Automation of Dice (Czekanowski-Sørensen) similarity index calculations in phyсological research
Section:
ProcedureIssue:
Vol. 34 No. 1 (2024)Pages:
80-90DOI:
https://doi.org/10.15407/alg34.01.080Abstract
This paper examines the trends in the use of the Dice (Czekanowski-Sørensen) similarity index in studies of algae and cyanoprokaryotes. A concise overview of the characteristics of this metric is provided, considering its positive aspects and limitations. The relevance of the work is justified by the researchers' need for automation of Dice index calculations and the construction of resulting matrices. The article proposes a method for automating calculations using macros in the Excel environment. The authors provide an overview of the possibilities of this approach and offer their own macro for fast and convenient calculation of the Dice index without the need for third-party programs or formulas.
Keywords:
algae, cyanoprokaryotes, similarity measure, Dice (Czekanowski-Sørensen) indexFull text
References
Ataş İ. 2023. Performance Evaluation of Jaccard-Dice Coefficient on Building Segmentation from High Resolution Satellite Images. Balkan J. Electrical Comp. Engineer. 11(1): 100–106. https://doi.org/10.17694/bajece.1212563
Austin B., Colwell R.R. 1977. Evaluation of Some Coefficients for Use in Numerical Taxonomy of Microorganisms. Int. J. Syst. Bacteriol. 27(3): 204–210. https://doi.org/10.1099/00207713-27-3-204
Berezovska V. 2019. Species Diversity of Algae of the Kiev Upland Rivers (Ukraine). Int. J. Algae. 21(1): 43–66. https://doi.org/10.1615/InterJAlgae.v21.i1.30
Bertels J., Eelbode T., Berman M., Vandermeulen D., Maes F., Bisschops R., Blaschko M.B. 2019. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2019. Proc. 22nd Int. Conf. Shenzhen (China). Pp. 92–100. https://doi.org/10.1007/978-3-030-32245-8_11
Bray J.R. 1956. A study of mutual occurrence of plant species. Ecology. 37(1): 21–28. https://doi.org/10.2307/1929665
Cheetham A.H., Hazel J.E. 1969. Binary (Presence-Absence) Similarity Coefficients. J. Paleontol. 43(5): 1130–1136.
Czekanowski J. 1909. Zur differential Diagnose der Neandertalgruppe. Korrespbl. Dtsch. Ges. Anthropol. 40: 44–47.
Dice L.R. 1945. Measures of the amount of ecological association between species. Ecology. 26(3): 297–302. https://doi.org/10.2307/1932409
Eikelboom W., Van den Berg E., Coesmans M. Goudzwaard J. et al. 2023. Effects of the DICE Method to Improve Timely Recognition and Treatment of Neuropsychiatric Symptoms in Early Alzheimer's Disease at the Memory Clinic: The BEAT-IT Study. J. Alzheimer's Dis. 93(4): 1407–1423. https://doi.org/10.3233/JAD-230116 https://www.ncbi.nlm.nih.gov/pubmed/37182887 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10357139
Flores P., Salicrú M., Sánchez-Pla A., Ocaña J. 2022. An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment. BMC Bioinform. 23(1): 1–21. https://doi.org/10.1186/s12859-022-04739-2 https://www.ncbi.nlm.nih.gov/pubmed/35641928 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9158181
Graco-Roza C., Santos J., Huszar V., Domingos P., Soininen J., Marinho M. 2019. Downstream transport processes modulate the effects of environmental heterogeneity on riverine phytoplankton. Sci. Total Environ. 703(3): 1–10. https://doi.org/10.1016/j.scitotenv.2019.135519 https://www.ncbi.nlm.nih.gov/pubmed/31757554
Hammer O., Harper D., Ryan P. 2001. PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontol. Electron. 4(1): 1–9.
Hubalek Z. 1982. Coefficients of association and similarity, based on binary (presence-absence) data: an evaluation. Biol. Rev. 57(4): 669–689. https://doi.org/10.1111/j.1469-185X.1982.tb00376.x
Keil P. 2019. Z-scores unite pairwise indices of ecological similarity and association for binary data. Ecosphere. 10(11): e02933. https://doi.org/10.1002/ecs2.2933
Li X., Wang C., Zhang X., Sun W. 2020. Generic SAO Similarity Measure via Extended Sørensen-Dice Index. IEEE Access. 8: 66538–66552. https://doi.org/10.1109/ACCESS.2020.2984024
Mainali K.P., Slud E., Singer M.C., Fagan W.F. 2022. A better index for analysis of co-occurrence and similarity. Sci. Adv. 8(4): eabj9204. https://doi.org/10.1126/sciadv.abj9204 https://www.ncbi.nlm.nih.gov/pubmed/35080967
McCune B., Grace J. 2002. Analysis of Ecological Communities. Glenden Beach: MjM Software Design. 307 p.
Mironyuk A., Tkachenko F. 2020. Species Composition of Algae in Small Rivers of the Northwestern Black Sea Region. Int. J. Algae. 22(4): 359–372. https://doi.org/10.1615/InterJAlgae.v22.i4.50
Peipoch M., Miller S., Antao T., Vallett H. 2019. Niche partitioning of microbial communities in riverine floodplains. Sci. Rep. 9(1): 16384. https://doi.org/10.1038/s41598-019-52865-4 https://www.ncbi.nlm.nih.gov/pubmed/31705005 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6841707
Rogers D.J., Tanimoto T.T. 1960. A computer program for classifying plants. Science. 132(3434): 1115–1118. https://doi.org/10.1126/science.132.3434.1115 https://www.ncbi.nlm.nih.gov/pubmed/17790723
Shcherbak V., Semeniuk N., Lutsenko D. 2023. Diversity and Ecological Characteristics of Algae in the Water Column in the Subbasin of the Large Danube Lakes During the Autumn-Winter Period (Ukraine). Int. J. Algae. 25(1): 71–94. https://doi.org/10.1615/InterJAlgae.v25.i1.50
Sinnott Q.P. 1981. A Simple Similarity Coefficient for Taxonomic Comparisons. Taxon. 30(1): 18–26. https://doi.org/10.2307/1219383
Sneath P.H.A. 1957. The application of computers to taxonomy. J. Gen. Microbiol. 17(1): 201–226. https://doi.org/10.1099/00221287-17-1-201 https://www.ncbi.nlm.nih.gov/pubmed/13475686
Sørensen T. 1948. A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons. Biol. Skrifter/Kongel. Danske Videnskab. Selskab. 5(4): 1–34.
Zhang M., Shi X., Chen F. Yang Z. 2021. The underlying causes and effects of phytoplankton seasonal turnover on resource use efficiency in freshwater lakes. Ecol. Evol. 11(41): 1–13. https://doi.org/10.1002/ece3.7724 https://www.ncbi.nlm.nih.gov/pubmed/34257935 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8258203