Preview Software Manual - BioQUEST Curriculum Consortium
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1. If you discover that you want to edit a file marks can always be added or deleted In the current version of Sampling 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 old one Sampling 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 drive2. BioQUEST A n Sampling Version 1 2Beta DA ESK y Library VII User s Manual Daniel Udovic University of Oregon Will Goodwin University of Oregon Gordon Hennesy University of Oregon A BioQUEST Library VII Online module published by the BiOQUEST 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 Beloit College Managing Editor Ethel D Stanley Beloit College BioOQUEST Curriculum Consortium Associate Editors Sam Donovan University of Pittsburgh Stephen Everse University of Vermont Marion Fass Beloit College Margaret Waterman Southeast Missouri State University Ethel D Stanley Beloit College BioQUEST Curriculum Consortium Online Editor Amanda Everse Beloit College BioOQUEST Curriculum Consortium Editorial Assistant Sue Risseeuw Beloit College BioQUEST Curriculum Consortium Editorial Board Ken Brown University of Technology Sydney AU Peter Lockhart Massey University NZ Joyce Cadwallader St Mary of the Woods College Ed Louis The University of Nottingham UK Eloise Carter Oxford College Claudia
3. Sampling is designed to operate best on the Macintosh II family of computers or on Power Macintoshes color monitors are required to work with multiple species However it will run though slower on lower end models on Macintoshes of any type so long as at least 1 5 megabytes is available to the program However for a large run with many marks it may be necessary to set the partition size for Sampling to more than 1 5 megabytes 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 Sampling is System 7 compatible Summary of Hardware and Software Requirements e Macintosh computer with at least 1 5 megabyte of available random access memory RAM e Macintosh operating system 6 x or greater is required However system 7 x or greater is recommended e Sampling application installed on the hard disk or a floppy disk e A color monitor is strongly recommended On a monochrome monitor you will not be able to distinguish between individuals of different populations You should however be able to work with problems that are restricted to a single species Sampling User s Manual 31 Appendix 2 It Doesn t Work Even the best program has some bugs in it I
4. File M h Usrerssencieenieea oe idan r E a EE E E Ea 14 Control MTU ss scsescapsameantavnomaadanaas aena a E aa ie 16 Settings Mennie eieiei E E AE A a 18 Marks MEI sosaniavscnansdandiueel eonan n i a e a 22 Windows Me nU srcsecinsucnariesrasii anioni Seoienches nE nE E EEE 23 Appendix 1 Hardware and Software Requirements 05 30 Appendix 2 Tt Doesnt Work siuiainsetiertvntiiar minnie hinienemnertadinetiies 31 I can t open the progt aM sessiones nininini enep eane eei 31 I get an error message when I try to set a mark 31 I m having trouble creating quadrats ccceeeeeeeeeeee ones 31 Why is the Print command grayed out 2 0 eee eeee eee ee es 32 Appendix 3 Notes for Instructors ccs icietinnpvaneanees vie waaortiawenawwanncues 33 Using Sampling s Features to Prepare Learning Materials 33 Sampling User s Manual 1 Preface Sampling is a software tool designed to help biology students learn some of the fundamental concepts related to population estimation and experimental design Sampling allows students to ask a variety of what if questions and to design and perform their own investigations The direct manipulation graphical interface encourages exploration and makes the program accessible to introductory students Nevertheless many graduate students in population biology will find interesting and challenging questions that they can explore using the program Sa
5. Neuhauser University of Minnesota Angelo Collins Knowles Science Teaching Foundation Patti Soderberg Conserve School Terry L Derting Murray State University Daniel Udovic University of Oregon Roscoe Giles Boston University Rama Viswanathan Beloit College Louis Gross University of Tennessee Knoxville Linda Weinland Edison College Yaffa Grossman Beloit College Anton Weisstein Truman University Raquel Holmes Boston University Richard Wilson Emeritus Rockhurst College Stacey Kiser Lane Community College William Wimsatt University of Chicago Copyright 1993 2006 by Daniel Udovic Will Goodwin Gordon Hennesy 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 eithe
6. Sampling you may specify different distributions for each species CAUTION changing the number of species or pressing a button for a distribution other than the current distribution completely Sampling User s Manual 21 changes things in the program If you don t want to lose what you were doing before make sure you save your work in a separate file before making any of these changes Font Size 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 SORRY The Fonts menu is grayed out because it is not functional in the current version Make Correlation Graph This menu option is only available when you are working with more than one species In that case you may view a graph of the correlation between any two species Choose this command from the Settings menu to specify which two species will be displayed in the correlation graph The following dialog will be displayed Select two species fora correlation graph First Species Second Species Z 22 Sampling User s Manual Marks Menu Marks Set Go To gt Remove gt Set To set a mark place the cursor over the Marks menu press the mouse button and drag down until Set command is highlighted then release the mouse butt
