cross shape when you position it over the graph Click on the graph at the point you want to set or hold down the mouse button and drag the graph into the shape you want 32 Epidemiology User s Manual Appendix 3 Notes for Instructors In this section we provide some suggestions for instructors on how to use Epidemiology in the classroom and laboratory First we describe a series of activities used in a freshman seminar class at the University of Oregon Appendix 4 A Sample Learning Module contains the packet of materials that we handed out to our students Instruc
39. move from mark to mark in a presentation using each mark to set up a simulation demonstrating a different point or using two or more marks to make comparisons When setting up problem sets for students it may be better to create a number of files with only one or two marks per file rather than a single file with numerous marks The problem is that in the current version of the program there is no mechanism for grouping related marks If students choose to set marks of their own the latter approach would lead to a single file with a collection of marks that are difficult to keep organized Once you have created a file and set up all the marks that you need you may save the file using the SAVE or SAVE AS commands under the File menu Epidemiology will save all the initial values including model type and all the values displayed on the graphs for each mark that you set information about these marks such as the name and the notes that you entered for each mark and display information for each window such as the position and size of each window and whether or not it is open or closed If you discover that you want to edit a file marks can always be added or deleted In the current version of Epidemiology individual marks cannot be edited If you wish to change the settings for a particular mark e g re position some of the windows you will need to go to that mark make the desired changes create a new mark and then delete the
40. n R M and R M May 1991 Infectious diseases of humans dynamics and control Oxford University Press Oxford UK Epidemiology User s Manual 33 How we use Epidemiology at the University of Oregon The learning module in Appendix 4 was designed for use in introductory classes for non majors The first half of the module was tried out in Winter 1996 by Dan Udovic in a freshman seminar By the time students used the learning module in the seminar they had been learning in a very non technical way about the spread of infectious diseases for several weeks They had been reading and discussing Laurie Garrett s The Coming Plague and had seen videos on the eradication of smallpox and on issues surrounding the use of polio vaccines To learn more about this course and the resources used you may want to check out the class World Wide Web site http biology uoregon edu classes bi199 home html Before introducing the students to the computer program you might consider either or both of the following activities to lay the groundwork For more advanced biology majors these activities may not be important For most non majors however the activities prepare them for the computer exercises which follow The first is a simple hands on classroom simulation activity that illustrates how an infectious disease spreads The general idea is that one or two students in a class are somehow infected and infect other students through a series of cont
41. n dynamics of disease In any case we would like to hear from you both students and faculty about your experiences with the program We are particularly interested in knowing the kinds of issues that you have explored how Epidemiology helped and what kinds of limitations or problems you encountered Please write to the Biology Software Lab send us e mail BSL oregon uoregon edu or provide feedback through our World Wide Web site http Biology uoregon edu Biology_WWW bsl bsl html Epidemiology User s Manual 5 What You Should Read If you are unfamiliar with the Macintosh computer or computer terminology used in this manual Read the next section What You Need to Know see page 6 If you are unfamiliar with a biological term that is used in this manual Look in the section entitled Glossary page 28 If you want to know whether you have the right equipment to run the Epidemiology program Read Appendix Hardware and software requirements page 30 If you are familiar with the Macintosh but not with Epidemiology Read the section entitled Using Epidemiology page 7 If you have been through the features and want to know more details Read the section entitled Menus and Commands page 16 If you are an instructor and want to know how to use the program to prepare problem sets for students Read Appendix Ill Notes for Instructors page 32 Also see Appendix IV A Sample Learning Module page 36 If
42. n the models they use or in the parameters they explore Parameters gt Init Pop Size Init Pop Size vs vs Model Type Virulence Prob of Transmission Density Independent Group 1 Group 2 Contact Rate Density Dependent Group 3 Group 4 Contact Rate On the graph on the next page map out your predictions for the simulations that your group will do In your explanation discuss how your predictions would differ if you were using the opposite model Epidemiology User s Manual 49 Your Predictions High MOU PRRHAHZH Qu Low Med High VIRULENCE or PROB OF TRANSMISSION Explain your predictions 50 Epidemiology User s Manual Once you ve made your predictions you can go ahead and start doing some simulations with the object being to fill in the table below similar to the previous exercise Once again you may divide up the work among you Groups 1 and 3 should use a fixed probability of transmission of 0 01 and groups 2 and 4 should use a fixed disease death rate of 0 2 For the varying parameter use the values from the table in exercise 1 Be careful to let your simulations run for a long enough time to be sure that you know what will happen Sometimes the results may surprise you For example sometimes just when a disease looks like it has died out or will die out an epidemic can break out Medium Death rate gt 2 Prob of gt 0 01 Transmission Initial Pop Size Susc 10 000
