BioSim2 User`s Manual
Contents
1. eo 19 11 Opening Screen with Print Drop down Menu 20 12 Opening Screen with Edit Drop down Menu Opened 21 vii viii List of Tables 1 Example of CSV Spreadsheet as an Input File partial data set with titles and OpPUONS eI e Example of CSV Spreadsheet as an Input File partial data set without tles or user OpliOns cedes esee to omi rueda dadada Acknowledgement This project was supported in part by EPSCoR Baccalaureate College Summer Research Program under NSF Grant Number EPS 0236976 and by the generous donation of Dr Reid s time for the Java program from the Academic Computing Team Information Technology Department of Norwich University xi Xii Abstract The Pinkham Pearson index of similarity has been evaluated by EPA as one of the more powerful tools for comparing community structure in its rapid bioassessment protocol However its use has been limited because the program that ran it BioSim1 was only available in DOS format A user friendly version of BioSim2 is now available in a Java format that can run on Windows Mac OS Linux or any computer operating system that supports Java v1 4 or higher xiii Xiv Section 1 Introduction The index of similarity B Pinkham and Pearson 1976 was proposed as a means for determining the impact of pollution on communities Pinkham a2. the Help for BioSim2 provides access to an html version of this User s Manual 21 22 References Barbour M T J L Plafkin B P Bradley C G Graves and R W Wisseman 1992 Evaluation of EPA s rapid bioassessment benthic metrics metric redundancy and variability among reference stream sites Environmental Toxicology and Chemistry 11 4 437 449 Bonham Carter G F 1967 Fortran IV program for Q mode cluster analysis of non quantitative data using IBM 7090 7094 computers Kans Geol Surv Computer Contribution No 17 Gonzales D A J G Pearson and C F A Pinkham 1993 User s manual for BioSim1 Beta Version 1 0 A Program that Applies the Coefficient of Biotic Similarity B to Complex Data Matrices EPA 600 R 93 219 Environmental Monitoring Systems Laboratory Las Vegas NV Kaesler R L 1970 The Cophenetic Correlation Coefficient in Paleoecology Geological Society of America Bulletin Lawrence KS pp 1261 1266 Klemm D J P A Lewis and J M Lazorchak 1990 Macroinvertebrate Field and Laboratory Methods for Evaluating the Biological Integrity of Surface Waters Aquatic Biology Branch Quality Assurance Research Division Environmental Monitoring Systems Laboratory Cincinnati OH EPA 600 0 90 000 U S EPA Washington D C Pankhurst Richard J 1991 Practical Taxonomic Computing Cambridge University Press Cambridge 201 pp Pearson J G and C F A Pinkham 1992 Strategy for data analysis in environm
3. 0 12 20 0 7 7 4 CC725R3 76 8 80 PC725R1 73 90 10 80 6 14 PC725R2 30 27 PC725R3 27 2 Aa gt n CPCTestData Ready Important There must be a value in column A row 6 the word Data is written here by BioSim2 when saving the file As indicated above the titles and options data may be entered directly on the screen accessed with the Input amp Options tab The maximum number of characters for these titles is 256 but long titles can cause some problems with the data displays Data may also be entered directly using the table portion of this screen and the buttons Add Row Add Column Insert Row Insert Column Delete Row and Delete Column directly below the data input table You can also just import the data using the Open Data File option This file must follow the format as shown in Table 2 The first row always contains the titles for the columns and the first column always contains the titles for the rows Important There must be a value in column A row 1 the word Data is written here by BioSim2 when saving the file It is also possible to use the standard copy Ctrl C cut Ctrl X and paste Ctrl V features of Windows to move data from a spreadsheet directly into the table on the nput amp Options tab When doing this make sure that cell A 1 has something in it otherwise the column titles in row 1 shift to the left one column Save Data File The Save Data F
