DATA TITLE: Guadua micromorphology data, data wrangling, analysis, graphics, and associated documents
PROJECT TITLE: Foliage leaf and floral bract micromorphology vary by habitat and habit in Guadua (Poaceae: Bambusoideae: Bambuseae)
DATA ABSTRACT: This repository contains the raw data, tidied data, associated documents, and code for data wrangling, data analysis, and graphics generation for the manuscript "Foliage leaf and floral bract micromorphology vary by habitat and habit in Guadua (Poaceae: Bambusoideae: Bambuseae)"
AUTHORS:
Author: Elizabeth K. McMurchie ORCID: 0000-0002-4917-4314 Institution: Iowa State University Email: elkamcmurchie@gmail.com; mcmurch@iastate.edu
Author: Josephine A. Crock Institution: Iowa State University Email: jaccrock@iastate.edu
Author: Devin Molnau Institution: Iowa State University Email: d.molnau3172@gmail.com
Author: Haldre S. Rogers ORCID: 0000-0003-4763-5006 Institution: Virginia Tech Email: haldre@vt.edu
Author: Dean C. Adams ORCID: 0000-0001-9172-7894 Institution: Iowa State University Email: dcadams@iastate.edu
Author: Lynn G. Clark ORCID: 0000-0001-5564-4688 Institution: Iowa State University Email: lgclark@iastate.edu
Corresponding author: Elizabeth K. McMurchie
ASSOCIATED PUBLICATIONS: Foliage leaf and floral bract micromorphology vary by habitat and habit in Guadua (Poaceae: Bambusoideae: Bambuseae)
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'analysis'
-'README_analysis.MD' contains the README information for the 'analysis' subdirectory
-'guadua_leaf_micromorphology_analysis.Rmd' contains R code used analyze Guadua foliage leaf data. The 'RRPP' (Collyer and Adams, 2024, 2018), 'geomorph'(Baken et al, 2021; Adams et al., 2025), 'tidyverse' (Wickham et al., 2023, 2019),'ade4' (Bougeard and Dray, 2018; Chessel et al., 2004; Dray et al., 2023, 2007; Dray and Dufour, 2007; Thioulouse et al., 2018), 'vegan' (Oksanen et al., 2025), and 'pander' (Daróczi and Tsegelskyi, 2022) R packages were used to assist in data analysis, including visualization of statistics using tables and principal coordinates analysis (PcoA).
-'guadua_floret_micromorphology_analysis.Rmd' contains R code used analyze Guadua floral bract data. The 'RRPP' (Collyer and Adams, 2024, 2018), 'geomorph'(Baken et al, 2021; Adams et al., 2025), 'tidyverse' (Wickham et al., 2023, 2019),'ade4' (Bougeard and Dray, 2018; Chessel et al., 2004; Dray et al., 2023, 2007; Dray and Dufour, 2007; Thioulouse et al., 2018), 'vegan' (Oksanen et al., 2025), and 'pander' (Daróczi and Tsegelskyi, 2022) R packages were used to assist in data analysis, including visualization of statistics using tables and principal coordinates analysis (PcoA).
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'data' contains 'README_data.MD', which includes the README information for the 'data' subdirectory, and two further subdirectories:
A. 'data_raw' contains 'README_data_raw', the README information for the 'data_raw' subdirectory, was well as the raw data files 'guadua_leaf_raw_3.xlsx' and 'guadua_lemmas_paleas_raw_3.xlsx'.
-'guadua_leaf_raw_3.xlsx' is the original raw data file for raw Guadua leaf micromorphology data. For definitions of all variables, see 'Appendix A data_dictionary_leaf.docx' for the foliage leaf data dictionary.
-'guadua_lemmas_paleas_raw_3.xlsx' is the original raw data file for raw Guadua floral bract micromorphology data. For definitions of all variables, see 'Appendix B data_dictionary_floret.docx' for the floral bract data dictionary.
B. 'data_tidy' contains 'README_data_tidy', the README information for the 'data_tidy' subdirectory, 'guadualeaf.csv', and 'guaduafloret.csv'.
-'guadualeaf.csv' includes tidied Guadua foliage leaf data prepared for analysis. It is the product of using 'tidying_guadua_leaf.Rmd' on 'guadua_leaf_raw_3.xlsx' for tidying.
-'guaduafloret.csv' includes tidied Guadua floral bract data prepared for analysis. It is the product of using 'tidying_guadua_floret.Rmd' on 'guadua_lemmas_paleas_raw_3.xlsx' for tidying.