43. ndividuals in the total population and in each category It also indicates whether the simulation is currently running or is stopped When the simulation is running the status window is updated each display interval The Population Size vs Time window displays a graph of the number or proportion of individuals in different population categories through time To change from total Epidemiology User s Manual 13 numbers to proportions or back again click on the icon on the tool bar at the top of the window The Deaths vs Time window displays the number of individuals dying each time interval It displays both the number of natural deaths and the number dying from the disease If you watch the above graph of population size or mortality as the simulation runs you will notice that they automatically re scale whenever necessary It may take you several runs to get used to the unexpected sudden changes in the shape of these graphs that occur during re scaling Both of these windows may also be viewed in spreadsheet format Click on the table icon on the tool bar at the top of the window The graphical display is now replaced by a table To return to the graphical display click the graph icon on the tool bar at the top of the window At times you may want to simplify the Population Size vs Time window and the Status window by only displaying values for a subset of the available population categories By choosing
44. old one Epidemiology and associated files are standard Macintosh files and can be copied in the usual ways when you are in the Finder for example by choosing the Finder s Duplicate command from the File menu or by dragging the file from one disk to another You will probably want to copy each of the files you have prepared onto a floppy disk that each student will use or copy the files onto each computer s hard drive 36 Epidemiology User s Manual Appendix 4 Modeling the Spread of a Disease A Sample Learning Module Note The Introduction and Exercise 1 of this Appendix can also be found in a slightly different form in the file called Modeling Diseases Introduction When a new disease enters a population we can envision several different kinds of outcomes 1 the disease could quickly die out 2 the disease could remain in the population at more or less stable levels perhaps settling down after a major outbreak i e become endemic 3 the disease could cycle in incidence causing periodic epidemics the cycles could increase or decrease in amplitude or remain about the same 4 epidemics could come and go at more or less random intervals perhaps exhibiting chaotic behavior or 5 the disease could cause the population to go extinct Which of these outcomes can we expect from diseases like AIDS or Ebola Examining simulation models may give us some insights We might also learn something about the fac
45. ons or back again click on the icon on the tool bar at the top of the window The display can either be in a graphical form or in tabular form To switch from one to the other click on the table or graph icon in the tool bar above the graph The values displayed are calculated from other population values you cannot change the values in this window directly To see this window if it is not already shown choose the Host Deaths vs Time command from the Windows menu 28 Epidemiology User s Manual Glossary Below are some of the key terms used in Epidemiology and in this manual Asymptomatic Individuals who have been infected but who do not yet show any signs of the disease Birth rate The number of births per individual in the population during a specified time interval Death Rate The fraction of the population that dies during a specified time interval Density dependent A factor that changes values depending on the density of the host population In Epidemiology 2 1 the user may set the contact rate average number of contacts per individual per time interval to be density dependent or density independent Disease Death Rate The fraction of the population that dies during a specified time due to the disease Doubling Time The time it would take a population to double given no changes in age specific mortality or fertility rates Any change in the fertility or the mortality graphs will result in a
46. oose which windows to print and how to arrange them Saving and Opening Problems The Open command under the File menu allows you to open a problem file that has been saved to disk You can do this only if there is not another problem file already open If another file is open the Open command will be inactive will appear grayed out on the screen when you select the File menu Save the current file first if you want to then choose the Close command from the File menu Any parameter windows which are displayed will disappear Now choose the Open command under the File menu Notice that the Open command is now available The Save command under the File menu allows you to save a problem file along with any marks that you have set and any notes you have made for those marks It will remember the last time interval you reached and the position of all the parameter windows The Save As command under the File menu allows you to save a problem file under a different name from the one you opened For instance if you open a class problem file but you make changes to it and want to save it to a name you choose you would choose the Save As command from the File menu A window will appear asking you to name the file Enter in your new name and click on the SAVE button to save the file Epidemiology User s Manual 15 under your new name The old file will be the same as it was before and still have the old name Quitting To quit Epid