4. 6424 0 5897 1 0 2457 0 2366 0 2035 IPC725R1 0413 0230 0444 2735 343 45 1 0 5521 039 1 10 PC 25R3 0 3242 Matrix of Similarity Values Version B CPCRW 02 0 0 Matches 1 0 po Tubfic DCD Diam DCD Paga DCO Crco DCO Euki DCO Lapp DCO Syno DE Cheli Ds Meta DCD Paga 0 2833 0 1667 1 0 1882 0 3222 0 4960 0 3056 0 2815 0 1708 DCO Syno 0 0231 0 3762 0 3056 0 1743 0 0500 0 2398 1 0 0222 0 3357 DE Cheli 0 3112 0468 02415 2245 0538 222 022 1 02453 DS Meta DS Pros 0 3170 0 1764 0 1522 0 1677 0 3708 0 1830 0 1491 0 1869 0 4538 DS Sim 0 0686 0 3519 0 4017 0 1612 0 1642 0 2460 0 2222 0 3247 0 2543 Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 5 Tab B Matrices Showing the Similarity Values B for Rows top and Columns bottom 14 BioSim 2 0 03 File Print Edit Actions Help CPCRW 02 Version B unweighted average 0 0 Matches 1 r 0 892 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 t Sites 0 642 CCT25R3 0 578 CC725R1 CC725R2 PC725R2 PC725R1 PC725R3 CPC720R3 CPC720R2 CPC720R1 0 9 1 0 Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 6 Tab Row Dendrogram Showing the Dendrogram for Rows 15 BioSim 2 0 03 File Print Edit Actions Help
5. Cophenetic Correlation Plot for Sites CPCRW 02 Version B unweighted average 0 0 Matches 1 r 70 892 0 4 0 6 Average B Value Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 7 Tab Row Cophenetic Plot Showing the Cophenetic Correlation Plot for Rows 16 BioSim 2 0 03 File Print Edit Actions Help CPCRW 02 Version B unweighted average 0 0 Matches 1 0 685 0 2 0 3 D 4 0 5 0 6 0 7 0 8 0 666 0 424 0 382 0 574 Taxa EA Amel DCD Diam PN Isop EB Drun DCO Syno DS Sim DT Dicr DCD Paga DCO Lapp Tr Rhya EH Epeo DCO Euki PNZ cint DE Cheli TL Eccl PNZ hays DCO CrCo EH Ciny Tubific DS Pros DS Meta EB Baet Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot JE Reordered Data Figure 8 Tab Column Dendrogram Showing the Dendrogram for Columns 17 BioSim 2 0 03 File Print Edit Actions Help Cophenetic Correlation Plot for Taxa CPCRW 02 Version B unweighted average 0 0 Matches 1 r 0 685 0 6 Average B Value Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot k Column Dendrogram Column Cophenetic Plot Reordered Data Figure 9 Tab Column Cophenetic Plot Showing the Cophenetic Correlation Plot for Columns 18 amp BioSim 2 0 03 CC725R3 CPC
6. Delete Row Delete Column Input amp Options BMatrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 11 Opening Screen with Print Drop down Menu Opened 20 4 1 4 Edit Drop down Menu Figure 12 represents the opening screen with the Edit drop down menu opened From this menu you can highlight any of the input data fields and use the standard cut copy or paste functions The standard keyboard shortcuts Ctrl X Ctrl C and Ctrl V also work for these functions BioSim 2 0 03 File Print Edit Actions Help Cut Ctrl X Copy pverallanalysis CPCRW 02 Paste Ctl Title for rows Sites Title for columns Taxa Sire ote rn m matches Q1 1 ior cote sat ona E TIIMIN Low denominators 0 0 Matches 1 0 v Threshold 0 Data First Row is for Column labels First Column is for Row labels DCD Diam DCD Paga Dem CrCo 299 Euki De Lapp DCO Syno Cheli DS Meta DS Pros CPC720R1 CPC720R2 CPC720R3 CC725R1 Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 12 Opening Screen with Edit Drop down Menu Opened 4 1 5 Help Drop down Menu The Help menu has two options The About BioSim2 option provides information on the authors and the version number of BioSim2 At present
7. titles for the rows The values in column A rows 1 5 are fixed and must appear as in Table 1 The values in column B rows 1 3 are user entered titles and the values in rows 4 and 5 are options for calculating the similarity index see Pearson and Pinkham 1992 for a complete explanation of these options B is the standard similarity index and B1 is the same index but the raw data values are converted to relative abundances The Low denominators field allows the user to define how 0 0 matches and other matches with low denominators will be dealt with during the calculation of the similarity index The 0 0 