README file for B.A. Kohli and M.A. Jarzyna. 2021. Pitfalls of ignoring trait resolution when drawing conclusions about ecological processes. Global Ecology and Biogeography. Data Dryad DOI:10.5061/dryad.0k6djhb03 Corresponding author contact information (as of February 2021): Brooks A. Kohli Department of Evolution, Ecology and Organismal Biology Ohio State University 318 W. 12th Ave. Columbus, OH, 43210 Email: brookskohli@gmail.com ORCiD ID: 0000-0002-9703-536X ### The 13 files stored on Dryad include the initial species pool data (abundance matrices and continuous trait values) used for the simulation results reported in the main text (9 files; names starting with "MainSims_") of the article to enable exact replication of our results. In addition, all simulation data and outputs relevant to Supplementary Methods and Results described in Appendix S1 and S2 (4 files; names starting with "SI_Methods_") of the article are also provided, including the initial regional pools and trait values, summary output of SES values, Wilcoxon tests, and p-values across all simulation iterations. Associated R code for main results and supplementary results can be found at https://github.com/Jarzyna-Lab and on Zenodo: https://doi.org/10.5281/zenodo.4497961. Associated R code is deposited on Zenodo: https://doi.org/10.5281/zenodo.4497961. ### Brief Methods ### All data in this project are simulated following previously developed approaches to generate species pools and trait values to serve as the starting data for simulation iterations. The primary method, reported in the main text, follow those of Botta-Dukát & Czúcz, 2016 (Testing the ability of functional diversity indices to detect trait convergence and divergence using individual-based simulation. Methods in Ecology and Evolution, 7, 114–126). An alternate method based largely on McPherson et al. 2017 (A simulation tool to scrutinise the behavior of functional diversity metrics. Methods in Ecology and Evolution, 9, 200–206) and Kraft & Ackerly, 2010 (Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest. Ecological Monographs, 80, 401–422) was also used, with results reported primarily in the Supporting Information of the paper. ### Detailed File Information ### #Main simulations files MainSims_RegPool50.csv, MainSims_RegPool100.csv, MainSims_RegPool500.csv, MainSims_RegPool1000.csv: These are the 4 initial regional species pools of varying size (50, 100, 500, or 1000 species) created and used as the base for all iterations. Column headings are species and values are the simulated abundance of each species in 100 simulated community (rows). Rows sum to 300. MainSims_RegPool50_Traits.csv, MainSims_RegPool100_Traits.csv, MainSims_RegPool500_Traits.csv, MainSims_RegPool1000_Traits.csv: These are the companion trait matrices for each of the 4 initial regional species pool. Rows are species (repeated in column "sp"; matching those in the regional pool files above). Remaining columns hold simulated values for three traits: TrEF = environmental filtering trait, TcComp = competition trait, TrNeut = neutral trait. MainSims_Skewness_FullResults.csv: Mean and standard deviation (indicated in column "value") of the skew of SES test statistic null distributions averaged across simulation iterations of regional pool size (column "poolSize", values" 50, 100, 500, 1000 species) per combination of functional structure index (column "index"; values: FDis = functional dispersion, MNTD = mean nearest neighbor trait distance, Rao = Rao's quadratic entropy, MPD = mean pairwise distance), community structure process (column "process"; values: Conv = convergence due to environmental filtering, Div = divergence due to competition), and trait resolution (columns 1-6; TrContin = continuous trait values, Rounded = rounded continuous values, Cat16-Cat02 = categorical trait values of N states (16, 8, 4, or 2)). These values are summarized in Table S2.2 in Supporting Information. #Supplemental simulations files SI_Methods_InitialSimulationPools.xlsx: An Excel spreadsheet containing 3 worksheets with initial regional pools, trait values, and simulation parameters for the methods used and R code of McPherson et al. 2017. A simulation tool to scrutinise the behavior of functional diversity metrics. Methods in Ecology and Evolution, 9, 200–206. -Sheet "RegPoolsPools_1": Rows are regional species pools (COM1-4) of varying size, columns are species (SP1-1500) found in the universal species pool, values are presence/absence (1/0) of the species in each pool. -Sheet "RegPoolsTraits_1": Rows are species (SP1-1500; mathcing those in Sheet 1), columns are traits (TR1-24), values are simulated continous trait values. The last column, LIKELIHOOD, equates to the joint (multiplied) density functions of each of the species’ trait values (see McPherson et al. 2017 for more). -Sheet "RegPoolsParams_1": contains characteristics and summary statistics of the simulated universal pool and 4 regional pools (rows; matching those on Sheet 1) and each trait (T# headings). See McPherson et al. 2017 for complete description of all headers and parameters. SI_Methods_MedianSESs_including1traitResults_appended.csv: Median SES values for simulated communities from the full range of supplemental simulation methods. These values were used to produce Figure S2.1 in Supporting Information. Column headings: -community structure process (column "process"; values: Conv = convergence due to environmental filtering, Div = divergence due to competition, Rdm = random assembly), -coarseness (trait resolution; values: TrContin = continuous trait values, Rounded = rounded continuous values, Cat16-Cat02 = categorical trait values of N states (16, 8, 4, or 2), -functional structure index (column "index"; values: FDis = functional dispersion, MNTD = mean nearest neighbor trait distance, MPD = mean pairwise distance, FD = dendrogram-based functional diversity, FDIavg = mean dendrogram-based functional distinctness). We included a braoder array of indices in the supplemental simulations than the ultimate set used in the Main Simulations. -tr = trait number -p = pool size -nc = size of communities relative to pool size (1/3, 1/4, 1/5 the pool size) SI_Methods_MediansSESs_MIX_MNND.csv: Median SES values of Mean nearest neighbor distance index as a function of mixing variable numbers of high and low resolution traits. These values were used to produce Figure S2.2 in Supporting Information. Column headings: -community structure process (column "proc"; values: Conv = convergence due to environmental filtering, Div = divergence due to competition, Rdm = random assembly), -coarseness (trait resolution; values: TrContin = continuous trait values, Rounded = rounded continuous values, Cat16-Cat02 = categorical trait values of N states (16, 8, 4, or 2), Mixed1-5 = (the number after "Mixed" reflects the number of continous trait values randomly drawn, the rest were either 2 or 4 state categorical values; not all levels possible in all iterations due to trait number limitations), -tr = trait number (only 3 and 6 used in this mixed resolution analysis) -p = pool size -nc = size of communities relative to pool size (only 1/4 the pool size used in this mixed resolution analysis) -cat = the resolution of the categorical traits randomly drawn to use in combination with continuous values of the remaining number of traits (values: 2 = 2-state categorical; 4 = 4-state categorical trait values) SI_Methods_WilcoxEstsPvals.csv: Simulated median SES shift estimates (columns 3-7) and associated p-values (columns 8-12) based on Wilcoxon signed ranks tests comparing the distribution of values generated by using baseline continuous trait data to coarser traits from the supplemental simulation results. Includes all process-based patterns (convergent, divergent, random), trait resolution levels, and pool sizes, column headings and values same as above. ###end