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BugStats:

Why BugsEcoCodes?
Generate environmental reconstructions for a site
   & produce BugsEcoGraphs
See a sample by sample species breakdown of
   BugsEcoCodes for a site
Compare samples with correlation coefficients
BugStats output files explained
Tips for improving graphs externally
The BugStats methods explained
- BugsEcoGraphs
- Correlation coefficients

 

BugStats produces multi-sample environmental summary diagrams from coded habitat data. When used with stratigraphic sequences or repeated pitfall trapping, these diagrams can be used to identify environmental changes through time as reflected in the taxa present in the samples. When used with archaeological samples they can be used to illustrate spatial variation in human impact.

The method is simple, transparent and uses broad (eco)habitat classifications. Ca. 4995 taxa have been assigned to 22 habitats (BugsEcoCodes, ca. 8317 designations) through a combination of examination of various published habitat descriptions and the detailed ecology codes assigned by Koch (1989-92). 125 Koch codes are included in BugsCEP for ca. 2920 species (ca. 11192 designations), but are yet to be included in graphical outputs.

The categories are based on those most commonly used in Quaternary research, with a little adjustment to cater for archaeological investigations. In particular, the work of the Bugs authors, and Mark Robinson (e.g. 2000), Philippe Ponel (e.g. 1995) and Harry Kenward (e.g. 2001) have influenced the category definitions. The species designations are those of the Bugs authors, with a considerable influence from Klaus Koch's work. Due to the nature of these influences the codes are most likely to be more ecologically useful in Central to Northern Europe.

Taxa may be assigned to more than one habitat, but may exist in only one 'indicator' class at a time.

Despite a probable northern bias the use of a constant system enables reproducibility in any fauna, and thus the system could even be useful where the habitat coding is less accurate.

More information is available in Buckland (2007). The BugsEcoCode system produces quantitative reconstructions from qualitative habitat descriptions/designations. It is thus a reproducible semi-quantitative system which allows advanced inter-site comparisons. Raw and calculated data is always output in the export files, and a sample by sample breakdown of species and their codes and abundances can be obtained.

BugStats is to some extent a work in progress, and we would very much appreciate feedback on the usefulness and problems with the BugsEcoCode calculation system and outputs.


Why BugsEcoCodes & BugStats
  1. There is need for a standardized (i.e. regionally comparable) & transparent system for summarizing palaeoentomological interpretations & reconstructions (from 100's of taxa, or very few).
  2. Ordination method results (PCA, CA etc.) not comparable in terms of inter-site reconstruction - habitat definitions derived in this way are only applicable within the context of the original study.
  3. There is currently no existing routinely used software for numerically reconstructing habitats from fossil insects - there is a need for (at least semi-)quantitative environmental reconstruction software.
  4. No existing system works as well on modern data as fossil - allowing long term (palaeo)biodiversity studies.
  5. Palaeo-data often violates/confuses assumptions needed for many advanced statistical methods (differential taphonomy, uncertain representation, many 0's). BugStats does not.
  6. No current habitat summary system has its species designations fully and publicly available.

 

Generate environmental reconstructions for a site & produce BugsEcoGraphs
BugStats can produce sample habitat summary diagrams for any site which includes taxa that have been assigned BugsEcoCodes. The graphs allow direct comparison of the environments represented by samples between samples and sites. A number of standardization and calculation options are available.

BugStats uses the concept of environmental representation (env. rep.) as follows:
1 environmental representation = 1 environment represented by 1 individual or taxon. A taxon can represent more than one environment.
The raw results are counts of environmental representation in each habitat class for each sample.
These can (optionally) be standardized by dividing by the sample sum to allow samples to be compared on a common (percent) scale.


  1. To open the BugStats interface click the [BugStats] button on the main toolbar.
  2. Make sure MS Excel is closed and not running in the background.
  3. If you have created a site, and entered abundance data for it then it will be available from the 'Site' drop down box towards the top of the screen. (Use the [Refresh sites list] button if it is not there).
    Sites without abundance data are not shown.
    BugsCEP already contains abundance data for over 550 published sites - try some!
  4. If the site has more than one countsheet, then select the required one from the 'Select Countsheet' drop down box.
  5. Select the desired options, as described below (and in more detail further below)...