7. have supported the development of Sampling and related materials For more information about Workshop Biology contact Deborah Morris Coordinator Workshop Biology Project Department of Biology 1210 University of Oregon Eugene OR 97403 1210 phone 503 346 5092 internet dmorris 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 Sampling User s Manual 3 An Overview of Sampling What is the most effective way to find out the size of a population How is the accuracy of an the estimate of a population s size related to the size and number of samples How are population estimates influenced by the way the population is distributed in space How can you determine whether the spatial distributions of two or more populations are correlated These are some of questions that can be addressed using Sampling a computer tool designed to help biology students obtain a qualitative understanding of basic concepts related to estimation and statistics Sampling presents the user with a group of hypothetical populations distributed throughout an area and with tools for sampling these populations to estimate characteristics such as population size and density the nature of each population s spatial patterning and spatial correlations in abundance between populations By manipulating the number of samples the size of each sample and the spatial location and pa
8. in an early stage of development Many of the features that we have planned are not yet implemented You may find it frustrating that the program will not do all the things that you would like it to The silver lining in this cloud is that you can have a big impact on the next version of the program 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 questions that you have explored how Sampling 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 Workshop_biol wb html Sampling 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 If you are unfamiliar with a biological term that is used in this manual Refer to your textbook or course materials or ask your instructor If you want to know whether you have the right equipment to run Sampling Read the Appendix entitled Hardware and software requirements If you are familiar with the Macintosh but not with Sampling Read the section entitled Using Sampling If you have been through the features and want to know more details Read the section entitled Menus and Com
9. most option display button Note statistics are still updated and species are still there they are just not displayed The cursor position display shows the position of the cursor It often helps in positioning quadrats to have an idea of the exact position within the field It is presented as x y x is the horizontal position from left to right and y is the vertical position from top to bottom The entire field is 400 X 400 Count Per Quadrat Count per Quadrat Quad Count per Quadrat Displays the number of individuals of each species found in each quadrat The quadrats are numbered in the order they were generated The display can either be in a graphical form or in tabular form To switch from one to the other click on the T or G in the lower left corner of the window 26 Sampling User s Manual To see this window if it is not already shown choose the Count Per Quadrat command from the Windows menu Freq Dist Freq Dist 20 40 60 50 No Quad T Freq Dist The Frequency Distribution window displays a bar graph which shows the number of quadrats in which the number of individuals of a particular species falls within specified intervals The shape of this frequency distribution will depend on the spatial distribution pattern on population density and on the size of the quadrats The display can either be in a graphical form or in tabular form To switch from one to the other cl
10. Info box and start the program over again I m having trouble creating quadrats Make sure you click on the map 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 map Click on the map at the point that you want the upper left corner of the quadrat to be If the quadrat is too large to fit within the map area you will not be able to position a quadrat there 32 Sampling User s Manual Why is the Print command grayed out Printing has not been implemented in the current version of sampling If you plan to use the program in a setting that requires printing please contact the Biology Software Lab By the time you need it there may be an upgrade Sampling User s Manual 33 Appendix 3 Notes for Instructors In this section we provide some suggestions for how instructors can take advantage of some of Sampling s features to help prepare learning materials Using Sampling s Features to Prepare Learning Materials Sampling 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 prese
11. e see Close command below Sampling User s Manual 15 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 If you have 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 a new 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 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