47. p icon from the Control Panel This only stops the simulation it doesn t quit the program or end the problem you are working on so don t worry You can stop and start the simulation as often as you like If you wish to return to the initial state of a simulation with the fertility mortality and age distribution graphs as they were before you started the current simulation choose Reset from the Control menu or the Reset icon from the Control Panel A dialog box will appear asking whether you wish to mark the current spot before returning to the initial state see Menus and Commands Control Menu Reset for more details The Control Panel is a convenient way to run simulations Because of limited screen space however you may want to hide the Control Panel You may do so by clicking in the palette s close box or by choosing Hide Control Panel from the Control menu If the palette is hidden you may display it again by choosing Show Control Panel from the Control Menu Viewing Results Results are displayed in three types of windows 1 the Status window 2 the Population Size vs Time window and 3 the Deaths vs Time window These windows are updated every display interval If you are using a model with vector populations or reservoir populations enabled you will be able to view status windows and population windows for each population The Status window displays the current time and the number of i
48. pment of Epidemiology and related materials We would like to thank those faculty and students who have tested earlier versions of Epidemiology for their feedback and support and G Z Brown and his co workers for stimulating discussions regarding program design Our colleagues Gordon Hennesy and Jasper Barber contributed numerous ideas during the development of Epidemiology They are also responsible for many aspects of the common interface design of BSL programs The staff of the Workshop Biology Project John Postlethwait Alan Dickman Peter Wetherwax Deborah Morris Stacey Kiser and Nan Perigo and participants in our Biology Education Journal Club over the past several years have contributed many ideas about teaching and learning that have influenced our software tools and the curricular materials that use these tools Finally we d like to thank the staff of the BioQUEST Consortium for their continued support of our development efforts 4 Epidemiology User s Manual An Overview of Epidemiology Are emerging diseases like Ebola a serious threat to the world population Under what conditions would we expect a new infectious disease to spread through a population Can we predict whether a specific vaccination policy or other public health policy will be effective in preventing the spread of a disease These are a small sample of the kinds of questions that can be addressed by Epidemiology a computer program that simulates the s
49. pread of a disease in a population By manipulating values such as population death rates birth rates the length of time infected individuals are infectious the probability of disease transmission and initial population characteristics and then using the simulation to see how population characteristics change through time users of Epidemiology can investigate important questions in population biology and public health develop a deeper understanding of fundamental population concepts and explore issues related to public health policy A key feature of Epidemiology is the easy to use interface that allows you to rapidly and intuitively alter population characteristics even while a simulation is running and to instantaneously see the effects of your alterations For example changing the probability of disease transmission can be done quickly and easily and if the simulation is running you will immediately see the effect of your changes on the spread of the disease Epidemiology is designed to make it easy for you to creatively explore and experiment Just as importantly it is designed to help you organize your explorations and keep track of your experiments You may stop a simulation at any time and mark your place so that you can return to it later to make comparisons to perform controlled experiments or simply to refresh your memory We hope that you find Epidemiology to be an interesting and productive way to learn about the populatio
50. r s Manual deadly the disease should die out There is no basis for the predictions made here It is just a hypothetical example Your Predictions ZLOHMUNHZUADDAH Low Med High VIRULENCE Use the graph above to map out your predictions Give the rationale for your predictions below Your Rationale Epidemiology User s Manual 45 Once we ve all thought about and written down our expectations we can start our experiment Basically we need to fill in a chart similar to the graph above Rather than all of us doing all of the simulations we can divide up the workload and collate all our results Death rate Very Low Low Medium High Very High gt 0 0 0 1 0 2 0 3 0 5 Trans mission Medium Very High It may of course take more room to explain the outcome of each run As a class when we look at the different results we can decide what it is that we think is important and what is not so important We will discuss this as we go along Once we have collated all our results each of you should compare your results with your predictions and attempt to explain what we have observed Fill in the graph on the next page Are there major surprises 46 Epidemiology User s Manual Class Results High ZOnMnNHZUuALrA4 Low Med VIRULENCE High Epidemiology User s Manual 47 Exercise 2 How would immunization affect these results Make and test predictions about how the pattern of outcomes observed
