CLAMP banner rotating CLAMP plot

How do I do a CLAMP analysis online?

If you are already familiar with the classic CLAMP procedure and have a completed scoresheet you can go straight to paragraph 3 below,

  or if you are familiar with the online analysis procedure go straight to Go to Analysis Button

 

As with the 'classic' CLAMP analysis there are several stages to doing a CLAMP analysis online:

  1)   After collecting the fossil sample for analysis you will have to divide your specimens up into morphotypes. In an ideal world these are equivalent to biological species but, as with all fossil material, this is an ideal rarely achieved. The criteria used for this taxonomic partitioning should include characters not used in the CLAMP analysis. In most cases venation characters should be used in addition to shape and margin features. It is not necessary to identify (i.e. name or establish relationships to published taxa) the morphotypes. At least 20 morphotypes of leaves of woody dicotyledonous plants are required for each fossil assemblage. Any less than this and the statistical uncertainties rise dramatically, so degrading the reliability of the results.
       
  2)   Next you will need to score your fossil leaf assemblage using the CLAMP criteria and character definitions. It is important that the scoring scheme is adhered to rigorously or the fossil score will not be compatible with the modern reference data sets. If you download the scoresheet you will be able to add your scores easily to the reference data sets prior to the analysis. With a little experience the scoring of each morphotype should take no more than 2-3 minutes.
       
  3)   To run the analysis select the combinations of calibration files from the dropdown menu given on the online analysis page.To access the online analysis page click the "Set up Analysis" button at the bottom of this page. There are several physiognomic calibration files available - Physg3arcAZ, Physg3brcAZ, PhysgAsia2 and PhysgGlobal378.Physg3arcAZ consists of physiognomic data from leaves collected from 173 modern day stands of vegetation growing in a variety of climates predominantly in North America and Japan. These have been collected in a comparable manner and all the reference material is in the form of dried herbarium type samples stored at the U.S. National Museum, Smithsonian Institute, Washington D.C. (contact: Scott Wing).
       
      Each sample consists of leaves covering the full range of morphologies seen in the living vegetation at each calibration site. It is important that the full range of morphologies is represented in the sample and for this reason herbarium material collected for purposes other than CLAMP are rarely suitable.The Physg3brcAZ file consists of a subset of 144 sites from the Physg3arcAZ file, the difference being that the Physg3brcAZ file lacks sites that experience significant cold. The Physg3brcAZ file yields higher precision. It is recommended that you either use the spreadsheet available to help you decide which calibration file is most suitable for your sample, or that you first run your sample using the PhysgarcAZ calibration, see where your sample sits in physiognomic space relative to cold sites, and if it plots away from them it is safe to use the higher precision Physg3brcAZ calibration.
       
      There are two types of meteorological files to choose from. The data from the meterological stations associated with the calibration sites is contained in the MET3arcAZ and MET3brcAZ files. These record the climate close to, and affected by, the vegetation. The other option is to use gridded meteorological data (files called GRIDMET3arcAZ and GRIDMET3brcAZ). The data in these files are derived from globally gridded meteorological data (New et al., 1999) adjusted for elevation (Spicer et al., 2009) and are more representative of modern regional climates used in climate modelling. Which one you use is up to you, but you should always specify in any subsequent publication which calibration data sets, physiognomic and meteorological, that you have used in your analysis. The Asian and global physiognomic files have ony gridded climate data available for calibration.
       
      PhysgAsia2.csv is a data set made up of 177 sites. It is built upon Physg3brcAZ with the addition of 45 sites from China, plus sites from India and Thailand (Khan et al., 2014). This dataset is particularly useful for warm monsoonal climates. It is accompanied by a high resolution gridded meteorological data set HiResGRIDMetAsia2.csv.
       
      PhysgGlobal378.csv is the last data set currently available for online analysis. This is an experimental a global data set that, because it offers less precision than the other calibrations, should not be used for routine analyses. It can be used, however, to determine where a fossil site sits in physiognomic space and so indicated which calibration data set is most appropriate for a detailed analysis. It is accompanied by a high resolution gridded meteorological calibration file HiResGRIDMetGlobal378.csv.To download a file summarising the precision associated with each climate parameter prediction click here.
       
  4)   You then need to upload a file containing the scores of the samples you wish to analyse. For instructions on how to construct this file click here. This files should be saved as a .csv file giving it a single word name beginning with an alphabetical character. In Excel on a Mac you will be given a choice of 'MS-DOS" or 'Windows' .csv format. Use the 'MS-DOS' format. Note that this format demands a decimal point be denoted by a '.' (point) and the values separated by a ','(comma). Some regionalised versions of Excel may not generate this kind of file and you may need to use a text editor to configure the file correctly. Once configured in the correct .csv format either enter the pathway to this file in the dialogue box or, more simply, use the browse button to identify and attach the file. Click here to download a zipped example file (Fossils.csv) that you can run as a test.
       
  5)   You now have the option to select colour or greyscale output and if you want the data points labelled or not. The default option is without labels. This is useful for publication when you may want to add your own form of labelling. The labelled versions can get very 'busy' with labels overlapping but you will need this form of output to properly interpret your results.
       
  6)   You are now ready to run your analysis. To do this simply click on the "Analyse" button on the online analysis page. Your results will be stored in a file that will appear on the online analysis page. Click on the results file to download it.
       
      When downloading these files please be patient. Sometimes for complex analyses, or on slow links, it can take a little while to return the results. To see an example of a results page and how to interpret it click here.
       

 

Please note that you should check the position of your fossil sites in physiognomic space. If your fossil site resides outside of the physiognomic space occupied by the calibration sites your result will have higher uncertainties that those given and may not be reliable.

Go to Analysis Button

Page Top

hotspot linking to the Institute of Botany., Chinese Academy of Sciences, Beijing Hotspot linking to the Open University