Flora ve Vejetasyon Verilerinin R Yazılım Paketleri ile Analizi: Türkiye’nin Güneyinden Bir Örnek Çalışma

Year 2025, Volume: 30 Issue: 1, 13 - 25, 29.04.2025

Yusuf Kurt , İlker Çinbilgel

https://doi.org/10.53433/yyufbed.1357339

Abstract

Flora ve vejetasyon araştırmalarını istatistiksel olarak karşılaştırmak için benzerlik ve farklılık indeksleri kullanılmaktadır. R yazılım ortamı, ekoloji ve diğer birçok disiplinde istatistiksel analiz ve grafiksel görselleştirme yapmak için kullanılan güncel ve popüler yaklaşımlardan biridir. Bu çalışmada, Türkiye'nin güneyindeki sekiz alanın floristik çalışmaları beta çeşitlilik indeksleri ile karşılaştırılmış ve numerik ekoloji ve taksonomik çalışmalarda kullanılan bazı R paketlerinden bahsedilmiş ve tartışılmıştır. Karşılaştırılan alanlarda tespit edilen tüm taksonlar baz alınarak birleşik takson listesi oluşturulmuş ve var/yok verileri hazırlanmıştır. Sekiz floristik alanı karşılaştırmak için beta çeşitlilik indeksleri hesaplandı. UPGMA (Aritmetik Ortalamaları Kullanan Ağırlıksız Çift-Grup Yöntemi) yöntemlerinin benzerlik ve farklılık dendrogramları ile ısı haritaları iki farklı ana grubun olduğunu gösterdi. Floristik alanlardan elde edilen küme dendrogramları ve ısı haritaları, flora ve vejetasyon çalışmalarında alanların kolay karşılaştırılmasını ve nicel farklılaşmasını ortaya koyar. R paketleri diğer birçok disiplinde olduğu gibi flora ve ekoloji alanlarında da ücretsiz olarak yayın kalitesinde grafiklerle verileri analiz etmek, yönetmek ve manipüle etmek için kullanılmaktadır.

Keywords

Bitki ekolojisi, Çeşitlilik indeksleri, R yazılım ortamı, Vegan paketi

Analysis of Flora and Vegetation Data by R Software Packages: A Case Study from Southern Türkiye

Abstract

Similarity and dissimilarity indices have been used to statistically compare flora and vegetation research. R software environment is one of the current and popular approaches to doing statistical analysis and graphical visualizations in ecology and many other disciplines. In the study, floristic studies of eight areas in southern Türkiye were compared by beta diversity indices, and some R packages for numerical ecology and taxonomic applications are mentioned and discussed for more detailed analysis. A unified taxa list was compiled based on all the taxa that are detected in compared areas and then a presence/absence data were prepared. Beta diversity indices were calculated to compare the eight floristic fields. Similarity and dissimilarity dendrograms and heatmaps of UPGMA (Unweighted Pair-Group Method using arithmetic Averages) methods were shown in two different main groups. The obtained cluster dendrograms and heat maps of floristic fields allow easy comparison and quantitative differentiation of areas in flora and vegetation studies. The R packages are used to analyze, manage, and manipulate data with publication quality graphics for free in flora and ecology fields like many other disciplines.

Keywords

Diversity indices, Plant ecology, R software, Vegan package

Thanks

We would like to thank researchers of studied floristic sites and contributions of different R package developers.