Calculations

  • To species id's only - only use taxa identified to species level (i.e. omit sp. spp. and indet. from calculations). Creates a more precise reconstruction, but may miss information in poorly resolved faunas.
  • Transform abundance log(n+1) - applies a natural logarithm transformation to the raw reconstruction counts (plus 1) before standardization. Some authors believe this compensates for inter-sample variation in a number of ways, including log/normal abundance distributions.
    Note that this will not be indicated on the output file, so please name your file accordingly.
 
  • Standardization
    • No abundance, % sumrep - Taxa occurrence only (presence/absence).
      Env. rep. sum for habitat class expressed as percent of sum of env. rep. for sample (sumrep).
    • No abundance, raw - Taxa occurrence only (presence/absence).
      Env. Rep. counts for habitat class only.
    • Abund. weighted, % sumrep - Taxa env. Rep. multiplied by its abundance in sample.
      Env. Rep. sum for habitat class expressed as percent of sum of env. Rep. for sample (sumrep).
    • Abundance weighted, raw - Taxa env. Rep. multiplied by its abundance in sample.
      Env. Rep. counts for habitat class only

 

Charts

  • Use Ref as sample names- Use sample Reference/Context field to label samples rather than database sample code (recommended).
  • Descriptive titles - use real words for habitat titles, rather than BugsEcoCodes.
  • Autoscale x-axis - BugStats will scale diagrams to fit all data. Uncheck this to specify a maximum and interval yourself.
  • Include sum graphs - Output graphs showing (shown to the right):
    Sumrep - sample environmental representation sums.
    Abundance - sample abundance sums.
    NSpec - number of taxa per sample.
  • Graph title - Use this box to give the graph a meaningful title (BugStats will append the chosen standardization option to this name on output).
  1. Click the [Create Bugs Ecofig] button, choose a save location and provide a filename, click [Save] then stand back and watch it calculate.
    Do not touch the computer until the 'Completed' message appears - BugStats needs full control of your system, and could crash if you interrupt it.
  2. When finished, the name and path of the export file will be given in the 'Ecofig file created' box towards the bottom of the screen. Click the [Open Results in Excel] button to the right of this to see the results.
    See below for an explanation of the results and some tips for preparing the graphs for presentations/publications.

 

See a sample by sample species breakdown of BugsEcoCodes for a site

The BugStats species breakdown report allows you to see exactly which represent which environments, and how abundant they are, in each sample. This is a useful too when trying to understand the environmental reconstruction diagrams.

  1. To open the BugStats interface click the [BugStats] button on the main toolbar.
  2. Make sure MS Excel is closed and not running in the background.
  3. If you have created a site, and entered abundance data for it then it will be available from the 'Site' drop down box towards the top of the screen. (Use the [Refresh sites list] button if it is not there).
    Sites without abundance data are not shown.
  4. If the site has more than one countsheet, then select the required one from the 'Select Countsheet' drop down box.
  5. Click the [Explore EcoCodes for Selected Site] button, and the report will be shown in preview mode...


  1. As always in BugsCEP the report can be browsed in the preview window; printed directly (check the number of pages first!), exported to MS Word or exported to MS Excel using the buttons at the top of the window.
    Remember to save the file after exporting in the application exported to.

 

Compare samples at a site using correlation coefficients

Correlation coefficients can be used to compare the similarity/dissimilarity of the species composition of samples. This is especially useful when trying to identify samples that represent similar environments in Quaternary geology and environmental archaeology.

BugsCEP currently only supports one correlation coefficient - the 'modified Sørensen's' coefficient of similarity of Southwood (1978), which is the inverse (1-B) of the Bray-Curtis coefficient of dissimilarity (Krebs, 1989). Additional coefficients will be added with time.

The results are exported as MS Excel files and can be used as the basis for building cluster diagrams/dendrograms, but no such feature is present (yet...) in BugsCEP.

NOTE: This feature is currently passworded and locked due to lack of development time - it's ugly, and we really don't know if it works on all systems! If you are particularly interested in the feature then please contact us and we will provide you with the password if you agree to help us debug the module... it will be opened up just as soon as we know it works properly.