51. registered trademarks or trademarks of Microsoft Corporation Helvetica Times and Palatino are registered trademarks of Linotype Hell The BioQUEST Library and BioQUEST Curriculum Consortium are trademarks of Beloit College Each BioQUEST module is a trademark of its respective institutions authors All other company and product names are trademarks or registered trademarks of their respective owners Portions of some modules software were created using Extender GrafPak by Invention Software Corporation Some modules software use the BioOQUEST Toolkit licensed from Project BioQUEST Table of Contents TABLE OF CONTENTS V PREFACE 1 ACKNOWLEDGMENTS 3 AN OVERVIEW OF EPIDEMIOLOGY 4 WHAT YOU SHOULD READ 5 WHAT YOU NEED TO KNOW 6 USING EPIDEMIOLOGY 7 Running Epidemiology 7 Opening a Problem 7 Setting up a Simulation 7 Running a Simulation 11 Viewing Results 12 Organizing Data and Reporting Results 13 Saving and Opening Problems 14 Quitting 15 MENUS AND COMMANDS 16 File Menu 16 Edit Menu 18 Control Menu 19 Settings Menu 22 Marks Menu 23 Windows Menu 24 GLOSSARY 28 APPENDIX 1 HARDWARE AND SOFTWARE REQUIREMENTS 30 APPENDIX 2 IT DOESN T WORK 31 APPENDIX 3 NOTES FOR INSTRUCTORS 32 The Simple SIR Model 32 How we use Epidemiology at the University of Oregon 33 Open ended Investigations with Epidemiology 2 1 34 Using Epidemiology s Features to Prepare Learning Materials 35 APP
52. sh to cut selected text from the Notes window associated with a mark see the Marks menu The selected text will be removed from the notes and placed on the clipboard for pasting somewhere else The Cut command is only active when the Notes window is active and some text has been selected Copy Use the Copy command from the Edit menu to copy objects and place them on the clipboard for pasting into other documents Copy takes the visible object from the currently active window a graph a table or the selected text and places it on the clipboard Graphs are handled as picts and tables are handled as tab delimited text Epidemiology User s Manual 19 Paste Use the Paste command from the Edit menu to take text from the clipboard and paste it into a Notes window associated with a mark see the Marks menu The Paste command is only active when the cursor is positioned within an active Notes window and there is text on the clipboard Clear Use the Clear command from the Edit to delete selected text from the Notes window associated with a mark see the Marks menu The selected text will be removed from the notes It will not be placed on the clipboard The Clear command is only active when the Notes window is active and some text has been selected Show Hide Clipboard The Show Hide Clipboard command from the Edit menu presents or hides a window which displays the current contents
53. start the simulation running choose the Go command from the Control menu The simulation will continue running and the display windows will continue updating until you stop the simulation using the Stop command The Go command is inactive except when the simulation is stopped and will appear grayed out whenever the simulation is running Step To run the simulation for only one time interval choose the Step command from the Control menu The simulation will update all the display windows for only one time interval then the simulation will stop You can continue the run of the simulation from this point by choosing the Go command or you can continue to choose the Step command as many times as you want Each time it will update the simulation for one time interval The Step command is always active If you choose this command while the simulation is running the simulation will immediately stop and then step through one more interval Epidemiology User s Manual 21 Stop After you choose the Go command the simulation will continue running and the display windows will continue updating until you stop the simulation Choose the Stop command from the Control menu The Stop command is inactive and will appear grayed out whenever the simulation is stopped Reset After you start Epidemiology but before you have run the simulation by selecting the Go or Step commands yo
54. t knowledge and misconceptions The activities in Appendix 4 introduce students to the following concepts e building and analyzing population models including construction of flow charts mapping out parameter space and testing the sensitivity of the model to certain parameters e why interactions between host populations and pathogen or parasite populations often lead to population cycles e how the virulence of a disease agent and its mode of transmission interact to influence whether a disease will spread in a population e how immunization rates can affect the spread of a disease perhaps leading to a disease dying out even if the percentage of the population immunized is much less than 100 e why a threshold population density is necessary for the spread of some diseases and what factors influence the level of that threshold Open ended Investigations with Epidemiology 2 1 Appendix 4 does not include a truly open ended investigation Once students have worked through those activities however they will be ready to use Epidemiology to build and analyze models of particular diseases of their own choosing They might be asked to find literature and materials on the Internet to help them decide how to build their model and what values to use for various parameters Does their disease have a latent period or an asymptomatic infectious stage How is it transmitted and what are the probabilities of transmission And so on They cou
