Software titles:
Axis
Community Analysis Package (CAP)
Density from Distance (DfD)
Ecom
Fish of the Amazon CD
Fuzzy Grouping
Growth II / Simply Growth
Hedgerow Assistant
QED Statistics
Removal Sampling
Simply Probit
Simply Tagging
-> Species Diversity & Richness (SDR)
Other tech support:
Contact Us
System requirements
Mac / Linux OS
Report Other Problems
Tech Support Front Page
Species Diversity & Richness - known issues & update history
Known Issues:
Some installations of SDR 4 did not include the LIFEScore.scr data file, so LIFE Score analyses will fail, with the error message "Cannot open file 'C:\Program Files\Species Diversity and Richness\LIFEScore.scr'. The system cannot find the file specified".
To fix this error, please download the missing file from here (right-click and choose 'Save As'). Unzip the file, and save 'LIFEScore.scr' into the \Species Diversity and Richness folder indicated in the error message. The analysis should now run correctly.
Issues with older versions of the program:
When running a comparison of the alpha diversity indices of two samples, if you press Stop before the program completes all its iterations, the program will from then on run only one randomisation. The solution is to close down and restart the program. This bug was fixed in version 2.6.
In the Renyi, Right-tailed sum and Rank Abundance calculations, selecting different years' data for analysis did not result in the correct data being plotted. This was fixed in version 2.6.
Other known issues and FAQs are described below:
I entered the data in a spreadsheet program, and saved it as a csv file. When I try to open it in SDR, the numbers are separated by ; not , so the analysis will not run.
This is because some non-British systems use ; instead of , to separate values in a csv file. Open Windows Explorer, and change the file extension from csv to txt (i.e. Filename.csv becomes Filename.txt). Open the txt file in Word or another word-processing program. Use the Find/Replace function to replace every ; with a , then save the file again. Change the txt file extension back to csv. It should now open and run perfectly in SDR.
When a data file is opened, all the data are dumped into the first cell, rather than opening in the grid properly
This is usually because there are one or more blank cells in the second row of data. If the blanks are replaced by zeros, or another row with no blanks is put in the second position, the problem should disappear. Row 2 is the crucial one; blank cells are tolerated elsewhere.
'' is not a valid floating point value.
This will occur if the raw data holds blank columns or rows. Remove blank columns and rows by using 0 issues in the working data window. It may also occur if the raw data holds a blank cell. In some cases SDR II will identify the problem cell which should be edited. Normally it is because the data has been prepared in a spreadsheet using blanks to represent zero values.
I/O error 32 - access denied
This will occur if the data file you are trying to open is currently being used by another program - normally the spreadsheet which was used to organise the data. Close the file in other programs and try again.
My files do not appear to be saved
This is often caused by the lack of the correct file extension. The program only shows files with the .csv extension. To see other files in the open file dialog type *.* into the file name box and press return. - WARNING this will show all the files in the directory - whether they are compatible with the program or not. If you have saved a file without an extension either add the extension outside the program or open the file and save with the correct extension using Save As.
How can I analyse biomass data?
With biomass data the Shannon index can be used to compare samples as this measures the information content. However, remember that you cannot compare the index calculated with that found using numbers. Species diversity & Richness also requires integer input so if your biomass data are real values you will need to multiply them by a suitable factor to use the program. e.g. if you have say 1.2 grams per sq. m. change it to 1200 mg per sq m. The Q statistic will probably also be useful.
A final approach worth examining is to see if your biomass data fits a parametric distribution e.g. log series or log normal. If it does then you can use the parameters of the model as an index. For example, if a log series fits reasonably well, the alpha parameter is an excellent diversity index.
Percentage frequency data is a problem. If you are dealing with percentage coverage data for plants then see if it fits a truncated log normal. But, you will need a lot of data for this to be testable.
How can I analyse real numbers (e.g. 4.5)?
Species Diversity and Richness is designed to work with whole numbers (integers). To work on a derived dataset that includes real numbers simply multiply the data set by a suitable factor to make all the values integers.
How can I analyse % cover data?
The Shannon-Weiner Index can be used with % cover data when you want to compare sites which have all been sampled in the same way. Care must be taken not to compare the diversity measures calculated with those generated from full quantitative data.
A site with cover values 4,1,1,1,1 will have a higher Shannon diversity than a site with 5,1,1,1,1 because the former is more equitable. A site with 5,5,5,5,5 will have a higher diversity still. This is all quite reasonable and works as one would expect. You should note that the Shannon-Weiner value calculated for percentage cover data will tend to just reflect the species number. This is because the values can only range from 1-5 rather than from 0-infinity thus the resolution of differences in equitability between sites is much reduced.
The question is, do you really need to use the Shannon index? Perhaps you might be better using species richness. From your vegetation surveys you could use one of the recently developed total species richness estimators such as the Chao equation to estimate the total species set for each sample and its variance. You could then consider if the sites are significantly different.
