This SAFEdataREADME.txt file was generated on 2021-06-14 by K. Ann Bybee-Finley GENERAL INFORMATION 1. Data for: Finding the right mix: a framework for selecting seeding rates for cover crop mixtures 2. Author Information A. Principal Investigator Contact Information Name: K. Ann Bybee-Finley Institution: USDA-ARS, Sustainable Agricultural Systems Laboratory Email: kabfin@gmail.com B. Associate or Co-investigator Contact Information Name: Matt Ryan Institution: Cornell University, Sustainable Cropping Systems Laboratory Address: Ithaca, NY Email: mrr232@cornell.edu C. Associate or Co-investigator Contact Information Name: Stéphane Cordeau Institution: Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France Address: Univ. Bourgogne Franche-Comté, F-21000 Dijon, France Email: stephane.cordeau@inrae.fr D. Associate or Co-investigator Contact Information Name: Séverin Yvoz Institution: Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne Address: Univ. Bourgogne Franche-Comté, F-21000 Dijon, France Email: Severin.Yvoz@inrae.fr E. Associate or Co-investigator Contact Information Name: Steven Mirsky Institution: Sustainable Agricultural Systems Laboratory, USDA-ARS Address: Beltsville, MD, 20705, USA Email: Steven.Mirsky@usda.gov 3. Date of data collection: Main experimental data: 2014-07-07 to 2014-08-21; Validation data: 06-01-2013 to 09-01-2013, 06-01-2014 to 09-01-2014 4. Geographic location of data collection: Main experiment data: Cornell Musgrave Research Farm in Aurora, NY (42º45’N, 76 º35’W); Validation data: Cornell Musgrave Research Farm in Aurora, NY--the same as the main experimental data; the Cornell Willsboro Research Farm in Willsboro, NY (44°21’ N, 73°23’ W); and the USDA–ARS Beltsville Agricultural Research Center in Beltsville, MD (39°02’ N, 76°54’ W). 5. Information about funding sources that supported the collection of the data: National Institute of Food and Agriculture, USDA, Hatch Project 2013-14-425: Expanding the role of cover crops in sustainable cropping systems; Northeast Sustainable Agriculture Research and Education Graduate Student Project GNE14-073: Selecting seeding rates for diverse summer annual forage crop mixtures SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: CC0 2. Links to publications that cite or use the data: Main experiment data: Bybee-Finley, K. Ann, Stéphane Cordeau, Séverin Yvoz, Steven B. Mirsky & Matthew R. Ryan. 2021. Finding the right mix: a framework for selecting seeding rates for cover crop mixtures. Ecological Applications. https://doi.org/10.1002/eap.2484 Validation data: Bybee‐Finley, K. Ann, Steven B. Mirsky, and Matthew R. Ryan. “Functional Diversity in Summer Annual Grass and Legume Intercrops in the Northeastern United States.” Crop Science 56, no. 5 (September 2016): 2775–90. https://doi.org/10.2135/cropsci2016.01.0046. Bybee-Finley, K. Ann, Steven B. Mirsky, and Matthew R. Ryan. “Crop Biomass Not Species Richness Drives Weed Suppression in Warm-Season Annual Grass–Legume Intercrops in the Northeast.” Weed Science 65, no. 5 (September 2017): 669–80. https://doi.org/10.1017/wsc.2017.25. 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: N/A 5. Was data derived from another source? No 6. Recommended citation for this dataset: TBD DATA & FILE OVERVIEW 1. File List: Main experiment data: kendallcorr.csv longtestsppMonoBi.csv observedandseededdensity.csv seed_costs.csv testspp.csv tricoefflong.csv plotmap2014.jpg SAFEclean.Rmd Validation data: safe9_h2_poly_long.csv 2. Relationship between files, if important: Main experiment data files: testspp.csv (main file), longtestsppMonoBi.csv (data from testspp.csv and competition coefficient estimates from model), kendallcorr.csv (data uses NDI-a calculation based on the normalized competition coefficient estimates), tricoefflong.csv (three and four-species mixtures biomass and densities from testspp.csv in a long format with competition coefficient estimates from model) observedandseededdensity.csv (seeding rates and observed seeding densities found in testspp.csv), Validation data: safe9_h2_poly_long.csv (validation data and competition coefficient estimates from model) 3. Additional related data collected that was not included in the current data package: N/A 4. Are there multiple versions of the dataset? No METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Main experiment data: Methods for collecting experiment data can be found in the related Ecological Applications article (DOI will be linked) Validation data: Methods for collecting validation can be found here: 10.2135/cropsci2016.01.0046. Only data from the second harvest that was harvested around 45 days after planting (DAP) were used. 2. Methods for processing the data: Most data processing took place in R. Some data manipulation took place in Excel, particularly adding the appropriate estimates of competition coefficients to the experimental data in the required structure. 