55. tal Population Sere eee The status window shows the population sizes or proportions at the current time interval It also shows you whether the simulation is running or is currently stopped The Control Panel m E oe be The control panel works in much the same way that control buttons on a CD player or VCR work This is the Stop button When the simulation is running press this button when you are ready to stop it l This is the Go button Click on this button when you want to run the simulation It will continue to run until you stop it For greater control over the amount of time that a simulation runs choose Go Until or Go For from the Control Menu This is the Step button Click on this button to run the simulation for one time interval Since the simulation model runs quite fast especially on Power Macs stepping can be useful if you want to watch the progress of the simulation more carefully This is the Reset button It will reset the time to 0 and the population sizes to their original values It does not change the parameters that are set via the flow chart Epidemiology User s Manual 41 Setting Up the Model The simple model that we will be exploring allows you to set values for the following factors Birth rates You enter the number of individuals born per individual in the population per time unit For example if the time unit is years and we are dealing with a human pop
56. te to public policy see Sample Teaching Module These activities provide a starting point for instructors interested in using Epidemiology in their classes and labs The module is in an early stage of development and does not take full advantage of the features and flexibility of the program Whether you choose to adopt this module or to adapt it to your setting or to build a module of your own we would like to know how you are using the program Epidemiology is still evolving New features and interface changes will occur over time We are quite anxious to hear your views of Epidemiology and of the teaching module We would greatly appreciate any suggestions for improvement including ideas about the incorporation of new features 2 Epidemiology User s Manual For more information about Workshop Biology contact Daniel Udovic Director Workshop Biology Project Department of Biology 1210 University of Oregon Eugene OR 97403 1210 phone 541 346 5092 internet udovic oregon uoregon edu or see the Workshop Biology home page on the World Wide Web http Biology uoregon edu Biology_ WWW Workshop_biol wb html Epidemiology User s Manual 3 Acknowledgments Workshop Biology has been developed through grants from the Department of Education FIPSE P116A1 0385 and P116A4 1049 and the National Science Foundation USE 9150760 and DUE 9455145 These grants plus a grant from the Howard Hughes Medical Institute have supported the develo
57. the mouse button Don t click the button Depress it and hold it down Now move the mouse the object is dragged around on the screen When you have positioned the object where you want it release the mouse button to drop the object e Selecting This operation is used to pick one or more objects from a group of objects Selecting is usually accomplished by clicking on the object to be selected Typically selected objects will become highlighted to indicate they have been selected Example Select the mortality value for ages 20 25 by clicking on it The concepts listed above are few but are central to the operation of almost any Macintosh program There are a number of less fundamental concepts which we will ignore or will introduce as we encounter them Epidemiology User s Manual 7 Using Epidemiology This section provides basic information on how to use Epidemiology The exercises in the sample teaching module illustrate ways to use the program as a learning tool In this section we describe how to start the program open files enter population data either graphically or in spreadsheet format run simulations organize your findings save your simulations in a file and quit the program Running Epidemiology In order to run Epidemiology first make sure it is installed on your computer s hard disk or on a floppy disk that you have inserted into the disk drive Make sure that you also have all the problem files that
58. time during a simulation even when it is running 10 Epidemiology User s Manual Defining a Model To choose the type of model users can select the Define Model command from the Settings menu For example if you wish to model a disease in which there is an asymptomatic stage when an individual is first infected as with AIDS or rabies one can choose the appropriate check box from the Define Model dialog box Figure 3 A new flow chart will appear reflecting your choices The model choices available allow you to use Epidemiology to study the dynamics of a large variety of diseases In Epidemiology 2 5 you may also choose to model infectious diseases that are transmitted by vectors e g mosquitoes fleas or that affect other populations reservoir populations besides the host e g rats monkeys If you choose to include vectors and or reservoir populations in your models you will see separate flow charts for each population Warning changing these parameters during the run will cause the run to start over from the beginning time interval so only change these parameters before you begin a simulation or when you are ready to start a new one Population Categories Host Population O ector Population v Susceptible Susceptible CLatent Li Latent Infectious Asymptomatic Infectious M Symptomatic Reservoir Population Infectious Susceptible M Recovered M Infectious CJ immune O Recovered