matches can be set to equal 1 highest weight 0 lowest weight any value between 0 0 and 1 0 using the Weight for 0 0 matches slider bar or ignored altogether in the calculations Matches with low denominators can be ignored by setting the threshold to the value of the denominator at or below which matches should not be used in calculating B This value is entered in the Threshold box on the opening screen Table 1 Example of CSV Spreadsheet as an Input File partial data set with titles and options Microsoft Excel CPCTestData csv Format Tools ata Window Help Title CPCRW 02 Rows Sites Columns Taxa B Version B Low Denominators 0 0 Matches 1 Data Tubific DCD Diam DCD Paga DCO CrCo DCO Euki CPC720R1 17 1 4 71 3 CPC720R2 16 3 3 53 27 CPC720R3 33 2 8 87 15 CC725R1 96 54 0 0 30 CC725R2 88 24
8. 720R3 CPC720R2 CPC720R1 PC725R3 CPC720R3 CPC720R2 CPC720R1 0 0 0 0 0 0 0 i i I EB Drun DCO Syno DS Sim DT Dicr Tr Rhya 8 0 4 0 EH Epeo DCO Euki PNZ cint Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 10 Tab Reordered Data Showing the Data Reordered According to Both Row and Column Dendrograms 19 4 1 3 Print Drop down Menu Figure 11 represents the opening screen with the Print drop down menu opened From this menu you can select and print any of the following outputs Row Dendrogram Column Dendrogram Reordered Data Transposed Reordered Data Row B Matrix Column B Matrix Row Cophenetic Plot or the Column Cophenetic Plot You can also print all of these outputs by selecting Print All or the keyboard shortcut Ctrl P BioSim 2 0 03 File Print Edit Actions Help Print All Original Data Row B Matrix Row Dendrogram Weight for 0 0 matches Row Cophenetic Plot Column B Matrix Version B Column Dendrogram Column Cophenetic Plot 0 0 Matches 1 0 Threshold 0 ux d Reordered Data Transposed Reordered Data olumn is for Row labels CPC720R1 CPC720R2 CPC720R3 4 gt Add Row Add Column Insert Column
9. Average B Value Column Dendrogram 0 0 0 1 0 2 0 169 0 0 0 1 0 2 CPCRW 02 Version B unweighted average 0 0 Matches 1 Fos 0 685 03 0 4 0 382 0 278 0 367 0 322 0 349 0 368 0 328 0 3 0 4 0 424 0 5 0 6 0 7 0 666 0 611 0 574 0 63 0 446 0 605 0 458 0 563 0 524 0 453 0 5 0 6 0 7 0 8 0 8 0 9 0 9 Taxa EA Amel DCD Diam PN Isop EB Drun DCO Syno DS Sim DT Dier DCD Paga DCO Lapp Tr Rhya EH Epeo DCO Euki PNZ cint DE Cheli TL Eccl PNZ hays DCO CrCo EH Ciny Tubific DS Pros DS Meta EB Baet 27 Column Cophenetic Correlation Plot Cophenetic Correlation Plot for Taxa CPCRW 02 Version B unweighted average 0 0 Matches 1 r 70 685 08r 04 0 2 O OOO Average B Value 28 gt Please make all necessary changes on the below label PRESORTED STANDARD up and return to the address the upper POSTAGE amp FEES PAID United States EPA Environmental Protection If you do not wish to receive these reports CHECK HERE Ol PERMIT No G 35 Agency detach or copy this cover and return to the address in the Office of Research upper left hand corner and Development 8101R Washington DC 20460 Official Business Penalty for Private Use 300 EPA 600 R 05 150 November 2005 www epa gov Recycled Recyclable Printed with vegetable based ink on paper that contains a minimum of 50 post consumer fibe
10. BioSim2 User s Manual Version 2 0 03 EPA 600 R 05 150 November 2005 www epa gov BioSim2 User s Manual Version 2 0 03 A Program that Applies the Coefficient of Biotic Similarity B to Complex Data Matrices by J Gareth Pearson U S Environmental Protection Agency Environmental Sciences Division P O Box 93478 Las Vegas Nevada 89193 3478 Carlos F A Pinkham Visiting Professor Department of Biology Norwich University Northfield Vermont 05663 Brian P Reid DMS Computing Dartmouth Medical School 1 Rope Ferry Road Hanover New Hampshire 03755 Victor T Chevalier 431 Isom Road Suite 125 San Antonio TX 78216 November 2005 Notice The information in this document has been funded in part by the United States Environmental Protection Agency in collaboration with Norwich University It has been subjected to the Agency s peer and administrative review and has been approved for publication as an EPA document Mention of trade names or commercial products does not constitute endorsement or recommendation by the EPA for use Contents Section Page Notice mS iii E Ege cc decia vii B qmd E ix Acknowledgement oet ii xi xiii 25 ee 1 Section 2 Use of This Manual 3 Section 3 Installing and Starting 2 2 22 5 Section 4 Using Blo