Alternatively a vegetation classification procedure such as TWINSPAN might be the best approach. This is designed to use % cover data.
We sell programs which can help you with all the above tasks - contact us.
My data set has a large number of columns (sites/samples), but Excel will only allow me to have up to 255
A common problem with large data sets. Use our ListCombiner utility to combine large data sets effortlessly!
Some installations of SDR 4 did not include the LIFEScore.scr data file, so LIFE Score analyses will fail, with the error message "Cannot open file 'C:\Program Files\Species Diversity and Richness\LIFEScore.scr'. The system cannot find the file specified".
To fix this error, please download the missing file from here (right-click and choose 'Save As'). Unzip the file, and save 'LIFEScore.scr' into the \Species Diversity and Richness folder indicated in the error message. The analysis should now run correctly.
Issues with older versions of the program:
When running a comparison of the alpha diversity indices of two samples, if you press Stop before the program completes all its iterations, the program will from then on run only one randomisation. The solution is to close down and restart the program. This bug was fixed in version 2.6.
In the Renyi, Right-tailed sum and Rank Abundance calculations, selecting different years' data for analysis did not result in the correct data being plotted. This was fixed in version 2.6.
Other known issues and FAQs are described below:
- I entered the data in a spreadsheet program, and saved it as a csv file. When I try to open it in SDR, the numbers are separated by ; not , so the analysis will not run.
- When a data file is opened, all the data are dumped into the first cell, rather than opening in the grid properly
- '' is not a valid floating point value
- I/O error 32 - access denied
- My files do not appear to be saved
- How can I analyse biomass data?
- How can I analyse real numbers (e.g. 4.5)?
- How can I analyse % cover data?
- My data set has a large number of columns (sites/samples), but Excel will only allow me to have up to 255
- None of the above
I entered the data in a spreadsheet program, and saved it as a csv file. When I try to open it in SDR, the numbers are separated by ; not , so the analysis will not run.
This is because some non-British systems use ; instead of , to separate values in a csv file. Open Windows Explorer, and change the file extension from csv to txt (i.e. Filename.csv becomes Filename.txt). Open the txt file in Word or another word-processing program. Use the Find/Replace function to replace every ; with a , then save the file again. Change the txt file extension back to csv. It should now open and run perfectly in SDR.
When a data file is opened, all the data are dumped into the first cell, rather than opening in the grid properly
This is usually because there are one or more blank cells in the second row of data. If the blanks are replaced by zeros, or another row with no blanks is put in the second position, the problem should disappear. Row 2 is the crucial one; blank cells are tolerated elsewhere.
'' is not a valid floating point value.
This will occur if the raw data holds blank columns or rows. Remove blank columns and rows by using 0 issues in the working data window. It may also occur if the raw data holds a blank cell. In some cases SDR II will identify the problem cell which should be edited. Normally it is because the data has been prepared in a spreadsheet using blanks to represent zero values.
I/O error 32 - access denied
This will occur if the data file you are trying to open is currently being used by another program - normally the spreadsheet which was used to organise the data. Close the file in other programs and try again.
My files do not appear to be saved
This is often caused by the lack of the correct file extension. The program only shows files with the .csv extension. To see other files in the open file dialog type *.* into the file name box and press return. - WARNING this will show all the files in the directory - whether they are compatible with the program or not. If you have saved a file without an extension either add the extension outside the program or open the file and save with the correct extension using Save As.
How can I analyse biomass data?
With biomass data the Shannon index can be used to compare samples as this measures the information content. However, remember that you cannot compare the index calculated with that found using numbers. Species diversity & Richness also requires integer input so if your biomass data are real values you will need to multiply them by a suitable factor to use the program. e.g. if you have say 1.2 grams per sq. m. change it to 1200 mg per sq m. The Q statistic will probably also be useful.
A final approach worth examining is to see if your biomass data fits a parametric distribution e.g. log series or log normal. If it does then you can use the parameters of the model as an index. For example, if a log series fits reasonably well, the alpha parameter is an excellent diversity index.
Percentage frequency data is a problem. If you are dealing with percentage coverage data for plants then see if it fits a truncated log normal. But, you will need a lot of data for this to be testable.
How can I analyse real numbers (e.g. 4.5)?
Species Diversity and Richness is designed to work with whole numbers (integers). To work on a derived dataset that includes real numbers simply multiply the data set by a suitable factor to make all the values integers.
How can I analyse % cover data?
The Shannon-Weiner Index can be used with % cover data when you want to compare sites which have all been sampled in the same way. Care must be taken not to compare the diversity measures calculated with those generated from full quantitative data.
