Create a new site (& summary data)
Add species, samples & abundances
- add samples
- create a species list
- add abundance
Import an Excel countsheet file
Add references to a site
Assign dates to samples at a site
Create a presence only species list

Enter species data

Create a new site (and add summary information)

1. Open the Site Manager from the main toolbar.
2. Click the [Create New Site] Button.
3. Enter a name for the site in the popup box, and click [OK].
4. The Site Information screen will open - shown below - so that you can enter summary data.
   Note that you will need an Administrator password to change this data later, or delete the site. This is so that students may create their own sites, but not alter any existing data.

• Interpretation - summarise the site, and add any other data that will enable others to understand the relevance of the countsheet data. Include anything that doesn't fit anywhere else in this box.
• Identified by - name of the person(s) that identified the species.
• Specimens stored at - location of the identified material (i.e. the contents of the samples)
• Location - geographical reference - this will be used through GIS later.
  • Latitude & Longitude - either enter as decimal degrees (+/-180°E/W, +/-90°N/S)* or click the [Enter Location in D°M'S"] to enter it in Degrees, Minutes and Seconds form.
    The [DD]/[DMS] button allows you to toggle the lat/long view.
  • Altitude - in metres above sea level.
  • National Grid Reference if available.
• Other Proxies - check boxes to indicate any other palaeo evidence available for the site.

5. To add a reference to the site click the [Add Reference] button and follow the instructions below.
6. Click [SAVE SITE] when finished.
   Remember - you will not be able to edit this data later without an Administrator password. Contact the developers for more information.

Add samples, species and abundances to a site

All abundance data is stored in 'countsheets'. It is up to the user to decide how to use these, but we recomend that each countsheet represents a cohesive sampling/analysis activity for a site. For example:
- a particular year's pitfall trapping
- the data from a year's excavation at an archaeological site
- a particular author's reworking of previously identified material

The 'Sample' is the nodal unit - all abundances and dates are tied to samples, and cannot exist without one. Similarly a zero abundance species cannot be stored - it must have an abundance in a sample. BugsCEP can create a dummy sample where the abundance of each species is 1 on request.

See the diagram above for a graphical explanation of site-sample-data hierarchy.

1. Select the site in the Site Manager (available from the main toolbar).
2. Click the [Manage Countsheets & Create Reports] button.
   If the site contains no countsheets (e.g. a newly created site) then you will be presented with the popup to the right, giving you the option to either create a new countsheet or import data.
   Click here to see how to import data or continue reading to add data in BugsCEP.

3. Click [Create empty countsheet], and a new blank countsheet will be created for the site.
4. Give the countsheet a name - THIS IS IMPORTANT as it allows you to easily identify the countsheet in other parts of the program - and then select the appropriate descriptive information from the drop down boxes for 'Context' and 'Data Type', as shown below.

5. Click [Save], and you now have an empty countsheet ready to receive sample, species and abundance data.

6. Click the [Show/Edit abundance data] button to open the Countsheet Explorer - a spreadsheet like interface for the entry of abundance data.
   You can delete the 'Please add species and samples' entry using the instructions below...
   
   
7. To create/modify a species list:
   1. Click the [Manage Species List] button to open the Species List Editor
   2. To add a species (taxon):
      1. use the 'Genus' dropdown box to find the Genus
      2. select the species from the (now updated) 'Species in Genus' list
      3. either double click on it in the list, or click the [Add to Species List] button
   3. To replace a species (taxon):
      1. select the species to be replaced in the 'Current Species List' to the right of the form
      2. Use the 'Genus' box and 'Species in Genus' list to find the species to replace it with and select it (single click)
      3. click the [Replace Selected] button
   4. To delete a species (taxon):
      1. select the species to be deleted in the 'Current Species List' to the right of the form
      2. Click the [Delete Selected] button
   5. When you are finished click the [Apply Changes] button so save the species list. Remember to add at least one sample with abundance values for every species - otherwise they will not be saved between editing sessions.
      
