BioDen Documentation Release 0.4.0 GiMaRIS
Contents
1. Release 0 4 0 Date May 19 2015 3 2 1 Starting BioDen On Windows go to Start menu gt All Programs gt GiMaRIS gt BioDen gt BioDen GNU Linux users can just execute bioden Once bioden is started you ll be presented with its main window The main window has the following components Select input data file The CSV or XLS file containing the biomass and or density data to be processed This file must be in a specific format This format is described in the nput File Format section Select output folder Select the folder to which all output files should be saved The output files are described in the Output Files section Property for calculations The property to perform the calculations on You have a choice between biomass and density Note that the input data file must contain data for the specified property If this is not the case an error message will be displayed Format for output files The format to save the output files in You have a choice between Comma Separated Values csv and Microsoft Excel 97 2000 XP xls Note Microsoft Excel files xls support a maximum of 256 columns Columns that exceed this limit will not be exported Advanced Options Clicking this toggle button shows hides the advanced options Target sample surface The sample surface used for AMBI files Default is 0 2 66 7 Round values to n decimals Number of decimals to round values in the output files2. Get the source code BioDen Documentation Release 0 4 0 6 Chapter 2 Developers CHAPTER 3 Contents 3 1 Installation Release 0 4 0 Date May 19 2015 3 1 1 Requirements BioDen has the following dependencies e GTK gt 3 6 Python gt 2 7 PyGObject gt 3 10 xird xlwt On Debian based systems the dependencies can be installed from the software repository sudo apt get install python gobject python xlrd python xlwt More recent versions of some Python packages can be obtained via the Python Package Index pip install r requirements txt Windows users can install the PyGObject Windows installer with Gtk3 support Then use pip as described above to install the remaining dependencies Note This step is not needed if you have the Windows installer for BioDen which comes bundeled with all the requirements 3 1 2 Installation From the GitHub repository git clone https github com figure002 bioden git pip install bioden BioDen Documentation Release 0 4 0 Or if you have a source archive file pip install bioden x x tar gz Windows installers can be obtained from SourceForge Note The Windows installer for BioDen comes bundled with third party dependencies The third party tools bundled with BioDen are property of their individual authors and are governed by their individual applicable license 3 2 User Manual
3. appear In the Text Import window set e Language to English USA e Separator options to Separated by to Comma Press OK The data from the output file should now be displayed in the correct columns 3 2 User Manual 11 BioDen Documentation Release 0 4 0 3 2 5 Copying Permission Statement BioDen is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version BioDen is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with the program If not see http www gnu org licenses 3 2 6 Troubleshooting This application has failed to start because the application configuration is incorrect Reinstalling the application my fix this p This error is most likely caused by a missing DLL The installer for BioDen has the option to install the required DLL To fix this problem run the installer for BioDen and make sure that the Microsoft Visual C option is checked This will install the required DLL for BioDen 12 Chapter 3 Contents CHAPTER 4 Indices and tables e genindex
4. BioDen Documentation Release 0 4 0 GiMaRIS May 19 2015 Contents Users 3 Developers 5 Contents 7 JA Installation a sste 10 a u e e A a la a 7 3 2 User Manual hada dd da dd a de eid ced E 8 Indices and tables 13 BioDen Documentation Release 0 4 0 BioDen is a data normaliser and processor for files containing taxon biomass density data for ecotopes In general the input file of BioDen includes a list of records rows in a table that give species name an abundance measure biomass and or density a sample code the surface sampled and the ecotope see input example This list is transformed to a table in which the rows represent species and the columns represent samples see ouput examples This table can serve as the input file for various software applications that conduct species community analyses a BioDen u Mt Help Input data file test data xls DO Output folder E tmp Property for calculations biomass dl Format for output files Comma Separated Values csv 4 Advanced options Target sample surface 0 2 Number of decimals to round to 3 P CSV input file options Process Data Fig 1 BioDen screenshot Contents 1 BioDen Documentation Release 0 4 0 2 Contents CHAPTER 1 Users SourceForge Project page Download BioDen BioDen Documentation Release 0 4 0 4 Chapter 1 Users CHAPTER 2 Developers e
5. e modindex e search 13
6. matically corrects numbers that have been stored in non English format This means that commas are replaced by dots e g 12 5 will be converted to 12 5 Also see the example of an input data file with a header containing the required column names 3 2 3 Output Files BioDen produces several output files in the specified output folder in the spcified format Output files are saved in either CSV Comma Separated Values format or in XLS Microsoft Excel 97 2000 XP format and can be opened with any spreadsheet application e g Microsoft Excel OpenOffice Calc The output files are described below Raw ecotope files raw_ lt property gt _ lt ecotope gt csv The original data is split by ecotope So one data file per ecotope is exported The non grouped values are exported but the data has been re ordered Each column is a sample and each row contains the abundance measures for a species see example output Grouped files grouped_ lt property gt _ lt ecotope gt csv One data file per ecotope is exported Each file con tains the calculated sample groups for that ecotope Sample groups were created by summing samples for that ecotope until the sum of the sample surfaces reached the target sample surface default is 0 2 or higher The groups have not been corrected to the exact target sample surface Each column is a sample group and each row contains the abundance measures for a species see example output AMBI group files ambi_ l