12. e 1 A Frequency Distribution graph In this case there are 7 quadrats containing between 45 and 50 individuals and 6 quadrats containing 50 55 individuals etc Sampling User s Manual 11 Raw data is presented in the window entitled Count per Quadrat available from the Windows menu This data presented either graphically or in tabular form shows the number of individuals of each species in each quadrat sampled the quadrat number represents the order in which they were generated When working with multiple species see Changing the Settings Sampling also calculates covariances and correlation coefficients between species These statistics are available in tabular form from the Windows menu In addition you may view a correlation plot for any two species by specifying which species using the Settings menu and then choosing Correlate Btwn Species from the Windows menu For a more complete description of the meaning of the statistics or graphs that appear in these windows refer to Menus and Commands Windows to the Glossary or to a relevant textbook Changing the Settings Some of Sampling s settings are under user control By choosing the appropriate commands from the Settings menu for example the user can change the number of species displayed in the Species Distribution window and therefore sampled the size and shape of quadrats the interval size used for the horizontal axis in the frequency distribution g
13. e versions where the population may change through time this value will become meaningful In the current version of Sampling the name of the main statistics window is the same as the name of the current file To see the statistics window if it is not already shown choose the file name from the Windows menu When working with multiple species another statistics window is available that presents these descriptive statistics for all species in tabular form see below To see this window if it is not already n shown choose Statistics Sample Size n from the Windows menu Statistics MM variance istdDey istderr 0 000 0o00 0000 0 000 0 000 0 000 ooo 0 000 6 000 Statistics 1 Species 1 T orrelate btwn species 1 and JD This window shows a graph plotting the numbers of one population against the numbers of another Each point on the graph represents a different quadrat For example the leftmost point in the figure Sampling User s Manual 29 above represents a quadrat in which there were 10 individuals of species 1 and 15 individuals of species 3 The display can either be in a graphical form or in tabular form To switch from one to the other click on the icon in the lower left corner of the window To see this window if it is not already shown choose the Correlation Btwn Species command from the Windows menu 30 Sampling User s Manual Appendix 1 Hardware and Software Requirements
14. er will appear 10 Sampling User s Manual Automatic quadrat selection Another option for setting quadrats is to allow the program to set them randomly for you Under the Control menu select the Sample Automatically command by holding the mouse button down on it To the right of this command several options appear 5 10 15 20 25 50 75 100 200 and Custom Quadrat Selection Drag the cursor over one of the numbers and release the mouse button The program will then add the desired number of quadrats you selected and will update the statistics accordingly If you don t see the number you want use the Custom Quadrat Selection option This will bring up a box which asks you to type in the number of quadrats you want to set It also asks you for a second number Set a mark every quadrats Leave this number as zero for now We will discuss marks later Displaying Population Statistics Population statistics are presented in several different windows The Statistics window presents the mean density per quadrat the variance the standard deviation and the standard error for each population The Frequency Distribution window displays a bar graph with the horizontal axis representing the number of individuals of each species divided up into fixed intervals such as 0 5 5 10 and the vertical axis representing the number of quadrats having population numbers in each interval Freq Dist 40 60 50 No Quad Freq Dist Figur
15. ession 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 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 The concepts listed above are few but are central to the operation of almost any Macintosh program There are a number of less ie Sampling User s Manual 7 fundamental concepts which we will ignore or will introduce as we encounter them 8 Sampling User s Manual Using Sampling This section provides basic information on how to use Sampling 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 run simulations organize your findings save your simulations in a file and quit the program Running Sampling In order to run Sampling first make sure it is installed on your computer s hard disk or on a floppy disk that you have inserted into the di
16. f you find one please let us know However there are many situations in which there is some other problem something that is not an error at all can t open the program If Sampling 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 5 megabytes 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 1500K in order for the system to run If it is not and there are no other applications currently running then Sampling can not be run on that machine If there are other applications currently running try quitting those applications in order to free up memory get an error message when try to set a mark If Sampling 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 You may have to quit Sampling increase the memory partition in the Get