      

   Notes for species list editing:

   • The Synonyms Browser is available through a button at the bottom left - it allows you to look up synonyms, but not move to them in the Species List Editor (sorry - we'll fix this later).
   • When creating long lists APPLY CHANGES OFTEN! At least every 30 species or so.
   • You can limit the species available for addition to only those with climate data by selecting the [ ] Show only MCR Species checkbox.

8. To add/modify samples:
   1. From the Countsheet Explorer click the [Manage Samples] button
   2. To add a sample click the [Add New Sample] button, and give the sample a name/reference, and fill in coordinates and depth data if relevant.
      Important!
      Sample Names must begin with a letter to ensure all outputs from BugsCEP work.
      We recommend adding samples in the order you would like them output on any diagrams - BugsCEP does not yet sort by depth or sample name in all areas.
   3. Remeber to always click [Save Sample] after entering or editing samples.
   4. Click [Apply changes and return to Countsheet] when all samples are entered
      (You can add more samples, or edit existing ones at a later date)

       

9. You are now ready to enter abundance data in the cells of the spreadsheet shown in the Countsheet Explorer.
10. Click the [Save Changes & Update Database] button when finished - but read the notes below first!
    Clicking [Cancel/Close] will abandon all the changes made since you entered this session of the Countsheet Explorer.
    

Notes for abundances:

• Zero abundance species cannot be saved - make sure that every species has a value for at least one sample, even if it is just '1' to indicate presence. In fact, BugsCEP will not let you save the countsheet until this is done - but it will let you know which species are the problem.
• Samples may be saved without any abundance values.
• Click the [Create 'Presence' dummey sample] button to create a pseudosample indicating the presence of each species at a site.

Import abundance data into a site

BugsCEP can import data from MS Excel files as long as:
i) The first column (A) contains species names in the format 'Genus species authority'
(authority can be omitted).
ii) The remaining columns contain abundance data with sample names in the first row (1).

An example is given to the right - a countsheet created by the previous version of Bugs.

See the notes below for more format tips.

1. Select the site in the Site Manager (available from the main toolbar)
2. Click the [Manage Countsheets & Create Reports] button.
   If the site contains no countsheets (e.g. a newly created site) then you will be presented with the popup to the right, giving you the option to either create a new countsheet or import data.
   Click the [Import data from Excel file] button.

3. The BugsCEP Import Wizard will open.
   Import is relatively simple, and follows an ordered process indicated by the numbers on the interface (see screenshots below). The buttons cannot be clicked in the wrong order.

4. Follow the numbers, and click the buttons:
   1. [Select countsheet for import] - will open the 'Open file' dialog box' with which you can locate your file.
      • If the file is not in the standard BugsCEP format (i.e. one exported by BugsCEP) then you will be informed, and asked whether you would like to try to convert it - click [YES] to do so, and click here to follow see instructions for conversion.
      • If the file is in BugsCEP format then it will be imported directly and the species list will be displayed underneath the [Select countsheet...] button.
        Button 2 will now become active.
   2. [Extract Sample Names] - retrieves the sample names from the first row of the spreadsheet.
   3. [Enter Sample Attributes] - opens a popup box to allow you to add sample coordinates and depth.

4. [Import abundance values] - extracts the abundance data from the spreadsheet, an dinforms you how many values were imported on completion.
5. [Review imported Abundances] - an optional stage to allow you to check that the data came over correctly
6. Use the drop down boxes to select the appropriate countsheet metadata

&

7. [Attach to Site] - the final stage links the imported data to the selected site.
   On completion the imported countsheet will be shown in the Countsheet Manager.