References

• Alçıtepe, E. (1998). Termessos Milli Parkı (Antalya) florası üzerinde bir araştırma [Yükseklisans tezi, Akdeniz Üniversitesi]. Yök Tez Merkezi.
• Aldhebiani, A. Y. & Howladar, S. M. (2013). Floristic diversity and environmental relations in two valleys, south west Saudi Arabia. International Journal of Science and Research, 4(2), 1916-1925.
• Allaire, J.J., Xie, Y., McPherson, J., Luraschi, J., Ushey, K., Atkins, A., … & Iannone, R. (2019). rmarkdown: Dynamic Documents for R. R package version 2.0. https://cran.r-project.org/web/packages/rmarkdown/index.html
• Alvarez, M., & Luebert, F. (2018). The taxlist package: managing plant taxonomic lists in R. Biodiversity Data Journal, 6, e23635. https://doi.org/10.3897/BDJ.6.e23635
• Alvarez, M. (2020). vegtable: Handling Vegetation Data Sets. R package version 0.1.5. https://cran.r-project.org/web/packages/vegtable/index.html
• Anderson, M. J., Crist, T. O., Chase, J. M., Vellend, M., Inouye, B. D., Freestone, A. L., Sanders, N. J., Cornell, H. V., Comita, L. S., Davies, K. F., Harrison, S. P., Kraft, N. J., Stegen, J. C., & Swenson, N. G. (2011). Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecology Letters, 14, 19-28. https://doi.org/10.1111/j.1461-0248.2010.01552.x
• Arnholt, T. A., & Evans, B. (2017). BSDA: Basic statistics and data analysis. R package version 1.2.0. https://cran.r-project.org/web/packages/BSDA/index.html
• Baddeley, A., Turner, R. & Rubak, E. (2020). spatstat: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests. R package version 1.63-3. https://cran.r-project.org/web/packages/spatstat/index.html
• Barton, K., & Barton, M.K. (2019). MuMIn: Multi-Model Inference. R package version 1.43.15. https://cran.r-project.org/web/packages/MuMIn/index.html
• Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19(1), 134-143. https://doi.org/10.1111/j.1466-8238.2009.00490.x
• Baselga, A., Orme, D., Villeger, S., De Bortoli, J., Leprieur, F., Logez, M., & Henriques-Silva, R. (2018). betapart: Partitioning Beta Diversity into Turnover and Nestedness Components. R package version 1.5.1. https://cran.r-project.org/web/packages/betapart/index.html
• Bates, D., Maechler, M., Bolker, B., Walker, S., Christensen, R.H.B., Singmann, H., Scheipl, F., Grothendieck, G., Green, P., Fox, J., Bauer, A., & Krivitsky, P.N. (2020). lme4: Linear Mixed-Effects Models using ‘Eigen’ and S4. R package version 1.1-23. https://cran.r-project.org/web/packages/lme4/index.html
• Bocci, G. (2015). TR8: an R package for easily retrieving plant species traits. Methods in Ecology and Evolution, 6(3), 347-350. https://doi.org/10.1111/2041-210X.12327
• Bollmann, S., Cook, D., Dumas, J., Fox, J., Josse, J., Keyes, O., Strobl, C., Turner, H., & Debelak, R. (2017). A first survey on the diversity of the R community. The R Journal, 9(2), 541-552.
• Calderon-Patron, J. M., Goyenechea, I., Ortiz-Pulido, R., Castillo-Ceron, J., Manriquez, N., Ramírez-Bautista, A., Rojas-Martínez, A. E., Sánchez-Rojas, G., Zuria, I., & Moreno, C. E. (2016). Beta diversity in a highly heterogeneous area: disentangling species and taxonomic dissimilarity for terrestrial vertebrates. PLoS ONE, 11(8), e0160438. https://doi.org/10.1371/journal.pone.0160438
• Carvalho, G. (2017). Flora: Tools for Interacting with the Brazilian Flora 2020. R package version 0.3.0. https://cran.r-project.org/web/packages/flora/index.html
• Cayuela, L., Macarro, I., Stein, A. & Oksanen, J. (2019). Taxonstand: Taxonomic Standardization of Plant Species Names. R package version 2.2. https://cran.r-project.org/src/contrib/Archive/Taxonstand/
• Chao, A., Chazdon, R. L., Colwell, R. K., & Shen, T. J. (2005). A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology Letters, 8(2), 148-159. https://doi.org/10.1111/j.1461-0248.2004.00707.x
• Charney, N. & Record, S. (2012). vegetarian: Jost Diversity Measures for Community Data. R package version 1.2. https://cran.r-project.org/src/contrib/Archive/vegetarian/