17. ick on the icon in the lower left corner of the window You may also control the level of detail of this graph by altering the setting of the frequency distribution interval in the Sampling Parameters dialog box For example if you are using small quadrats that rarely have more than ten individuals of a given species you may want to set the interval to 1 or 2 If you change the value to 2 it will display the number of quadrats with either O or 1 individual in the first interval 2 3 in the second 4 5 in the third etc To see this window if it is not already shown choose the Freq Dist command from the Windows menu Sampling User s Manual 27 Statistics Untitled Statistics for Current Time O0 N Sample Size 15 Mean per Quadrat 50 53 Variance 20 65 Std Deviation 4 54 Std Error 1 17 z Untitled Statistics for Current Time 0 M Sample Size 30 Species 1 Species 2 Mean per Quadrat 6 17 5 67 Variance 5 41 6 55 Std Deviation 2 42 2 57 Std Error O 42 0 47 Mean crowding 6 04 5 99 Patchiness rds 0 98 1 02 Covariance 51 53 Correlation Coefficient 0 29 The Statistics window displays current estimates and variance measures for various population statistics Statistic which are reported are e Total number of quadrats set e Mean e Variance e Standard Deviation e Standard Error 28 Sampling User s Manual Note Current time is always zero in the current version of the program In futur
18. l 19 e Quadrat Width enter a number for the width this doesn t need to be the same number if you don t want square quadrats Sampling will discard all previous quadrats when you change the size of the quadrats This is because the statistics don t mean anything if the quadrats are of different sizes Display e Frequency Dist Interval This parameter controls the size of the interval reported in the Frequency Distribution graph For example a frequency distribution interval of five will group all quadrats with a sampling of zero to five from five to ten etc The following dialog will appear Enter the Frequency Distribution interval Size 20 Sampling User s Manual Populations Enter the following parameters for species populations Number of species Random Clumped Even Species 1 Species 2 Species 3 Species Species 5 Species 6 E 8 a E E E E Species f e Number of Species enter a number between 1 and 7 Sampling can display up to seven species e Density enter a number between 0 0 and 1 0 to represent the density of each species e Distribution radio buttons press the button which represents the desired distribution of species randomly distributed or clumped The even distribution would distribute species according to a statistically even distribution but has not been implemented if you press this button you will get a random distribution In the current version of
19. lready been placed in the area You may place additional quadrats by positioning the cursor at the appropriate spot over the map and clicking or by choosing Sample Automatically from the Settings menu The tool bar at the top of the Species Distribution window is used to display information about the window and to control the display options There are three regions of the tool bar e Quadrat display region displays quadrat number and a count of individuals of each species within that quadrat e Display options buttons you can choose to display all the individuals in the distribution map only the individuals appearing within a quadrat or none of the individuals e Cursor position display tells you the location of the cursor when it is over the species distribution portion of the screen Sampling User s Manual 25 The quadrat display region is only active when the cursor is positioned above a quadrat Then the cursor changes from a cross to a white arrow and the quadrat display region will display the quadrat number and a count one number for each species of individuals found in that quadrat If you want the Species Distribution window to display all the individuals press the right most display option button If you want the Species Distribution window to only display individuals that are found inside the quadrats press the middle display option button If you want to display no individuals at all press the right
20. mands If you are an instructor and want to know how to use the program to prepare problem sets for students Read the Appendix entitled Instructor Guidelines If you ve read through the manual but have found something that doesn t seem to work in Sampling Read the Appendix entitled IT DOESN T WORK 6 Sampling 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 succ
21. mpling 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 and as with our other software modules Sampling 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 this goal may be less obvious in Sampling than in some of our other programs such as Demography As we add new features to the program however connections to population and conservation issues will become more apparent Sampling is in an early stage of development New features and interface changes will occur over time We are quite anxious to hear your views of Sampling We would greatly appreciate any suggestions for improvement including ideas about the incorporation of new features 2 Sampling User s Manual 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
22. nd still have the old name Quitting To quit Sampling choose the Quit command from the File menu or use the Command Q option to quit hold down the Command key which has the symbol on it and press the Q key on the keyboard If you have made any changes a dialog box will appear giving you the opportunity to save your work before exiting the program ie 14 Sampling User s Manual Menus and Commands This section will describe the menu structure of Sampling 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 ELE PPEP Close 36 gape HES Save As Reuyeri ip Saved Page Setup Print P 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 The Species Distribution window and the Statistics window 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 on