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'data_wrangling'
-'README_data_wrangling.MD' contains the README information for the 'data_wrangling' subdirectory
-'tidying_guadua_leaf.Rmd' contains R code used to tidy data from 'guadua_leaf_raw_3.xlsx' for analysis. The 'tidyverse' (including 'readr') (Wickham et al., 2023, 2019) and 'readxl' (Wickham and Bryan, 2023) R packages were used to assist in tidying of data.
-'tidying_guadua_floret.Rmd' contains R code used to tidy data from 'guadua_lemmas_paleas_raw_3.xlsx' for analysis. The 'tidyverse' (including 'readr') (Wickham et al., 2023, 2019) and 'readxl' (Wickham and Bryan, 2023) R packages were used to assist in tidying of data.
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'documents'
-'README_documents.MD' contains the README information for the 'documents' subdirectory
-'specimen_data.csv' contains basic information about all specimens used in this study. These data include specimen collector and number, species (and subspecies, when applicable) identification, country in which specimens were collected, general habit for the species, general habitat for the species, Index Herbariorum (Thiers, 2025) code corresponding to the herbarium at which the specimen is deposited, photographer (Elizabeth K. McMurchie, EKM, or Lynn G. Clark, LGC) who imaged each floral bract and/or foliage leaf specimen, which researcher (Elizabeth K. McMurchie, EKM, or Josephine A. Crock, JAC) classified presence/absence of micromorphological features on foliage leaves and floral bracts, and metal sputter coating used on foliage leaves and floral bracts (Au, gold, Pt, platinum, or Ir, iridium) prior to imaging. Instances of 'x' in the spreadsheet indicate when values were not applicable, such under subspecies when a species has no recognized subspecies and under photographer, coating, and classification for leaves or floral bracts when a specimen lacked either leaves or floral bracts so that these parts could not be imaged or leaves or floral bracts were unusable. Specimen information for specimens from the Missouri Botanical Garden (MO) is searchable at: https://www.tropicos.org/specimen/Search . Specimen information for specimens from the Smithsonian Herbarium (US) is searchable at: https://collections.nmnh.si.edu/search/botany/ . Specimen information for specimens from the Harvard University Herbaria (including A) is searchable at: https://kiki.huh.harvard.edu/databases/specimen_index.html .
-'Appendix A data_dictionary_leaf.docx' contains the data dictionary for foliage leaf micromorphology classification. This includes the definitions for all variables used in 'guadua_leaf_raw_3.xlsx'. Variables are primarily defined with reference to Ellis (1979), with additional reference to Cunha Santana (2017) and ICPT (2019).
-'Appendix B data_dicitonary_floret.docx' contains the data dictionary for floral bract micromorphology classification. This includes the definitions for all variables used in 'guadua_lemmas_paleas_raw_3.xlsx'. Variables are primarily defined with reference to Ellis (1979), with additional reference to Cunha Santana (2017) and ICPT (2019).
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'graphics'
-'README_graphics.MD' contains the README information for the 'graphics' subdirectory
-'guadua_leaf_micromorphology_graphics.Rmd' contains R code used to create the graphics related to foliage leaf micromorphology data used in the manuscript and supplementary material. 'tidyverse' was used to run 'ggplot2', which was required for graphics (Wickham et al., 2023, 2019). The packages 'ade4' (Bougeard and Dray, 2018; Chessel et al., 2004; Dray et al., 2023, 2007; Dray and Dufour, 2007; Thioulouse et al., 2018) and 'vegan' (Oksanen et al., 2025) were required for PCoA. Correlation tables were created using 'ggcorrplot' (Kassambara, 2023; Kassambara and Patil, 2023). ColorBrewer 2.0 was used to assist in selection of colors used in the PCoA (Brewer et al, 2013).
-'guadua_floret_micromorphology_graphics.Rmd' contains R code used to create the graphics related to floral bract micromorphology data used in the manuscript and supplementary material. 'tidyverse' was used to run 'ggplot2', which was required for graphics (Wickham et al., 2023, 2019). The packages 'ade4' (Bougeard and Dray, 2018; Chessel et al., 2004; Dray et al., 2023, 2007; Dray and Dufour, 2007; Thioulouse et al., 2018) and 'vegan' (Oksanen et al., 2025) were required for PCoA. Correlation tables were created using 'ggcorrplot' (Kassambara, 2023; Kassambara and Patil, 2023). ColorBrewer 2.0 was used to assist in selection of colors used in the PCoA (Brewer et al, 2013).
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