11. SiIm2 oie eee en ht ERE RE REIR bend 7 4 1 Standard Menu FUNCIONS assa ee ea een 8 41 1 Eile Drop down Mental 8 4 1 2 Actions Drop down Menu a re een 11 4 1 3 Print Drop down Men tt a Essen 20 4 1 4 Edit Drop down Menu inicio nee 21 4 1 5 Help Drop down Menu 21 Referenc Sii M 23 o E 25 vi List of Figures Number Page 1 Opening Screen Of BIOSIM 2 ante rtc bis 8 2 Opening Screen with File Drop down Menu Opened 9 3 Opening Screen with Actions Drop down Menu Opened 12 4 Files Created and Saved Using the Save Report 13 5 Tab B Matrices Showing the Similarity Values B for Rows top and Columns DOOM en estu inus 14 6 Tab Row Dendrogram Showing the Dendrogram for 15 7 Tab Row Cophenetic Plot Showing the Cophenetic Correlation Plot TO 16 8 Tab Column Dendrogram Showing the Dendrogram for Columns 17 9 Tab Column Cophenetic Plot Showing the Cophenetic Correlation Plot for sad ti 18 10 Tab Reordered Data Showing the Data Reordered According to Both Row and Column Dendrograms u
12. abs E BioSim 2 0 03 BAR Title for overall analysis BioSim Analysis Title for rows Rows Title for columns Columns A ONL Imole be Index of Biotic Similarity VersionB gt DRA RN Low denominators oo Matches 1 Threshold 0 Data First Row is for Column labels First Column is for Row labels AAA M M Add Row Add Column Insert Row Insert Column Delete Row Delete Column Welcome to BioSim 2 0 03 Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 1 Opening Screen of BioSim2 4 1 Standard Menu Functions 4 1 1 File Drop down Menu Figure 2 represents the opening screen with the File drop down menu opened This menu contains four options New Data File Open Data File Save Data File and Exit The first three options are also available using the keyboard shortcut in the drop down menu New Data File If an existing file is open the New Data File will clear the data in the spreadsheet portion of the screen Currently it does not clear the title data or the options selected These data require manual entry Open Data File The Open Data File option opens existing data files that are in CSV format comma separated values also referred to as comma delimited data Most of the modern spre
13. adsheet programs allow you to save files in this CSV format Titles and options data may be entered manually using the Input amp Options tab and its associated drop down menus or by opening a CSV spreadsheet containing these data When importing all of the data titles options and numerical data from a spreadsheet file the data must follow the format shown in Table 1 and must be saved as a CSV file E BioSim 2 0 03 File Print Edit Actions Help New Data File Open Data File ctio erall analysis BioSim Analysis Save Data File ct S Title for rows Rows Exit Weight for 0 0 matches e for columns Columns Index of Biotic Similarity VersionB Kod PDE PMD Low denominators om Matches 1 Threshold 0 Data First Row is for Column labels First Column is for Row labels Add Row Add Column Insert Column Delete Row Delete Column Welcome to EloSim 2 0 03 Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 2 Opening Screen with File Drop down Menu Opened The first five rows of an external spreadsheet must contain the input titles and program options data selected by the user The sixth row must contain the titles to be used for the columns and the remaining rows contain the actual data set with the first column being the