23. ntations 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 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 Sampling will save all the initial values the positions of all the quadrats on the map 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 34 Sampling User s Manual and display information for each window such as the position and size of each window and whether or not it is open or closed
24. on In the current version of the program a mark is automatically created and given a name e g Mark after quad 3 Future versions will allow you to choose your own names for marks Go To After you have set a mark you can restore the program 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 This new mark will show up in the Go to and Remove lists so you can treat it like any other mark The program will go to the mark you requested Remove If you decide you no longer need a mark that you have previously set you can remove the mark Move the cursor over the Marks Sampling User s Manual 23 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
25. ou plan to use the program in a setting that requires printing please contact the Biology Software Lab 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 Gf 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 Sampling User s Manual 13 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 under your new name The old file will be the same as it was before a
26. r 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 BioOQUEST 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 BioQUEST Toolkit licensed from Project BioQUEST Table of Contents Table Of Co ntentSr icorisindo ei i EE Eaa vii NPT Sh Ss ame wes lv ht a ah eh oe eh dich EEES AO 1 An Overview of Sampling iscicows dersarexranebeeonde ont bacsawsirorepiranaepioreh aces 4 What You Should IRAs j acnias onnonernstia ciate danieanantnenasaravlaiedinsavadubeutuns 6 What vou Need to KNOW pceucissieistesiatioustieiaariatiaiaienaious 7 Using APE diowexsvandviooras naan enwannee TT EEIE E E ETENEE E 8 Ru unning Sampling sisrcnrorrrsri rires iinei aa i AAEE RETE 8 Opening a Problem cacicictsasrevieaeninieieueiaas EE EEE A 8 Working with the program ci xciiedinncianddiners Gartmore dneties 9 Or rgani ins D t emesnysrno renin nonn EER tian EEEE 11 Saving and Opening Pradlemsey scecicniepesnieriounvveervdvveetey entered 12 Ouattaraa a E EETA E EEEE E EE E E TOE 13 Men s and Command Sic iniesrisies teense inier EEEE ESEA a EEE 14
27. raph and the pattern of the spatial distribution of populations random clumped or even the latter is not implemented in this version of Sampling For a detailed description please see the section on the Settings menu under Menus Organizing Data Marking The Mark feature allows you to set a mark at any particular time while you are running the program You can then enter a note to keep track of additional information in association with the mark 12 Sampling User s Manual When you set a mark Sampling 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 whenever you need to Marking makes comparisons easy and provides a simple way to summarize your work If you want to show someone what happened at various stages while you were running the program you can set a mark at each point of interest For example if you wish to investigate the relationship between the standard error of an estimate and the sample size you could select Sample Automatically from the Settings menu choosing Custom from the hierarchical menu By entering say 100 quadrats and by specifying that you would like to set marks every ten quadrats you would be able to easily track the value for the standard error after 10 20 30 quadrats etc Printing SORRY Printing is not available in this version of Sampling It may be available soon however So if y
28. sk drive Make sure that you also have any problem files that you will need if any check with your instructor to find out what they are called They will look like this icon of course the names will be different JJH Sampling file Double click on the Sampling icon BOEDA Sampling v1 1 B The program will start up Opening a Problem To open a problem file choose the Open command from the File menu If the Open command 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 Sampling User s Manual 9 Working with the program When you open the Sampling program by double clicking on the Sampling 1 18 icon two windows will appear the statistics window the title is Untitled until you save the file with some other name and the Species Distribution window which has a distribution of blue dots in a random pattern Other windows will appear when you begin using the program or may be selected from the Windows menu Positioning Quadrats Estimating population parameters occurs when you sample the populations in the Species Distribution window by placing quadra