A site with cover values 4,1,1,1,1 will have a higher Shannon diversity than a site with 5,1,1,1,1 because the former is more equitable. A site with 5,5,5,5,5 will have a higher diversity still. This is all quite reasonable and works as one would expect. You should note that the Shannon-Weiner value calculated for percentage cover data will tend to just reflect the species number. This is because the values can only range from 1-5 rather than from 0-infinity thus the resolution of differences in equitability between sites is much reduced.
The question is, do you really need to use the Shannon index? Perhaps you might be better using species richness. From your vegetation surveys you could use one of the recently developed total species richness estimators such as the Chao equation to estimate the total species set for each sample and its variance. You could then consider if the sites are significantly different.
Alternatively a vegetation classification procedure such as TWINSPAN might be the best approach. This is designed to use % cover data.
We sell programs which can help you with all the above tasks - contact us.
My data set has a large number of columns (sites/samples), but Excel will only allow me to have up to 255
A common problem with large data sets. Use our ListCombiner utility to combine large data sets effortlessly!
Here is the update history for SDR. To upgrade to the latest version:
Version 1.x / 2.x / 3.x to latest version - £34, plus postage/VAT (Buy online NOW, or see How To Buy)
Users who have already purchased Version 4.x can upgrade to the latest version FREE. Please contact Pisces.
Version 4.1.2 released 28/11/07
Version 1.x / 2.x / 3.x to latest version - £34, plus postage/VAT (Buy online NOW, or see How To Buy)
Users who have already purchased Version 4.x can upgrade to the latest version FREE. Please contact Pisces.
Version 4.1.2 released 28/11/07
- Alteration to saving of .ini files and list of previously-used data files, to ensure compatibility with Windows Vista
- Improvement to import of data from Excel files
- Minor bug fix
- Fixed issue where, if a data set has only two columns, the program did not allow the user to compare diversity indices.
- An improved user interface and graphics
- No maximum size for the data set - all arrays are dynamically sized
- Increased range of evenness measures, (Smith & Wilson - B, 1/D, -ln(d), and 1-D, Camargo, NHC, Simpson E, Heip, etc)
- Addition of Menhinick, Gini and Strong's alpha diversity indices
- Addition of Harrison's beta diversity measures
- Jackknife estimation of standard error implemented
- Improved rarefaction methods and sample interpolation
- Improved help system with tutorials
- Improved BMWP scores for water quality assessment
- New species richness estimator for open systems studied long-term - Henderson
- A sample comparison feature quickly finds the species in common
- Maximum size of any observation increased to 2147483647.
- Greatly increased number of individuals allowed in each cell of data set.
- Minor bug fix to disappearing buttons on 'Edit Data set' window.
- Corrected minor error in saving of new data sets
- Corrected minor error in calculation of % zero/non-zero cells on Summary Data page
- An improved user interface and graphics
- Increased range of evenness (equitability) measures
- 2nd order jackknife species richness measure
- K-Dominance plots
- SHE analysis for beta diversity
- LIFE scores as used in water quality monitoring
- Fixed error in data selection for Renyi, Right-tailed Sum and Rank Ab. calculations
- Bug fixed in Deselect/Select All option of Edit Data.
- Selected data randomisation improved
- Chart tab issue corrected in Distribution analyses
- Chi-squared calculations grouped for expected values < 3.
- Q statistic small data set zero error corrected.
- Printing bug on grids fixed (introduced in version 2.6).
- Improvements made to output of randomisation test.
- Data selection bug fixed in Reyni, Right-tailed sum and Rank Abundance calculations.
- Fixed problem with number of randomisations performed in comparison of alpha diversity indices of two samples.
- 'File not found' error with BMWP score corrected.
- Data checking improved.
- Deals with leading and trailing spaces.
- Warns if non integer values are entered.
- Improved grid printing.
- Rarefaction added.
- Implemented full chart editing.
- Correction to plot of Irish Q, both lines now showing.
- Data checking improved.
- Updated chart titles.
- Last used files now appear on the file menu.
- now includes Irish Q Rating
- New file structure.
- Many new methods including - Fishers Alpha, Brillouin and Q Statistic
- Right-tailed sum
- Fitting and simulating Geometric, log series, truncated log normal and broken stick distributions
- Beta Diversity including Whittaker Bw, Cody Bc, Routledge Br, Bi and Bt and Wilson and Shmida Bt Special index
- ASPT
- Closes all windows on opening new dataset
- Handles 3500 species by 250 samples
- Improved graphics
- Number of runs now defaults to 1.
- Hourglass cursor now shows while calculating.
- Help links from Heterogeneity, Species Accumulation and BMWP Score Fixed.
- Beta reference corrected to Tothmeresz in Instruc.doc.
- Minor corrections to instruction booklet.
- Correction to new dataset creation. No longer stores old data by accident.
All content © Pisces Conservation Ltd, 1995 -