59. tors should feel free to modify these materials to suit their needs We then describe how instructors can take advantage of some of Epidemiology s features to help prepare learning materials Note that Winter 1996 was the first term in which these exercises were tried The learning module should definitely be considered a rough draft The Simple SIR Model The simple models used in Epidemiology 2 5 are all variants of the mathematical model for the spread of an infectious disease caused by a microparasitic agent as described in Chapter 6 in Anderson amp May 1991 This model is generally referred to as an SIR model because it tracks the number of Susceptible Infected and Recovered individuals in a host population The system of equations appears below dX dt birthRate N t deathRate transmissionRate Y t X t dY dt transmissionRate Y t X t mortalityRate diseaseDeathRate recoveryRate Y t dZ dt recoveryRate Y t deathRate lossOf mmunityRate Z t where X t the susceptible population at time t Y t the infected population at time t Z t the recovered population at time t N t the total population at time t Our models are discrete time versions with the number of iterations per time interval under user control The variants of our simple model differ in the way that they calculate the transmission rate and in the number of additional population variables that they track Anderso
60. tors that influence the severity of epidemics or the levels of endemism Finally models may help us understand the impact of public health policies and practices How would we go about building a model of the spread of a disease One important step is to identify the variables that we want to track through time For example a demographer tracks the size of populations through time perhaps divided into population categories such as gender groups racial ethnic groups or age groups To track changes in population size we must look at the processes that could bring about change In this simple case there are only three things that can happen 1 individuals can come into the population via birth or immigration 2 they can leave the population through death or emigration or 3 the can move from one category to another e g by getting older or by having a sex change operation or by changing their economic status That s it So if we could model the processes by which the number of individuals in each category change then we could make predictions about the future state of the population Of course the challenge is to figure out what influences birth rates death rates etc and that may be very hard especially when all of the influencing factors may interact in complex ways In the case of epidemiological models the population variables can be divided into individuals that are susceptible to infection those that are infected currently
61. u can set the initial state for the run of the simulation At any time you are running the simulation you may want to return to this initial state The Reset command from the Control menu or the Reset button on the Control panel will set the population size and age distribution back to their initial values It does not however change the fertility or mortality settings After choosing Reset a window will appear asking you whether you want to save the current state before returning to the initial state If you click Save you will be setting a mark see the Mark menu and you will be asked to give it a name Reset All The Reset All command from the Control menu is similar to Reset In addition to resetting the population size and age distribution however Reset All resets all the parameter values e g birth and death rates and transmission probabilities to the values selected before you ran the last simulation the simulation After choosing Reset All a window will appear asking you whether you want to save the current state before returning to the initial state If you click Save you will be setting a mark see the Mark menu and you will be asked to give it a name Show Hide Control Panel The Control Panel is a window that contains four buttons one for each of the four commands above Stop Go Step and Reset The control panel provides an easy and
62. ue many mammals and birds harbor lyme disease Of course from the point of view of rats humans are a reservoir of plague Symptomatic Infected individuals who show signs of having the disease Vector Populations Populations that transmit disease causing organisms from one host individual to another e g mosquitoes fleas 30 Epidemiology User s Manual Appendix 1 Hardware and Software Requirements Epidemiology is designed to operate best on the Macintosh II family of computers or on Power Macintoshes However it will run nicely though slower on lower end models on Macintoshes of any type so long as at least 1 megabyte is available to the program However for a large run with many marks it may be necessary to set the partition size for Epidemiology to more than 1 megabyte Choose Get Info from the Finder In order to run the program you only need to have the application itself All of the resources that the program requires are already installed in the application Of course if you have saved an experiment and want to open it you will need to have the file into which you saved that experiment Epidemiology 2 5 is System 7 and MacOS 8 compatible and is accelerated for PowerPC s Summary of Hardware and Software Requirements e Macintosh computer with at least 1 megabyte of available random access memory RAM e Macintosh operating system 6 x or greater is required However system 7 x or OS 8 is recommended e Epidem
