Journal of Paleolimnology

, Volume 10, Issue 2, pp 147–152 | Cite as

WACALIB version 3.3 — a computer program to reconstruct environmental variables from fossil assemblages by weighted averaging and to derive sample-specific errors of prediction

  • J. M. Line
  • Cajo J. F. ter Braak
  • H. J. B. Birks


A computer program for reconstructing environmental variables (e.g. lake-water pH) from fossil assemblages (e.g. diatoms) by weighted averaging regression and calibration is described. The estimation of sample-specific errors of prediction by bootstrapping is outlined. The program runs on IBM-compatible personal computers.

Key words

weighted averaging regression calibration bootstrapping maximum likelihood reconstruction error estimation 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Agbeti, M. D., 1992. Relationship between diatom assemblages and trophic variables: a comparison of old and new approaches. Can. J. Fish. aquat. Sci. 49: 1171–1175.Google Scholar
  2. Anderson, N. J., B. Rippey & C. E. Gibson, 1993 A comparison of sedimentary and diatom-inferred phosphorus profiles: implications for defining pre-disturbance nutrient conditions, Hydrobiologia 253: 357–366Google Scholar
  3. Battarbee, R. W., J. Mason, I. Renberg & J. F. Talling, 1990. Paleolimnology and lake acidification. The Royal Society, London.Google Scholar
  4. Birks, H. J. B., J. M. Line, S. Juggins, A. C. Stevenson & C. J. F. ter Braak, 1990a. Diatoms and pH reconstruction. Phil. Trans. Roy. Soc. Lond. B, 327: 263–278.Google Scholar
  5. Birks, H. J. B., S. Juggins & J. M. Line, 1990b. Lake surface-water chemistry reconstructions from palaeolimnological data. In The Surface Waters Acidification Programme (ed. B. J. Mason), pp. 301–313. Cambridge University Press, Cambridge.Google Scholar
  6. Charles, D. F. & J. P. Smol, 1990. The PIRLA II Project: Regional assessment of lake acidification trends. Verh. Int. Ver. Limnol. 24: 474–480.Google Scholar
  7. Cumming, B. F. & J. P. Smol, 1993a. Development of diatom-based salinity models for paleoclimatic research from lakes in British Columbia (Canada). Hydrobiologia 269/270: 179–196.Google Scholar
  8. Cumming, B. F. & J. P. Smol, 1993b. Scaled chrysophytes and pH-inference models: the effects of converting scale counts to cell counts and other species data transformations. J. Paleolimnol. 9: 147–153.Google Scholar
  9. Cumming, B. F., J. P. Smol, J. C. Kingston, D. F. Charles, H. J. B. Birks, K. E. Camburn, S. S. Dixit, A. J. Uutala & A. R. Selle, 1992b. How much acidification has occurred in Adirondack region lakes (New York, USA) since preindustrial times? Can. J. Fish. aquat. Sci. 49: 128–141.Google Scholar
  10. Dixit, S. S., B. F. Cumming, H. J. B. Birks, J. P. Smol, J. C. Kingston, A. J. Uutala, D. F. Charles & K. E. Camburn, 1993. Diatom assemblages from Adirondack lakes (New York, USA) and the development of inference models for retrospective environmental assessment. J. Paleolimnol. 8: 27–47.Google Scholar
  11. Effon, B., 1982d. The jackknife, the bootstrap and other resampling plans. Society for Industrial and Applied Mathematics NSF-CBMS Monograph 38: 1–92.Google Scholar
  12. Fritz, S. C., S. Juggins, R. W. Battarbee & D. R. Engstrom, 1991. Reconstruction of past changes in salinity and climate using a diatom-based transfer function. Nature 352: 706–708.Google Scholar
  13. Gaillard, M.-J., H. J. B. Birks, U. Emanuelsson & B. E. Berglund, 1992. Modern pollen/land-use relationships as an aid in the reconstruction of past land-uses and cultural landscapes: an example from south Sweden. Veget. Hist. Archaeobot. 1: 3–17.Google Scholar
  14. Gallant, A. R., 1975. Nonlinear regression. Am. Statist. 29: 73–81.Google Scholar
  15. Hall, R. I. & J. P. Smol, 1992. A weighted-averaging regression and calibration model for inferring total phosphorus concentration from diatoms in British Columbia (Canada) lakes. Freshwat. Biol. 27: 417–434.Google Scholar
  16. Hill, M. O., 1973. Diversity and evenness: a unifying notation and its consequences. Ecology 54: 427–432.Google Scholar
  17. Hill, M. O., 1979. DECORANA- a FORTRAN program for detrended correspondence analysis and reciprocal averaging. Cornell University, Ithaca, New York, USA.Google Scholar
  18. Hill, M. O. & H. G. Gauch, 1980. Detrended correspondence analysis — an improved ordination technique. Vegetatio 42: 47–58.Google Scholar