3. Instrument- or software-specific information needed to interpret the data: R version 3.6.1 (2019-07-05) -- "Action of the Toes" 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: K. Ann Bybee-Finley, Matt Ryan, Stephane Cordeau, Severin Yvoz, Steven Mirsky ------------------------------- ------------------------------- MAIN EXPERIMENT DATA-SPECIFIC INFORMATION FOR: [testspp.csv] This is the main experimental data. Each row is a unique plot. Plots labeled 'RMS' in key2 and plots labeled 'none' were not included in the analysis. 1. Number of variables: 19 2. Number of cases/rows: 128 (including header) 3. Variable List: plot: plot number, seen on plot map year: year data collection took place key: seed treatments, decimal in front relates to the proportion (p) of recommended seeding rate and letter denotes species included key2: same thing as key, except that replicates are not differentiated spp: species contained in the plot. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. Combinations of letters indicate multiple species are in the plot. richness: number of species in the plot. nbspecies same as richness pM: proportion of the recommended monoculture rate for M seeded in the plot pS: proportion of the recommended monoculture rate for S seeded in the plot pH: proportion of the recommended monoculture rate for H seeded in the plot pC: proportion of the recommended monoculture rate for C seeded in the plot dC: density, the number of C plants per square meter observed in the plot bC: the dry matter biomass per square meter of C species observed in the plot dM: density, the number of M plants per square meter observed in the plot bM: the dry matter biomass per square meter of M species observed in the plot dS: density, the number of S plants per square meter observed in the plot bS: the dry matter biomass per square meter of S species observed in the plot dH: density, the number of H plants per square meter observed in the plot bH: the dry matter biomass per square meter of H species observed in the plot Missing data: 0.6M was excluded from dataset as it was missing density. ------------------------------ EXPERIMENT DATA DATA-SPECIFIC INFORMATION FOR: [longtestsppMonoBi.csv] testspp.csv was subset for 1- and 2-species mixtures and made long in Excel so that each row represents a focal species. Estimates from model included for monocultures and bicultures and generic column naming so that d1 is the density of the focal species and d2 is the other species in the biculture. This dataset was used to generate the R^2 values for the predicted and observed biomass of the monocultures and bicultures using a yield-density model. Observations missing information were excluded (0.6M was excluded from dataset as it was missing density.) 1. Number of variables: 14 2. Number of cases/rows: 128 (including header) 3. Variable List: ref: identifier column of treatment column and species column plot: plot number, seen on plot map treatment: species contained in the plot. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. Combinations of letters indicate multiple species are in the plot. species: the focal species. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. nbspecies number of species in the plot proportion: proportion of the recommended monoculture rate for the focal species (listed in the species column) seeded in the plot d1: density, plants per square meter of the focal species in the plot d2: density, plants per square meter of the other species in the plot if a biculture biomass: the dry matter biomass per square meter of the focal species observed in the plot b01:intercept generated from the yield-density model of the focal species b11:intraspecific competition coefficient generated from the yield-density model of the focal species b12:interspecific competition coefficient generated from the yield-density model of the focal species 4. Missing data codes: Monoculture treatments will have blank d2 and b12 columns ----------------------------------- DATA-SPECIFIC INFORMATION FOR: [kendallcorr.csv] This dataset is a subset of testspp.csv for 2-species mixtures and was used to calculate the kendall correlation between total biomass of a biculture and the niche differentiation index (NDI). Each row is a biculture plot. The NDI for each biculture was calculated by multiplying the two relative competitive abilities (RC) of a biculture together. The RC was calculated as a ratio of the intraspecific and interspecific competition coefficients that were generated from the yield-density models using the testspp.csv dataset. 