Important notes for importing files

• Make sure the abundace area of your spreadsheet is formatted as numbers, and really includes numbers. Excel sometimes retains other formats even if you apply the number format. To be really sure, either copy and paste special (values) the data into a new workbook, or use a tool such as PopTools to enforce the formatting.
• BugsCEP will not accept anything other than numbers in the abundance cells
  - for example: >10; some; x; etc. are not valid data for BugsCEP.
  If you must use such notation, then convert it something numerical and includes explanatory notes in the site summary information. Be really careful when using statistics with these values!
• Blank lines before the end of the import file will lead to everything below it being missed.
• Blank columns are not usually a problem (and Excel files often include 'ghost' columns after the data) - but try to avoid them.
• Prefixes before the Genus name can cause problems (e.g. space, '-')
• There is a theoretical limit to the number of samples per countsheet - it seems to be system and context dependent (!) - we recommend having no more than 70 samples in one countsheet. If you have more, then split it and import into two countsheets.

Add references to a site

Any number of references can be attached to a site to help users locate source data and interpretations.

(Skip numbers 1-4 if you are already in edit mode on the Site Information screen)

1. Select the site in the Site Manager (from the main toolbar).
2. Click the [Show Site Info.] button.
3. Click [Edit Site] and enter the Administrator password to enter edit mode.
4. Click the [Add Reference] button on the Site References panel (bottom right)
5. A popup window will open which allows you to either:
   1. Select an existing reference from the Bugs Bibliography, or
      (use the search or list boxes to find the reference and click the [Use this...] button)
   2. Add a New Reference to the Bugs Bibliography
      ...as explained here...
6. Click [Add a New Reference to BugsCEP] and the 'Add Ref...' window will pop up.
   This requests the abbreviated form of the reference - as you would use within the text of a publication. Enter the abbreviated reference and click [OK].
   You may notice that references concerning fossil beetles have the date in brackets, and modern ecology references don't - feel free to prolong the tradition, but it's not essential.

Bibliography notes

can be edited from Edit Bibliography on the Tools dropdown on the toolbar , in edit more... maybe need to change this later!

Assign dates to samples at a site

1. Either create a new site or select an existing one in the Site Manager.
2. If the site has no samples, then add some using the Countsheet Explorer (accessible thorugh the Counthsheet Manager).
3. Click the [Dates Explorer] button to open the form with the same name.
4. The samples for the first countsheet at the site will be shown to the left, arranged by depth (or order of entry if no depths were given). To change countsheet within a site use the 'Select Countsheet' dropdown box.

5. Select the sample to be assigned a date.
6. Click the appropriate tab for the type of data - Calendar/Radiometric/Period - and click the [Add New Date to Sample] button.
7. You can then fill in the details - the fields are pretty self explanatory, and BugsCEP will let you know if you try to enter inappropriate data.
8. Always click [Save Date] when you finish entering one.
9. Dates can be deleted by first clicking [Edit Date], and then the [Delete Date] button that appears.

Create a species list for a site with no samples or only presence values

BugCEP needs species lists to be assigned abundances in samples for them to be stored. The workaround is, then, to create a single sample with abundance '1' for every species.

As this could be a common problem, we've included the facility to generate single 'presence' samples.

1. Create a new site or select one in the Site Manager.
2. Click on the [Manage Countsheets & Create Reports] button.
   If no counthsheets are present then you will be prompted to either import or create one (as shown here). Choose to create one.
   If there are countsheets present, click the [Add Countsheet] button to create a new one.
3. Give the countsheet a name and fill in the appropriate context and type information.
   WARNING! BugsCEP may select the first countsheet for the site after you click [Add Counthsheet] - make sure you select the new blank one before entering the name.
4. Click [Show/Edit abundance data], then [Manage Species List] and add your species as instructed above. Click [Apply Changes] when done.
5. Back in the Countsheet Explorer click the [Create 'Presence' dummy sample] button, click [OK] to confirm the action, and then observe the changes.

6. Note that you can also use this button to update the 'BugsPresence' sample if you add mroe species at a later date.
7. Click [Save Changes & Update Database] to add the new countsheet to the database.

* Notes