• Cinbilgel, I., & Gokceoglu, M. (2010). Flora of Altınbeşik National Park (İbradı-Akseki, Antalya/Turkey). Biodicon, 3(3), 85-110. https://dergipark.org.tr/en/pub/biodicon/issue/55900/766064
• Cipullo, N. (2016). Biodiversity indicators: the accounting point of view. Procedia Economics and Finance, 39, 539-544. https://doi.org/10.1016/S2212-5671(16)30297-0
• Conord, C., Gurevitch, J., & Fady, B. (2012). Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basin. Ecology and Evolution, 2(10), 2595-2609. https://doi.org/10.1002/ece3.350
• Crawley, M. J. (2013). The R Book (2nd ed.). John Wiley & Sons Ltd.
• Dallas, T. & Pulliam, T. (2020). metacom: Analysis of the ‘Elements of Metacommunity Structure’. R package version 1.5.3. https://cran.r-project.org/web/packages/metacom/index.html
• Dauby, G. (2019). ConR: Computation of Parameters Used in Preliminary Assessment of Conservation Status. R package version 1.2.4. https://cran.r-project.org/src/contrib/Archive/ConR/
• De Cáceres, M. (2019). vegclust: Fuzzy Clustering of Vegetation Data. R package version 1.7. https://cran.r-project.org/web/packages/vegclust/index.html
• Demirelma, H. (2006). Derebucak (Konya)–İbradı ve Cevizli (Antalya) arasında kalan bölgenin florası [Doktora tezi, Selçuk Üniversitesi]. Yök Tez Merkezi.
• Dray, S., Dufour, A. B. & Thioulouse, J. (2020). ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences. R package version 1.7-15. https://cran.r-project.org/web/packages/ade4/index.html
• Duran, A. (2002). Flora of Tuzaklı, Otluk, Gidefi Mountains and surroundings (Akseki). Turkish Journal of Botany, 26, 303-349. https://journals.tubitak.gov.tr/botany/vol26/iss5/4/
• Fakir, H. (2006). Flora of Bozburun Mountain and its environs (Antalya-Isparta-Burdur, Turkey). Turkish Journal of Botany, 30, 149-169. https://journals.tubitak.gov.tr/botany/vol30/iss3/1/
• Fuka, D.R., Walter, M.T., Archibald, J.A., Steenhuis, T.S. & Easton, Z.M. (2018). EcoHydRology: A Community Modeling Foundation for Eco-Hydrology. R package version 0.4.12.1. https://cran.r-project.org/src/contrib/Archive/EcoHydRology/
• Giraudoux, P., Antonietti, J.P., Beale, C., Pleydell, D. & Treglia, M. (2018). pgirmess: Spatial Analysis and Data Mining for Field Ecologists. R package version 1.6.9. https://cran.r-project.org/web/packages/pgirmess/index.html
• Goslee, S. & Urban, D. (2020). ecodist: Dissimilarity-based Functions for Ecological Analysis. R package version 2.0.5. https://cran.r-project.org/web/packages/ecodist/index.html
• Hennig, C. & Hausdorf, B. (2020). prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data. R package version 2.3-2. https://cran.r-project.org/web/packages/prabclus/index.html
• Hope, R. M. (2013). Rmisc: Ryan Miscellaneous. R package version 1.5. https://cran.r-project.org/web/packages/Rmisc/index.html
• Hyndman, R., Athanasopoulos, G., Bergmeir, C., Caceres, G., Chhay, L., O’Hara-Wild, M., ... & Yasmeen, F. (2020). forecast: Forecasting Functions for Time Series and Linear Models. R package version 8.12. https://cran.r-project.org/web/packages/forecast/index.html
• Isik, K., Semiz, G., & Kurt, Y. (2005, Eylül 8-10). Farklı doğal alanların, içerdikleri türler açısından UPGMA kümelendirme yöntemine göre karşılaştırılması. Korunan Doğal Alanlar Sempozyumu, Süleyman Demirel Üniversitesi, Isparta, Türkiye. https://ormanweb.isparta.edu.tr/kdas/
• Jansen, F. (2019). vegdata: Access Vegetation Databases and Treat Taxonomy. R package version 0.9.7. https://cran.r-project.org/web/packages/vegdata/index.html
• Kahle, D., Wickham, H., Jackson, S. & Korpela, M. (2019). ggmap: Spatial Visualization with ggplot2. R package version 3.0.0. https://cran.r-project.org/web/packages/ggmap/index.html
• Karagoz, Y., & Aslan, A. (2012). Floristic lichen records from Kemaliye District (Erzincan) and Van Province. Turkish Journal of Botany, 36(5), 558-565. https://doi.org/10.3906/bot-1101-30
• Kindt, R. (2019). BiodiversityR: Package for Community Ecology and Suitability Analysis. R package version 2.11-3. https://cran.r-project.org/web/packages/BiodiversityR/index.html