14. an error message will appear to assist in trouble shooting problems with the input data Although the program processes small data sets almost instantaneously data sets with 50 or more rows or columns take somewhat longer When you select Process Data an hourglass appears to let you know that the program is running smoothly You can maximize the performance of BioSim2 by minimizing the number of other applications running on your computer at the time you process the data 11 BioSim 2 0 03 EOK File Print Edit Action Process Data Ctrl D Save Report Ctrl R Compress Row Dendrogram Ctrl 1 Expand Row Dendrogram Ctrl 2 Weight for 0 0 matches Compress Column Dendrogram Ctrl 3 0 i Expand Column Dendrogram Ctrl 4 Low denominators 0 0 Matches 1 0 v Threshold 0 Data First Row is for Column labels First Column is for Row labels Tubific DCD Diam CPC720R1 117 1 CPC720R2 16 3 2 CPC720R3 33 CC725R1 986 54 CC725R2 88 24 CC725R3 152 7B PC725R1 73 0 PC725R2 30 0 PC725R3 27 0 KK Add Row Add Column Insert Column Delete Row Delete Column Input amp Options B Matrices Row Dendrogram Row Cophenetic Plot Column Dendrogram Column Cophenetic Plot Reordered Data Figure 3 Opening Screen with Actions Drop down Menu Opened Save Report Selecting the Save Report option from the Actions menu gives the user the ability to identify or crea
15. ental surveys emphasizing the index of biotic similarity and BioSim1 Water Environ Res 64 901 909 Pfalkin J L M T Barbour K D Porter S K Gross and R M Hughes 1989 Rapid Bioassessment Protocols for Use in Streams and Rivers Benthic Macroinvertebrates and Fish EPA 444 4 89 001 U S EPA Washington D C Pinkham C F A and Pearson J G 1976 Applications of a new coefficient of similarity to pollution surveys J Water Pollut Control Fed 48 717 Pinkham C F A J G Pearson W L Clontz and A E Asaki 1975 A Computer Program for Calculations of Measures of Biotic Similarity Between Samples and the Plotting of the Relationship Between These Measures EATR EB TR 75013 Mar Sep 74 41pp Vermont Department of Environmental Conservation 1990 Indirect Discharge Rule Chap 14 Environmental Protection Rules Agency of Natural Resources Waterbury Vermont 23 24 Row Dendrogram 0 0 0 0 0 1 0 1 Appendix A CPCRW 02 Version B unweighted average 0 0 Matches 1 Fos 0 892 0 2 0 3 0 4 0 5 0 6 0 7 0 642 0 578 0 271 0 552 0 467 0 444 0 8 0 8 Samples of Saved Graphic Output Files 0 9 0 9 1 0 Sites CC725R3 CC725R1 CC725R2 PC725R2 PC725R1 PC725R3 CPC720R3 CPC720R2 CPC720R1 25 Row Cophenetic Correlation Plot 26 Cophenetic Correlation Plot for Sites CPCRW 02 Version B unweighted average 0 0 Matches 1 0 892
16. he opening screen see page 8 is used for most commands The data are imported or entered manually The program is run using the Process Data command under the Action menu Results are accessed through the various tabs at the bottom of the window Section 4 Using BioSim2 BioSim2 was written with an entirely new appearance and a simpler approach while retaining most of the features discussed in Pearson and Pinkham 1992 A major change was to drop the agglomerative clustering method for forming dendrograms used in former versions of BioSim Bonham Carter 1967 in favor of the simpler average link method Pankhurst 1991 This method searches through each possible pair of unlinked parameters and an average B value is calculated for the pair see Pearson and Pinkham 1992 for a definition of these terms This average B value is determined in three possible situations 1 Both parameters are not found in any other cluster formed already This normally happens toward the beginning of the process In this case the average is their single B value 2 One of these parameters is already part of another cluster All B values involving the unlinked parameter and every member of this other cluster are averaged 3 Both parameters belong to existing clusters All B values between the two clusters are averaged After searching the complete set of unlinked pairs the pair with the highest average B value is linked at that average value In addi