  19. Hjertholm, E., 1992. The autecology of four species ofSedum along a west-east climatic gradient, Sognefjorden, western Norway. Cand. Scient. thesis, University of Bergen, 83 pp.Google Scholar
  20. Janssens, J. A., B. C. S. Hansen, P. H. Glaser & C. Whitlock, 1992. Development of a raised-bog complex. In The Patterned Peatlands of Minnesota (eds. H. E. Wright, B. A. Coffin & N. E. Aaseng), pp 189–221. University of Minnesota Press, Minneapolis.Google Scholar
  21. Jonsgard, B. & H. J. B. Birks, 1993. Quantitative studies on saxicolous bryophyte-environment relationships in western Norway, J. Bryology 17: 579–611.Google Scholar
  22. Juggins, S., 1993. GLR — a program for Gaussian logit regression. Unpublished program.Google Scholar
  23. Juggins, S. & C. J. F. ter Braak, 1993. CALIBRATE — a program for species-environment calibration by [weighted-averaging] partial least squares regression. Unpublished program.Google Scholar
  24. Kingston, J. C. & H. J. B. Birks, 1990. Dissolved organic carbon reconstructions from diatom assemblages in PIRLA project lakes, North America. Phil. Trans. Roy. Soc. Lond. B, 327: 279–288.Google Scholar
  25. Kingston, J. C., H. J. B. Birks, A. J. Uutala, B. F. Cumming & J. P. Smol, 1992. Assessing trends in fishery resources and lake water aluminum from paleolimnological analyses of siliceous algae. Can. J. Fish. aquat. Sci. 49: 116–127.Google Scholar
  26. Le, J., 1992. Palaeotemperature estimation methods: sensitivity test on two western equatorial Pacific cores. Quat. Sci. Rev. 11: 801–820.Google Scholar
  27. Line, J. M. & H. J. B. Birks, 1990. WACALIB version 2.1 — a computer program to reconstruct environmental variables from fossil assemblages by weighted averaging. J. Paleolimnol. 3: 170–173.Google Scholar
  28. Pienitz, R., J. P. Smol & H. J. B. Birks, 1994. Assessment of freshwater diatoms as quantitative indicators of past climatic change in the Yukon and Northwest Territories, Canada. Arctic and Alpine Research (submitted).Google Scholar
  29. ter Braak, C. J. F., 1987. Unimodal models to relate species to environment. Doctoral thesis, University of Wageningen, 152 p.Google Scholar
  30. ter Braak, C. J. F., 1990a. CANOCO — a FORTRAN program for canonical community ordination. Microcomputer Power, Ithaca, New York, USA.Google Scholar
  31. ter Braak, C. J. F., 1990b. Update notes: CANOCO version 3.10. Agricultural Mathematics Group, Wageningen, 35 pp.Google Scholar
  32. ter Braak, C. J. F. & S. Juggins, 1993. Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblages. Hydrobiologia 269/270: 485–502.Google Scholar
  33. ter Braak, C. J. F., S. Juggins, H. J. B. Birks & H. van der Voet, 1993. Weighted averaging partial least squares (WA-PLS): definition and comparison with other methods for species — environmental calibration. In Multivariate Environmental Statistics (eds. G. P. Patil & C. R. Rao), North Holland, Amsterdam: 525–560.Google Scholar
  34. ter Braak, C. J. F. & I. C. Prentice, 1988. A theory of gradient analysis. Adv. Ecol. Res. 18: 271–317.Google Scholar
  35. ter Braak, C. J. F. & H. van Dam, 1989. Inferring pH from diatoms: a comparison of old and new calibration methods. Hydrobiologia 178: 209–223.Google Scholar
  36. Walker, I. R., R. J. Mott & J. P. Smol, 1991. Allerød-Younger Dryas lake temperatures from midge fossils in Atlantic Canada. Science 253: 1010–1012.Google Scholar
  37. Wilson, S. E., I. R. Walker, R. J. Mott & J. P. Smol, 1993. Climatic and limnological changes associated with the Younger Dryas in Atlantic Canada. Climate Dynamics 8: 177–187.Google Scholar
  38. van Tongeren, O. F. R., 1991. CEDIT program. Limnological Institute, Nieuwersluis, The Netherlands.Google Scholar

Copyright information

© Kluwer Academic Publishers 1994

Authors and Affiliations

  • J. M. Line
    • 1
  • Cajo J. F. ter Braak
    • 2
    • 3
  • H. J. B. Birks
    • 4
    • 5
  1. 1.University of Cambridge Computer LaboratoryCambridgeUK
  2. 2.Agricultural Mathematics Group-DLOWageningenThe Netherlands
  3. 3.DLO-Institute for Forestry and Nature ResearchWageningenThe Netherlands
  4. 4.Botanical InstituteUniversity of BergenBergenNorway
  5. 5.Environmental Research CentreUniversity College LondonLondonUK

Personalised recommendations