  1. To open the BugStats interface click the [BugStats] button on the main toolbar.
  2. Make sure MS Excel is closed and not running in the background.
  3. Click the [Calculate Coefficients] button and enter the required password to open the calculations pop-up window.
  4. Select a site from the 'Site' drop down box.
  5. If the site has more than one countsheet, then select the required one from the 'Select Countsheet' drop down box.
  6. Check [] Transform abundance ln(n+1) if required.
  7. Click [Calculate & Export to XLS], choose a save location and provide a filename, then click [Save].
  8. Stand back and let BugStats calculate - do not disturb it!
  9. You will be informed that calculations are complete and asked whether you want to open the results in Excel.
    See below for an explanation of the results file.

 

BugStats output files explained

BugStats produces three types of output:
- BugsEcoGraph files (XLS format)
- Site EcoCode breakdown reports (preview, print, export)
- Coefficient files (XLS format)


BugsEcoGraph files

Three worksheets: Graphs; PctResults; RawResults

Graphs

A horizontal series of 24-27 bar chart like figures (depending on options) as shown below:

The first figure shows sample names and the diagram title provided by the user. The next 23 figures show the BugStats results for each sample in each of the 23 habitat classes of the BugsEcoCode system. Each figure is titled by the class name, and has a scale at the bottom which is either in percent or counts depending on the options chosen.

The final three figures provide summary information for each sample if requested. See above for details.

 

PctResults and RawResults

RawResults shows the raw counts of environmental representations for each sample in each habitat class.
PctResults shows the raw counts recalculated according to the options selected in the BugStats interface. These values are used to construct the figures on the graphs worksheet.

'Indicator' classes are not included in standardization calculations as they are subclasses.

The last few columns show sample data, including reference/name, coordinates and depth.

 

Coefficient files

Results are exported as a matrix, with sample names in the first row and first column. The remaining cells show the coefficient of similarity values for each sample compared with every other one.
The data is formatted and colour scaled here for illustration.

A value of 1 represents total similarity, and 0 no similarity.

Tips for improving the graphs for presentation/publication

Copy and paste the figures into vector graphics editing software (e.g. CorelDraw)

  • With the 'Graphs' worksheet selected in a BugStats output, activate the 'Drawing' toolbar and select the 'Select Objects' tool.
  • Select all the figures - easiest done by scrolling to the bottom right and dragging a box around them.
  • Press CTRL+C to copy the images to the clipboard.
  • Switch to your graphics package and paste special as 'picture (metafile)'.
  • The figures will probably be grouped - ungroup the objects and then polish the image as you see fit for your purpose.
    We recommend deleting empty figures (environments not represented by the faunas), enlarging titles and scale texts.

 

The BugStats methods explained

BugsEcoGraphs

Please see Buckland (2007) for a detailed description.

 

Correlation coefficients

Please see Buckland (2007) for a detailed description.

 

 

References

BUCKLAND, P.I. (2007). "The Development and Implementation of Software for Palaeoenvironmental and Palaeoclimatological Research: The Bugs Coleopteran Ecology Package (BugsCEP)". PhD thesis, Environmental Archaeology Lab., Department of Archaeology & Sámi Studies. University of Umeå, Sweden. Archaeology and Environment 23, 236 pp + CD. Available online: http://www.diva-portal.org/umu/abstract.xsql?dbid=1105

KENWARD, H (2001). "Insect remains from the Romano-British ditch terminal at the Flodden Hill Rectilinear Enclosure". Reports from the Environmental Archaeology Unit, York 2001/49, 15pp.

KOCH, K. (1989-92). Die Käfer Mitteleuropas. Ökologie, 1-3. Goecke & Evers, Krefeld.

KREBS CJ, (1989), Ecological methodology. Harper Collins Publishers, New York, USA, p. 654.

PONEL, P. (1995). “Rissian, Eemian and Würmian Coleoptera assemblages from La Grande Pile (Vosges, France)”. Palaeogeography, Palaeoclimatology, Palaeoecology, 114, 1-41.

ROBINSON, M. A. (2001) Insects as palaeoenvironmental indicators. In, D. R. Brothwell & A. M. Pollard (eds.) Handbook of archaeological sciences, 121-133. J. Wiley & sons, Chichester.

SOUTHWOOD TRE, (1978), Ecological methods, with particular reference to the study of insect populations. John Wiley & Sons, New York, 2nd ed., 524p.

 

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Last edited:
October 15, 2006