Chapter 02 - An Introduction to Landscape-level variation across the Barro Colorado Nature Monument - Appendix S1 - R code and data files to analyze plant compositional variation among BCI trail segments.

Appendix S1. R code and data files to analyze plant compositional variation among BCI trail segments. Citation Please cite this code and data package as Muller-Landau, Helene C., and Jens-Cristian Svenning. 2024. Chapter 02 - An Introduction to Landscape-level variation across the Barro Colorado Nature Monument - Appendix S1 - R code and data files to analyze plant compositional variation among BCI trail segments. Smithsonian Figshare. https://doi.org/10.25573/data.22779260 This is supplemental material for the following book chapter: Muller-Landau, Helene C., and Jens-Cristian Svenning. 2024. An Introduction to Landscape-Level Variation Across the Barro Colorado Nature Monument. Chapter 2 (pages 19-27) in The First 100 Years of Research on Barro Colorado: Plant and Ecosystem Science, ed. H. C. Muller-Landau and S. J. Wright: Smithsonian Institution Scholarly Press. https://doi.org/10.5479/si.26814820 License and usage terms This code and data package is licensed as CC BY 4.0 and is thus freely available for reuse with citation. Data Description This is Appendix S1 for the book chapter Muller-Landau, Helene C., and Jens-Cristian Svenning. 2024. An Introduction to Landscape-Level Variation Across the Barro Colorado Nature Monument. In The First 100 Years of Research on Barro Colorado: Plant and Ecosystem Science, ed. H. C. Muller-Landau and S. J. Wright: Smithsonian Institution Scholarly Press. It contains R code and data files to analyze plant compositional variation among BCI trail segments and construct Figure 2 of that chapter. Files included here: Muller-Landau&Svenning_2024_AppendixS1_Metadata.rtf A file of metadata for this data and code publication. LandscapeCode.Rmd An Rmarkdown file containing the R code and associated documentation to do the NMDS analyses and make figure 2 of the book chapter. It requires files finaldata_BCIdist_350p_5mb.txt (available for download at Svenning et al. 2024, see reference below), SvenningSpeciesNamesWoody_spcode_RP.txt, trailcodewGPS.txt, BCI_outline.shp,, BCI_outline.dbf, and BCI_outline.shx LandscapeCode.html An html file produced by running LandscapeCode.Rmd, including the code, documentation, and output figures. SvenningSpeciesNamesWoodyUpdated.txt corrections/updates to woody plant species names, courtesy of Suzanne Loo de Lao and Rolando Perez trailcodewGPS.txt GPS coordinates for each BCI trail segment (1 set of coordinates per segment, representing a geographic center of the segment). Produced by code fixcoords.r. BCI_outline.shp , BCI_outline.dbf, and BCI_outline.shx shapefiles of island coastline woodybraycurtis3.rdata results of a 3-axis NMDS on Bray-Curtis analysis of the woody plant abundance data from Svenning et al. 2004 that are presented in Muller-Landau and Svenning 2024 Figure 2. Note that by their nature, NMDS analyses are not precisely repeatable - they will produce the same qualitative results when repeated, but the direction of axis may be flipped as these directions are entirely arbitrary. fixcoords.r R code to produce file trailcodewGPS.txt, based on published Svenning X and Y coordinates of trail segments and the GPS coordinates of trail markers. Requires files BCItrailsegmentSvenningXY.txt and BCI_Trail_Markers_and_POI.csv. BCItrailsegmentSvenningXY.txt has the trail segment X, Y, and Segment_length (m) from Svenning et al. 2004, along with fixes to trail codes that are inconsistent, and the corresponding start and end trail markers. BCI_Trail_Markers_and_POI.csv has coordinates of trail markers and other points of interest on BCI, it was downloaded from STRI GIS data server on Jan 18, 2022 from the following addresshttps://stridata-si.opendata.arcgis.com/datasets/SI::poi/explore?location=9.163675,-79.756294,11.00 Figure 2. Non Metric Multidimensional Scaling (NMDS) analysis of Bray-Curtis dissimilarities of abundances of selected woody plant species on trail segments of BCI, data from Svenning et al. (2004). (a) Beta diversity map, with one point per trail segment analyzed; the color of each point reflects its ordination score, with red, green, and blue channels used for the three axis following Baldeck et al. (2012). (b,c) Vectors showing individual species scores on the three axis, with colors reflecting scores on the NMDS axis as for the sites. Genus names (and when multiple congeners, first two letters of species names) are printed for species whose absolute scores on the displayed axis are above 0.40, indicating they vary strongly with that axis. References Svenning, J. C., D. A. Kinner, R. F. Stallard, B. M. J. Engelbrecht, and S. J. Wright. 2004. Ecological determinism in plant community structure across a tropical forest landscape. Ecology, 85: 2526-2538. https://doi.org/10.1890/03-0396 Svenning, J.-C., D. A. Kinner, R. F. Stallard, B. M. J. Engelbrecht, and S. J. Wright. 2024. Data on environmental characteristics and plant abundances associated with trail segments on Barro Colorado Island, Panama, for 2000-2001. Smithsonian Figshare. https://doi.org/10.25573/data.25331362