Supplement 1. Individual data files (.csv) and R script (.R) used to conduct all analyses.

2016-08-10T11:07:35Z (GMT) by Jonathan S. Lefcheck J. Emmett Duffy
<h2>File List</h2><div> <p><a href="initial_species_data.csv">initial_species_data.csv</a> (MD5: a18ff9ecba3416b181591c3e94277cf0)</p> <p><a href="final_species_data.csv">final_species_data.csv</a> (MD5: 37134e48f4d7b3de20bb25aaaecf5b4e)</p> <p><a href="final_afdm_data.csv">final_afdm_data.csv</a> (MD5: fc558a1f8f7a9db215b67126a94e8bd2)</p> <p><a href="trait_data.csv">trait_data.csv</a> (MD5: bc4d4f19b0fb4377c70ec8f1d72afde3)</p> <p><a href="Lefcheck_mesocosm_analysis.R">Lefcheck_mesocosm_analysis.R</a> (MD5: cbcfe9d5f8cb4a457332f4279e115374)</p> <p><a href="dbFD_new.R">dbFD_new.R</a> (MD5: dd2b3639948332c1751a5e997c509739)</p> </div><h2>Description</h2><div> <p>These supplements should allow the reader to exactly reproduce every analysis in the manuscript, including the generalized linear mixed effects models, analysis of individual traits, and structural equation models, as well as most graphics.</p> <p>The data set is broken up into four files: (1) initial_species_data.csv contains the stocked abundances of all organisms used in the experiment; (2) final_species_data.csv contains the final abundances for stocked and recruiting invertebrates in their respective sieve size classes; (3) final_afdm_data.csv contains the final biomasses for stocked predators and <i>Gracilaria </i>spp., as well as recruiting algae and invertebrates; and (4) trait_data.csv contains the traits used in the analysis of functional diversity, derived from literature values and field observations.</p> <p>The main analysis is in the Lefcheck_mesocosm_analysis.R file. The dbFD_new.R file is sourced from the main script and includes minor modifications to the <i>dbFD()</i> function in the <i>FD </i>package to account for missing cells when calculating functional diversity.</p> <p><b>Column metadata</b></p> <p><i>initial_species_data.csv</i></p> <p>id: the number of species (mono = 1, 3, 6, or poly = 9), the functional diversity treatment (low or high), and finally the replicate number (1-6).</p> <p>treatment: the level of functional diversity (individual species, low, high, or poly). ‘Low’ and ‘high’ values are followed by the number of species (3 or 6).</p> <p>block: experimental block.</p> <p>initial.fd: initial functional richness (min, low, high, or max).</p> <p>initial.gracilaria.biomass: initial wet weight of <i>Gracilaria </i>spp.</p> <p>initial.ampithoe.abund: initial abundance of Ampithoid spp.</p> <p>initial.bittium.abund: initial abundance of <i>Bittolium varium</i></p> <p>initial.callinectes.abund: initial abundance of <i>Callinectes sapidus</i></p> <p>initial.erichsonella.abund: initial abundance of <i>Erichsonella attenuata</i></p> <p>initial.fundulus.abund: initial abundance of <i>Fundulus heteroclitus</i></p> <p>initial.gammarus.abund: initial abundance of <i>Gammarus mucronatus</i></p> <p>initial.hippolyte.abund: initial abundance of <i>Hippolyte pleuracanthus</i></p> <p>initial.palaemonetes.abund: initial abundance of <i>Palaemonetes pugio</i></p> <p>initial.syngnathus.abund: initial abundance of <i>Syngnathus </i>spp.</p> <p>initial.callinectes.length: initial length of <i>Callinectes sapidus</i> (in mm)</p> <p>initial.fundulus.length: initial length of <i>Fundulus heteroclitus</i> (in mm)</p> <p>initial.hippolyte.biomass: initial biomass of <i>Hippolyte pleuracanthus</i> (in g)</p> <p>initial.palaemonetes.biomass: initial biomass of <i>Palaemonetes pugio</i> (in g)</p> <p>initial.syngnathus.length: initial length of <i>Syngnathus </i>spp. (in mm)</p> <p><i> </i></p> <p><i>final_species_data.csv</i></p> <p>date: date the sample was processed and weighed</p> <p>id: the number of species (mono = 1, 3, 6, or poly = 9), the functional diversity treatment (low or high), and finally the replicate number (1-6).</p> <p>group: the taxonomic group of the species (e.g., “Molluscs”, “Crustacean”, “Polychaete”,”Caprellids”) to be used in the calculation of ash-free dry mass from Edgar equations (see R script).</p> <p>Species: species whose dry mass whose abundance was recorded.</p> <p>8.0_mm: the number of individuals in the 8 mm sieve.</p> <p>5.6_mm: the number of individuals in the 5.6 mm sieve.</p> <p>4.0_mm: the number of individuals in the 4 mm sieve.</p> <p>2.8_mm: the number of individuals in the 2.8 mm sieve.</p> <p>2.0_mm: the number of individuals in the 2.0 mm sieve.</p> <p>1.4_mm: the number of individuals in the 1.4 mm sieve.</p> <p>1.0_mm: the number of individuals in the 1 mm sieve.</p> <p>0.71_mm: the number of individuals in the 0.71 mm sieve.</p> <p>0.5_mm: the number of individuals in the 0.5 mm sieve.</p> <p><i> </i></p> <p><i>final_afdm_data.csv</i></p> <p>date: date the sample was processed and weighed</p> <p>id: the number of species (mono = 1, 3, 6, or poly = 9), the functional diversity treatment (low or high), and finally the replicate number (1-6).</p> <p>species: species whose weight was recorded.</p> <p>number.length: the number of individuals or length (in mm) of the species in the sample.</p> <p>Tin: weight of drying tin by itself (g).</p> <p>Tin_Dry: weight of drying tin plus dried sample (g).</p> <p>Tin_Ash: weight of trying tin plus ashed sample (g).</p> <p>AFDM: ash-free dry mass (g) = (Tin_Dry – Tin) – (Tin_Ash – Tin)</p> <p>Notes: additional notes.</p> <p> </p> <p><i>trait_data.csv</i></p> <p>species: the species used in the experiment.</p> <p>armor: whether the organisms is defended. Categorical: None, shell (chitin, calcium carbonate).</p> <p>body.plan: the body plan of the organism. Categorical: Articulate (laterally-, ventrally-compressed, subcylindrical), shelled conic, filiform, fusiform).</p> <p>trophic.level: The general trophic level of the organism. Categorical: Grazer, omnivore, predator.</p> <p>max.biomass: Maximum observed biomass in field surveys of local eelgrass bed (mg).</p> <p>mean.biomass: Average observed biomass in field surveys of local eelgrass bed (mg).</p> <p>mobility: The average mobility of the organism. Categorical: Swimmer (low, high), tube-builder, crawler.</p> <p>reproductive.mode: The reproductive mode of the organism. Categorical: Direct, planktotrophic, ovoviviparous, oviparous.</p> <p>month.max.abund: The month of maximum abundance as observed in field surveys of local eelgrass bed (February – November).</p> </div>