7. n it in your spreadsheet application To open a CSV file however your spreadsheet application needs to know some basic information about the CSV file before it can view it properly For example it needs to know the character used as a field delimiter which is a comma So you need to tell your spreadsheet application to use the comma character as the field delimiter along some other properties Below is explained how to do this with the two most popular spreadsheet applications Microsoft Excel 2007 Start Microsoft Excel Make sure you have open the Excel 2007 worksheet that you would like to import the ouput data file into Go to the Data tab Click on the From Text button This will open the file select browser window Navigate to where the output files are stored Then select one of the output CSV files After selecting an output file the Text Import Wizard window is displayed In that window set e Original Data Type to Delimited e File origin to United States Click the Next button In the next window that appears you need to change the Delimiter from Tab to Comma Uncheck Tab and check Comma under Delimiters 6 Press Finish The data from the output file should now be displayed in the correct columns OpenOffice Calc 1 Right click on an output CSV file and select Open With gt OpenOffice Calc The Text Import window should now
8. rrent process 3 2 2 Input File Format The input data file must be a CSV or XLS file in a specific format For CSV input the default settings for BioDen have been set for the format in which Excel creates CSV files This means that by default BioDen expects a semicolon as a field separator The quote character defaults to a double quote The CSV Input File Options in BioDen allow you to change these defaults should your input CSV file use a different field delimiter or quote character BioDen also expects a format for the data stored in the CSV or XLS file BioDen expects the following data format 1 The first row in the CSV XLS file must be the header The header contains the column names BioDen expects at least the following columns compiled ecotope sample code standardised taxon density and or biomass and sample surface 2 BioDen isn t very strict with the column names The column names aren t case sensitive So a column with name BioMass works just as good Also BioDen uses any column that contains any of the expected column names So a column with name Sum Of Density would be used as the density column because it contains the name density 3 BioDen ignores the columns that don t match the expected column names So it s alright if the input file contains other columns 4 The header row must be followed by the actual data rows 5 BioDen auto
9. t property gt _ lt ecotope gt csv One data file per ecotope is exported Each file con tains the calculated sample groups for that ecotope Sample groups were created by summing samples for that ecotope until the sum of the sample surfaces reached the target sample surface default is 0 2 or higher The 10 Chapter 3 Contents BioDen Documentation Release 0 4 0 groups have been corrected to the exact target sample surface This means that each sample group has a surface of exactly the target sample surface Each column is a sample group and each row contains the abundance measures for a species see example output Representatives data file representatives_ lt property gt csv One data file is exported The file contains one normalized sample group for each ecotope The sample group that best represents the ecotope is exported The biodiversity for all sample groups are calculated and the group that comes closest to the median of the biodiversities is considered the representative sample group for an ecotope Each column contains the values from the most representative sample group for an ecotope and each row contains the abundance measures for a species see example output 3 2 4 Viewing Output Files The output files created by BioDen are stored in either CSV format or XLS format You can view these output files in any spreadsheet application e g Microsoft Excel OpenOffice Calc Double clicking an XLS file should ope
10. to Value do not round default means CSV Input File Options Clicking this toggle button shows hides the options for the CSV input file Field delimiter of the input file A one character string used to separate fields in the input CSV file It defaults to a semicolon By default Excel uses the semicolon for CSV files If the CSV file is exported by a different application make sure this character matches the delimiter in the data file You can check this by opening the data file in a text editor e g Notepad Quote character of the input file A one character string used to separate fields in the input CSV file It defaults to a double quote 8 Chapter 3 Contents BioDen Documentation Release 0 4 0 BioDen ORE Help Input data file test data xls DO Output folder tmp dl Property for calculations biomass dl Format for output files Comma Separated Values csv 4 Advanced options Target sample surface 0 2 Number of decimals to round to 3 MEE b CSV input file options Process Data Fig 3 1 BioDen main window 3 2 User Manual 9 BioDen Documentation Release 0 4 0 Process Data Clicking this button starts the data processing While it s processing the data a progress dialog is displayed Be patient the calculations could take some time to finish based on the amount of data in the data file Clicking the Details buttons shows more detailed information about the cu
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