17. ile option saves all of the values contained in the spreadsheet under the nput amp Options tab as a CSV file The results look like the file in Table 1 when opened in Excel and contain the user input titles options selected and the numerical data in the table Exit Exit option closes BioSim2 All data are lost if they have not been previously saved Table 2 Example of CSV Spreadsheet as an Input File partial data set withouttitles or user options Microsoft Excel CPCTestData csv Insert Format Tools Window Help a question for help 2 x j 3 0 3 Reply with Changes End Review 8 Tubific DCD Diam DCO CrCo DCO Euki CPC720R1 17 1 71 3 CPC720R2 16 3 53 27 CPC720R3 33 2 87 15 CC725R1 96 54 0 30 CC725R2 88 24 12 20 CC725R3 76 8 80 PC725R1 73 90 10 PC725R2 30 80 6 PC725R3 27 14 lt CPCTestData a Ready 4 1 2 Actions Drop down Menu Figure 3 represents the opening screen with all the data fields completed and the Actions drop down menu opened Process Data To run the program select Process Data from the Actions menu or via the keyboard shortcut Ctrl D If the program executes properly the following message will appear in green in the message window Data successfully processed see Figure 3 If the program does not execute properly the message window will be red and
18. nd Pearson showed that the index overcame many of the shortcomings inherent in other indexes used for the same purpose and was more versatile Its use was coded in a DOS program BioSim Pinkham et al 1975 Since its publication it has been widely used for diverse investigations In 1989 Pfalkin et a included it in EPA s rapid bioassessment protocols for use in streams and rivers In 1990 it was identified by EPA as one of six commonly used community similarity indexes in a manual describing guidelines and standardized procedures for using benthic macroinvertebrates to evaluate the biological integrity of surface waters Klemm et al 1990 At least one state Vermont has adopted B as a legal requirement for assessing surface water quality Vermont Department of Environmental Conservation 1990 Barbour et al 1992 in a systematic comparison of the metrics proposed in EPA s rapid bioassessment protocol Pfalkin et al 1989 concluded that B may be the most appropriate metric to serve as a measure of community similarity In almost all published cases of its use however it was not being used to its full potential Recognizing this Pearson and Pinkham 1992 published a strategy for using it in an improved DOS version BioSim1 Gonzales et al 1993 However this strategy also failed to encourage a widespread use of its full capabilities It soon became apparent that the major reason for this shortcoming was the DOS platform of Bi
19. nu Again these options are also available via the keyboard shortcuts Ctrl 1 and Ctrl 3 Figure 3 CPCRW 020utputFile File Edit View Favorites Tools Help ts m Folders a My Documents B 9 My Computer 8 u 31 Floppy A E Local Disk C 2 Biosim El 5 Biosim2 m Ene jpg E colDendrogram jpg Bil columnBMatrix csv amp index html BS originalData csv reorderedData csv BL owBMatrix csv E rowCophenetic jpg JPEG Image JPEG Image Microsoft Office Exc HTML Document Microsoft Office Exc Microsoft Office Exc Microsoft Office Exc JPEG Image 3 29 2005 11 49 AM 3 29 2005 11 49 AM 3 29 2005 11 49 AM 3 29 2005 11 48 AM 3 29 2005 11 49 AM 3 29 2005 11 49 AM 3 29 2005 11 49 AM 3 29 2005 11 49 AM E rowDendrogram jpg JPEG Image 3 29 2005 11 48 AM BI transposedData csv Microsoft Office Exc 3 29 2005 11 49 AM H EEE Figure 4 Files Created and Saved Using the Save Report Option Once you have successfully processed the data you can view the results by selecting the various tabs at the very bottom of the screen These are shown in Figures 5 10 Examples of saved graphics files are shown in Appendix A 13 E BioSim 2 0 03 File Print Edit Actions Help Matrix of Similarity Values Version B Sites CPCRW 02 0 0 Matches 1 0 PC720R1 CPC720R2 CPC720R3 CC725R1 03 4 0243 0194 1 7 105665 0 6424 0275 02136 0 CC725R3 0 3399 0 2381 0 2533 0