29. the Print command to ensure the page setup is the way you want it 16 Sampling User s Manual Print SORRY Printing is not available in this version of Sampling It may be available soon however So if you plan to use the program in a setting that requires printing please contact the Biology Software Lab Quit To quit Sampling 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 Control Menu Settings Marks Sample automatically In the current version of Sampling the Control menu only has two functions and the rest of the menu is therefore grayed out In future versions populations may change through time and individuals may be able to move around This menu will then allow users to control the simulation Sample Automatically Choose Sample Automatically from the Control menu to generate a given number of quadrats placed randomly on the Species Distribution map A hierarchical menu will appear to the right of the Settings menu Either choose a specified number or select Custom If you select Custom a dialog box will appear Sampling User s Manual 17 asking you to enter the number of quadrats you want to Sampling to generate Select number of quadrats to be randomly selected by program Set a mark every quadrats Type in the number of quadra
30. 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 window will appear asking you to enter the text for your note Type in your text then click on the OK button to finish entering the note Windows Menu Windows Untitled Count per Quadrat Species Distribution Freq Dist All the commands under the Windows menu display Sampling windows These commands cause the windows to appear if they are not already being shown 24 Sampling User s Manual Species Distribution Species Distribution Seo 126 135 ee n s u r t i B ste p pn me The Species Distribution window displays the distribution of individuals in populations over a two dimensional area Individuals of different species are represented by different colors Also displays the position of quadrats that have a
31. ts at specific points in the window Sampling will automatically count up the number of each species in each quadrat and update all of the relevant population estimates To place quadrats you have two options One is to place them by hand Drag the mouse until it is over the Species Distribution window Notice that the cursor changes to a cross Position the cursor over the area where you want to set a quadrat Now hold down the mouse button and keep holding it down Notice that a blue rectangle in this case a square will appear Without letting up on the mouse button drag this square around on the screen until it is in the position you want Let go of the mouse button and the blue rectangle will stay in that position Notice also that the Frequency Distribution window appears and shows that one quadrat has the number of individuals that are in your quadrat Now without pressing down on the mouse button position the cursor somewhere within the quadrat rectangle The cursor will change from the cross into a white arrow Notice in the upper left hand corner of the Species Distribution window in an area called the tool bar which we will discuss later some information about the quadrat is displayed First the quadrat number in this case 1 next the number of individuals of each species unless you have changed the number of species using the Sampling Parameters command under the Settings menu there is only one species and only one numb
32. ts you want to set It will also give you the option of setting marks at regular intervals If you wanted to study how certain statistics changed as sample size increased for example this feature could be very useful Enter zero if you don t want marks to be set during automatic quadrat selection When sampling automatically Sampling will not automatically discard any quadrats that have been previously created but will add the new ones to the ones already present Reset Reset clears the sampling field of all quadrats All statistics reflect a zero state 18 Sampling User s Manual Settings Menu i Marks Windows Quadrat Size Display gt Make correlation graph Populations Font Size Quadrat Size To change the number of species you want displayed or to change the size of the quadrat rectangle or the frequency distribution interval size select the Sampling Parameters command under the Settings menu To change the size of the quadrat rectangle either select one of the sizes specified in the popup menu which will display when you hold down the mouse button while the cursor is positioned over Quadrat Size under the Settings Menu or drag the cursor and release over Custom If you choose Custom the following dialog box will appear Custom Quadrat Size Quadrat Height P Quadrat Width 25 e Quadrat Height enter a number for the height in pixels Sampling User s Manua
33. tterning of samples users of Sampling can investigate important questions in population estimation and especially in conjunction with field studies develop a much deeper understanding of fundamental concepts than would likely be obtained solely from limited field studies that can be conducted in introductory courses Sampling has an easy to use interface that allows you to rapidly and intuitively sample a group of populations and to immediately see results in graphical or tabular format For example Sampling presents you with an aerial view of the populations By simply placing the cursor over a particular spot and clicking the mouse you can place a quadrat over a given area As soon as you release the mouse button Sampling will calculate the numbers of each species in the quadrat Each time you create a new quadrat Sampling will immediately update estimates of population statistics such as mean densities and standard deviations and will update any relevant graphs such as frequency distributions based on the new information 4 Sampling User s Manual Sampling 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 Sampling is
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