63. ulation that has a birth rate of 20 1000 per year you would enter 0 02 Death rates You enter the number of individuals dying per individual in the population per time unit For example if the time unit is years and we are dealing with a human population that has a death rate of 10 1000 per year you would enter 0 01 This is a background death rate due to factors other than the disease Disease death rate You enter the proportion of the infected population that dies of the disease each time interval For a disease such as the common cold this would be 0 0 For a disease like smallpox it might be something like 0 25 Number of contacts per time interval or Contact Rate How many contacts of the sort that might result in transmission does an individual make with other individuals during the course of a time interval on average This will depend on how the disease is transmitted and the nature of living conditions For example the value would be much lower for an STD than for the common cold It would also be lower in a rural area than in an urban area Try 100 to start out with Probability of transmission Given a contact between a susceptible individual and an infectious individual what is the probability that the susceptible individual will become infected Values entered must be below 1 Something like 0 01 might be reasonable to start with Duration of infection This is the average number of time units that an individua
64. ulence and Ease of Transmission We will concentrate our modeling efforts in this exercise on examining how the virulence of the disease agent how deadly it is and its ease of transmission affect its spread We should be able to use our results to help assess the potential threats of newly emerging diseases like Lassa Fever and Ebola The approach that we will take is to systematically explore parameter space seeing what happens for different combinations of parameter values Since we will start by just examining two parameters we will need to choose values for the other parameters and keep those constant We ll use the values that we had when we initially started the program The first thing you should do is to make some predictions about what you expect to happen The graph below shows a hypothetical and probably nonsensical mapping of parameter space In the empty graph on the next page you should generate your own mapping and explain your predictions Hypothetical Mapping of Parameter Space Disease levels fluctuate Population goes extinct Disease and population come to equilibrium ZOHNNHZWADAH Low Med High VIRULENCE The drawing above shows a hypothetical mapping of parameter space To interpret the map notice that it is divided into four regions This map for example predicts that when transmission rates are low and virulence rates are low Le the disease is not very 44 Epidemiology Use
65. xception of the Tile Windows command display Epidemiology windows Choosing a command from the Windows menu causes the window to appear if it is not already being shown and to become the active window The Tile Windows command will re size and reorganize Epidemiology s open windows so that they do not overlap each other Epidemiology User s Manual 25 i O Epid Activities 2 5 Current Time Tiz Status Stopped Susceptible 55 072 12 Infectious 191 11 Recovered 75 00 Total Population Sete Cee The Status window displays the current time and the number of individuals in the total population and in each category It also indicates whether the simulation is currently running or is stopped When the simulation is running the status window is updated each display interval You cannot change the values in this window directly To change the current numbers in any category choose Current State from the Settings menu You can select the categories that will be displayed by choosing Display Settings from the Settings menu and checking the appropriate boxes in the Display Settings dialog box The following are the values that can be displayed in this window To see the Status window if it is not already shown choose the Host Status command from the Windows menu The Flow Chart Flow Chart Uninfected Symptomatic Infectious g Infectious Disease Deaths The population ch
66. you ve read through the manual but have found something that doesn t seem to work in Epidemiology Read Appendix Il IT DOESN T WORK page 31 6 Epidemiology User s Manual What you Need to Know Throughout this manual we will assume that you are already familiar with basic Macintosh operations and concepts If you are not comfortable with these refer to the Macintosh Owner s Guide or some other introduction to the Macintosh before starting To help you on your way the following is a list of Macintosh concepts you will need to understand along with a brief explanation For more information consult one of the references mentioned above or simply ask someone who has worked with a Macintosh before to explain briefly e Pointing Pointing simply refers to positioning the cursor which is shaped like a pointer over some object e Clicking Also known as single clicking Position the cursor over the desired object and click the mouse button once For example Single click in a window to activate it means that if you position the cursor over a window and click once it will become the active window Clicking objects is typically used to select them see below e Double clicking Just like single clicking except that you click the mouse button twice in rapid succession instead of just once e Dragging This is used to move objects around on the screen To drag an object grab the object by pointing to it and depressing

Download Pdf Manuals

image

Related Search

Related Contents

ACTIVATIoN GuIdE GuÍA dE  RM008 Series 500 Quick Start Guide  KMR 1050 S BAT - Alfred Kärcher and Company  PDFダウンロード(739Kb)  Vantec EZ Swap M3500  Entidades Aseguradoras - Superintendencia de Seguros de la Nación  Philips QG3379  プレクストークリンクポケット 取扱説明書  PXN300F用  e+p C 1200  

Copyright © All rights reserved.
DMCA: DMCA_mwitty#outlook.com.