20. oSim1 This manual describes the use of BioSim2 a Java program that finally overcomes that shortcoming Section 2 Use of This Manual It is assumed that users of this manual are familiar with the index of similarity B Pinkham and Pearson 1976 and the use of dendrograms in the analysis of complex environmental data sets If not users should refer to previous publications on the topic Bonham Carter 1967 Pinkham and Pearson 1976 Kaesler 1970 Klemm et al 1990 Pearson and Pinkham 1992 and Gonzales et al 1993 Section 3 Installing and Starting BioSim2 Running BioSim2 requires that a Java Runtime Environment JRE of version 1 4 1 or higher be installed Sun Microsystems Inc offers the Java Runtime Environment for Windows Linux and Solaris Apple offers Java for the Mac OS Links to download the appropriate JRE can be found at http www java com BioSim2 will run on most modern computers with Windows 98 SE or higher or Apple OS X or higher Once the JRE is installed biosim2 jar is the only file needed to run BioSim2 The biosim2 jar file is a Java archive which uses the same format as a compressed Zip file To install copy the biosim2 jar file to any convenient location or network directory The most recent version of the program and its associated User s Manual are available at http www2 norwich edu pinkhame Start BioSim2 by double clicking on the biosim2 jar file The file menu at the top of t
21. r content processed chlorine free
22. te a folder in which to save all of the program outputs using a standard Windows dialog box This option is also available via the keyboard shortcut Ctrl R Figure 4 shows the files that are automatically created and saved to a folder when this option is selected The dendrograms and the cophenetic correlation plots for both rows and columns are saved as jpg files All of the data matrices original input data matrices of matrix of similarity values Bs and the reordered and transposed data files are saved as CSV files An html file index html is also created which allows the user to view the output from the program using any of the common Internet browsers Depending on the size of the data matrix and the speed of the computer this may take some time During this time the standard hourglass symbol will appear Once the output files have been saved you will get a green message in the message window that reads Report saved Expand and Compress Row and Column Dendrograms Selecting either the Expand Row or Column Dendrogram option from the Actions menu increases the size of the row or column dendrogram by 50 percent This is useful when the matrix size is greater than 50 rows or columns These options are also available via the keyboard shortcuts Ctrl 2 and Ctrl 4 Figure 3 Once a dendrogram has been expanded it can be compressed to its original size by 12 selecting either the Compress Row or Column Dendrogram option from the Actions me
23. tion to the above the authors decided 1 to reduce the presentation of the program to a single screen that would sequentially display the original data and then the results 2 to make the conditions of the original data matrix flexible enough that most presently used spreadsheet formats would be acceptable 3 to provide a plot of the actual B values used to calculate each average B value found on the dendrogram to visualize how well each joining branch of the dendrogram represents the actual distribution of B values that formed the joining branch 4 to reorient the dendrogram 180 so that the plot resulting from number 3 above could be easily compared with the dendrogram 5 to eliminate the matrix of cophenetic correlation coefficients Kaesler 1970 in favor of the simpler and more valuable cophenetic correlation coefficient for the entire dendrogram 6 to enable BioSim2 to accept and analyze data matrices with missing data points incomplete data matrices and 7 to eliminate many of the choices that needed to be made in BioSim1 by making most options automatic in BioSim2 Figure 1 represents the opening blank screen of BioSim2 The screen consists of four basic parts a standard menu bar along the top a data input results display area a message window near the bottom and a series of tabs at the very bottom that provide access to panels for data input and after running the program with data to display results with a different array of t
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