### READ ME FILE ### "Data and analysis scripts for: Co-occurrence patterns at four spatial scales implicate reproductive processes in shaping community assembly in clovers" ### Figure 1: METADATA FOR .CSV FILES ---------------------------------------------------- 1a_statewide_community_matrix.csv (rows represent sites, columns represent species) - values of 0/1 represent absence/presence at site or in plot/quadrat 1b_CAplots_community_matrix.csv (rows represent sites, columns represent species) - values of 0/1 represent absence/presence at site or in plot/quadrat 1c_Bodega_community_matrix.csv (rows represent sites, columns represent species) - values of 0/1 represent absence/presence at site or in plot/quadrat 1d_McLaughlin_community_matrix_Tbifi_Tgrac_combined.csv - values of 0/1 represent absence/presence at site or in plot/quadrat - column "Trifolium bifigracilentum" represents combined presence/absence of both T. bifidum and T. gracilentum Figure 1: Figure1_plot_occurrence_data.R - for each dataset, plots of the proportion of sites/plots with varying numbers of Trifolium species present ### Figure 2: METADATA FOR .R FILES ------------------------------------------------------ 2a_statewide_qs_floral_9mm_OBSERVED.Rdata 2a_statewide_qs_floral_9mm.Rdata 2b_CAplots_qs_floral_9mm_OBSERVED.Rdata 2b_CAplots_qs_floral_9mm.Rdata 2c_Bodega_qs_floral_9mm_OBSERVED.Rdata 2c_Bodega_qs_floral_9mm.Rdata 2d_McLaughlin_qs_floral_9mm_OBSERVED.Rdata 2d_McLaughlin_qs_floral_9mm.Rdata - each .Rdata file represents a null model of community assembly based on 10,000 randomizations from vegan the vegan R package, using the nullmodel and simulate functions, and quasiswap algorithm - each OBSERVED.Rdata file represents the empirical observation (i.e., the proportion of large-flowered species at sites hosting varying numbers of Trifolium species) Figure2_flower_size_expectations.R - plots expected community composition (curves) and observed proportion of large-flowered species - at sites hosting varying numbers of Trifolium species for each dataset ### Figure 3: METADATA FOR .R FILES ------------------------------------------------------ 3a_statewide_qs_floral_9mm_OBSERVED.Rdata 3a_statewide_qs_floral_9mm.Rdata 3a_statewide_qs_output_all_species_leaf_size_173_OBSERVED.Rdata 3a_statewide_qs_output_all_species_leaf_size_173.Rdata 3a_statewide_qs_output_all_species_plant_height_304_OBSERVED.Rdata 3a_statewide_qs_output_all_species_plant_height_304.Rdata 3b_CAplots_qs_floral_9mm_OBSERVED.Rdata 3b_CAplots_qs_floral_9mm.Rdata 3b_CAplots_qs_output_all_species_leaf_size_173_OBSERVED.Rdata 3b_CAplots_qs_output_all_species_leaf_size_173.Rdata 3b_CAplots_qs_output_all_species_plant_height_304_OBSERVED.Rdata 3b_CAplots_qs_output_all_species_plant_height_304.Rdata 3c_Bodega_qs_floral_9mm_OBSERVED.Rdata 3c_Bodega_qs_floral_9mm.Rdata 3c_Bodega_qs_output_all_species_leaf_size_173_OBSERVED.Rdata 3c_Bodega_qs_output_all_species_leaf_size_173.Rdata 3c_Bodega_qs_output_all_species_plant_height_304_OBSERVED.Rdata 3c_Bodega_qs_output_all_species_plant_height_304.Rdata 3d_McLaughlin_qs_floral_9mm_OBSERVED.Rdata 3d_McLaughlin_qs_floral_9mm.Rdata 3d_McLaughlin_qs_output_all_species_leaf_size_173_OBSERVED.Rdata 3d_McLaughlin_qs_output_all_species_leaf_size_173.Rdata 3d_McLaughlin_qs_output_all_species_plant_height_304_OBSERVED.Rdata 3d_McLaughlin_qs_output_all_species_plant_height_304.Rdata - each .Rdata file represents a null model of community assembly based on 10,000 randomizations from vegan the vegan R package, using the nullmodel and simulate functions, and quasiswap algorithm - each OBSERVED.Rdata file represents the empirical observation (i.e., the proportion of large-flowered (floral), large-leaved (leaf size), and large-statured (plant height) species at sites hosting varying numbers of Trifolium species) Figure3_vegetative_traits_and_floral_traits_in_single_species_sites.R - Plots the composition of tall-statured, large-leaved, and large-flowered Trifolium species - in single-species communities at multiple sites from across California ### Figure 4: METADATA FOR .CSV FILES ---------------------------------------------------- 4_Trifolium_species_in_study.csv (column metadata) - species: Trifolium species - life_history: annual or perennial - mean_corolla_mm: average corolla length (mm) - mean_height_cm: average plant height (cm) - mean_leaflet_length_mm: average leaflet length (mm) - mean_leaflet_width_mm: average leaflet width (mm) - Statewide: presence/absence (1/0) in statewide dataset - CA_plots: presence/absence (1/0) in California plots dataset - McLaughlin: presence/absence (1/0) in McLaughlin dataset - Bodega: presence/absence (1/0) in Bodega Bay dataset 4a_statewide_multi_co-occurence_summary.csv 4b_CAplots_multi_co-occurence_summary.csv 4d_McLaughlin_multi_co-occurence_summary.csv - n_alone: number of sites in which a species occurred alone - n_coexist: number of sites in which a species occurred with at least one other Trifolium congener - n_total: total number of sites for a which a given species occurred - n_one_or_two: number of sites in which a species occurred alone or with one other Trifolium congener - n_three_or_more: number of sites in which a species occurred with at least two or more Trifolium congeners - species: Trifolium species - dataset: description of dataset ### Figure 4: METADATA FOR .R FILES ------------------------------------------------------ multiplot.R - required source function for multi-panel plot using 'ggplot2' package Figure4_probability_of_cooccurrence.R - .R analysis and figure script to model/visual the probability of Trifolium co-occurrence in relation to flower size