• Kindt, R. (2020). WorldFlora: Standardize Plant Names According to World Flora Online Taxonomic Backbone. R package version 1.5. https://cran.r-project.org/web/packages/WorldFlora/index.html
• Koleff, P., Gaston, K. J., & Lennon, J. J. (2003). Measuring beta diversity for presence-absence data. Journal of Animal Ecology, 72(3), 367-382. https://doi.org/10.1046/j.1365-2656.2003.00710.x
• Lai, J., Lortie, C. J., Muenchen, R. A., Yang, J., & Ma, K. (2019). Evaluating the popularity of R in ecology. Ecosphere, 10(1), e02567. https://doi.org/10.1002/ecs2.2567
• Legendre, P., & Caceres, M. D. (2013). Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecology Letters, 16(8), 951-963. https://doi.org/10.1111/ele.12141
• Lortie, C. J., Braun, J., Filazzola, A., & Miguel, F. (2020). A checlist for choosing between R packages in ecology and evolution. Ecology and Evolution, 10(3), 1098-1105. https://doi.org/10.1002/ece3.5970
• Maechler, M., Rousseeuw, P., Struyf, A., Hubert, M., Hornik, K., Studer, M., ... & Murphy, K. (2019). cluster: Finding Groups in Data. R package version 2.1.0. https://cran.r-project.org/web/packages/cluster/index.html
• Marcon, E. & Herault, B. (2020). entropart: Entropy Partitioning to Measure Diversity. R package version 1.6-4. https://cran.r-project.org/web/packages/entropart/index.html
• Minka, T. P., & Deckmyn, A. (2018). maps: Draw Geographical Maps. R package version 3.3.0. https://cran.r-project.org/web/packages/maps/index.html
• Neuwirth, E. (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2. https://cran.r-project.org/web/packages/RColorBrewer/index.html
• Niesenbaum, R. A. (2019). The integration of conservation, biodiversity and sustainability. Sustainability, 11(17), 4676. https://doi.org/10.3390/su11174676
• Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., ... & Wagner, H. (2019). vegan: Community Ecology Package. R package version 2.5-6. https://cran.r-project.org/web/packages/vegan/index.html
• Özçelik, H., & Korkmaz, M. (2002). Contributions to the flora of Sütçüler-Isparta (Türkiye). Bulletin of Pure and Applied Sciences, 21B(1), 1-19.
• Özcelik, H., Tanrıverdi, F., Tel, A. Z., & Fakir, H. (2006). Köprülü Kanyon Milli Parkı (Antalya-Isparta) Flora Envanter Çalışması, 3. Raporu (GEF-II Projesi, T.C. Çevre-Orman Bakanlığı, Doğa Koruma ve Milli Parklar Genel Müdürlüğü), Ankara.
• Paradis, E., Blomberg, S., Bolker, B., Brown, J., Claude, J., Cuong, H. S., & de Vienne, D. (2019). ape: Analyses of Phylogenetics and Evolution. R package version 5.3. https://cran.r-project.org/web/packages/ape/index.html
• Peşmen, H. (1980). Olimpos-Beydağları Milli Parkının Florası (Türkiye Bilimsel ve Teknik Araştırma Kurumu Temel Bilimler Araştırma Grubu (TBAG), Proje No: 335), Ankara.
• Petzoldt, T. (2019). simecol: Simulation of Ecological (and Other) Dynamic Systems. R package version 0.8-13. https://cran.r-project.org/web/packages/simecol/index.html
• Phillips, N. (2017). Yarrr: A Companion to the e-book “YaRrr!: The pirate’s guide to R”. R package version 0.1.5. https://cran.r-project.org/web/packages/yarrr/index.html
• Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D., Heisterkamp, S., Van Willigen, B., & Maintainer, R. (2020). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-145. https://cran.r-project.org/web/packages/nlme/index.html
• R package (2022a). The R Project for Statistical Computing. https://www.r-project.org/
• R package (2022b). Cran Mirrors. https://cran.r-project.org/mirrors.html
• R package (2022c). The Comprehensive R Archive Network. https://cran.r-project.org/
• R package (2022d). Contributed Packages. https://cran.r-project.org/web/packages/
• Revelle, W. (2019). psych: Procedures for Psychological, Psychometric, and Personality Research. R package version 1.9.12. Northwestern University, Evanston. https://cran.r-project.org/web/packages/psych/index.html
• Roberts, D. W. (2019). labdsv: Ordination and multivariate analysis for ecology. R package version 2.0-1. https://cran.r-project.org/web/packages/labdsv/index.html
• Sarkar, D. (2018). Lattice: Trellis Graphics for R. R package version 0.20-38. https://cran.r-project.org/web/packages/lattice/index.html
• Signorell, A., Aho, K., Alfons, A., Anderegg, N., Aragon, T., Arppe, A., ... & Borchers, H. W. (2019). DescTools: Tools for Descriptive Statistics. R package version 0.99.31. https://cran.r-project.org/web/packages/DescTools/index.html
• Simpson, G. L. (2009). cocorresp: Co-correspondence Analysis Methods. R package version 0.4-1. https://cran.r-project.org/package=cocorresp
• Solymos, P. (2016). mefa: Multivariate Data Handling in Ecology and Biogeography. R package version 3.2-7. https://cran.r-project.org/web/packages/mefa/index.html
• Tantipisanuh, N., & Gale, G. A. (2018). Identification of biodiversity hotspot in national level-Importance of unpublished data. Global Ecology and Conservation, 13, e00377. https://doi.org/10.1016/j.gecco.2018.e00377
• Todou, G., Dedangsou, S., & Kemeuze, V. A. (2017). Floristic composition, diversity and ecological importance of woody plants in eastern part of National Park of Sena Oura, Chad. JBES, 11(2), 92-104.
• Trapletti, A., Hornik, K. & LeBaron, B. (2019). tseries: Time Series Analysis and Computational Finance. R package version 0.10-47. https://cran.r-project.org/web/packages/tseries/index.html
• Valero-Mora, P. M., & Ledesma, R. D. (2012). Graphical user interfaces for R. Journal of Statistical Software, 49(1), 1-8. https://doi.org/10.18637/jss.v049.i01
• Warnes, G. R., Bolker, B., Bonebakker, L., Gentleman, R., Huber, W., Liaw, A., ... & Galili, T. (2019). gplots: Various R programming Tools for Plotting Data. R package version 3.0.1.1. https://cran.r-project.org/web/packages/gplots/index.html
• Watson, K. B., Galford, G. L., Sonter, L. J., & Ricketts, T. H. (2020). Conserving ecosystem services and biodiversity: Measuring the tradeoffs involved in splitting conservation budgets. Ecosystem Services, 42, 101063. https://doi.org/10.1016/j.ecoser.2020.101063
• Wickham, H. (2018). Reshape: Flexibly Reshape Data. R package version 0.8.8. https://cran.r-project.org/web/packages/reshape/index.html
• Wickham, H. (2019). plyr: Tools for Splitting, Applying and Combining Data. R package version 1.8.5. https://cran.r-project.org/web/packages/plyr/index.html
• Wickham, H. & Henry, L. (2019). tidyr: Tidy Messy Data. R package version 1.0.0. https://cran.r-project.org/web/packages/tidyr/index.html
• Wickham, H., François, R., Henry, L. & Müller, K. (2019a). dplyr: A Grammar of Data Manipulation. R package version 0.8.3. https://cran.r-project.org/web/packages/dplyr/index.html
• Wickham, H., Chang, W., Henry, L., Pedersen, T.L., Takahashi, K., Wilke, C., ... & van Den Brand, T. (2019b). ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. R package version 3.2.1. https://cran.r-project.org/web/packages/ggplot2/index.html
• Xie, Y., Vogt, A., Andrew, A., Zvoleff, A., Simon, A., Atkins, A., ..., & Foster, Z. (2019). knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.26. https://cran.r-project.org/web/packages/knitr/index.html
• Yee, T. & Moler, C. (2019). VGAM: Vector Generalized Linear and Additive Models. R package version 1.1-2. https://cran.r-project.org/web/packages/VGAM/index.html
• Zeileis, A., Grothendieck, G., Ryan, J.A., Ulrich, J.M. & Andrews, F. (2020). zoo: S3 Infrastructure for Regular and Irregular Time Series (Z’s Ordered Observations). R package version 1.8-7. https://cran.r-project.org/web/packages/zoo/index.html
• Zhang, J., Pei, N. & Mi, X. (2017). phylotools: Phylogenetic Tools for Eco-Phylogenetics. R package version 0.2.2. https://cran.r-project.org/web/packages/phylotools/index.html
• Zhao, S., Yin, L., Guo, Y., Sheng, Q. & Shyr, Y. (2019). heatmap3: An Improved Heatmap Package. R package version 1.1.6. https://cran.r-project.org/web/packages/heatmap3/index.html
• Zhu, H., Yong, C., Zhou, S., Wang, H., & Yan, L. (2015). Vegetation, floristic composition and species diversity in a tropical mountain nature reserve in southern Yunan, SW China, with implications for conservation. Tropical Conservation Science, 8(2), 528-546. https://doi.org/10.1177/194008291500800216