1. Number of variables: 8 2. Number of cases/rows: 60 (including headers) 3. Variable List: spp: species contained in the plot. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. Combinations of letters indicate multiple species are in the plot. nbspecies: number of species in the plot bC: the dry matter biomass per square meter of C species observed in the plot bM: the dry matter biomass per square meter of M species observed in the plot bS: the dry matter biomass per square meter of S species observed in the plot bH: the dry matter biomass per square meter of H species observed in the plot biomass_total: sum of bM, bS, bH, and bC across a row. ndi: niche differentiation index of a biculture (unique for each spp) -------------------- DATA-SPECIFIC INFORMATION FOR: [tricoefflong.csv] This dataset is a subset of the 3- and 4-species mixtures from the testspp.csv data. It is used to generate biomass predictions for 3 and 4-species mixtures from biculture competition coefficients and intercepts. Each row contains the biomass of the focal species as well as the densities of all species in the mixture and the estimates of the intra- and interspecific competition coefficients and intercepts that are relevant to the mixture. These coefficients and intercepts were the model output using the testspp.csv file.The mixture MHC uses competition coefficients and intercepts from each species in monoculture and the output from the MH, MC, HC bicultures. For example, if M was the focal species: a0_mono, represents the model intercept for the focal species monoculture; a0_MH and a0_MC represent the model intercepts for the MH and MC biculture, respectively; i_mono represents the intraspecific competition coefficient for the focal species monoculture; intra_MH and intra_MC represent the intraspecific competition coefficients for the MH and MC bicultures, respectively and inter_MH and inter_MC represent the interspecific competition coefficients for the MH and MC bicultures respectively. 1. Number of variables: 34 2. Number of cases/rows: 81 (including headers) 3. Variable List: plot: plot number, seen on plot map year: year data collection took place key: seed treatments, decimal in front relates to the proportion (p) of recommended seeding rate and letter denotes species included key2: same thing as key, except that replicates are not differentiated mix: same thing as key2 spp: species contained in the plot. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. Combinations of letters indicate multiple species are in the plot. nbspecies number of species in the plot species: the focal species. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. proportion: proportion of the recommended monoculture rate for the focal species (listed in the species column) seeded in the plot density: plants per square meter of the focal species dC: density, the number of C plants per square meter observed in the plot dM: density, the number of M plants per square meter observed in the plot dS: density, the number of S plants per square meter observed in the plot dH: density, the number of H plants per square meter observed in the plot biomass: the dry matter biomass per square meter of the focal species observed in the plot a0_mono: intercept generated from the yield-density model of the focal species in monoculture a0_MS: intercept generated from the yield-density model of the focal species in the MS biculture and the focal species' monoculture a0_MH: intercept generated from the yield-density model of the focal species in the MH biculture and the focal species' monoculture a0_MC: intercept generated from the yield-density model of the focal species in the MC biculture and the focal species' monoculture a0_SH: intercept generated from the yield-density model of the focal species in the SH biculture and the focal species' monoculture a0_SC: intercept generated from the yield-density model of the focal species in the SC biculture and the focal species' monoculture a0_HC: intercept generated from the yield-density model of the focal species in the HC biculture and the focal species' monoculture i_mono: intraspecific competition coefficient generated from the yield-density model of the focal species in monoculture intra_MS: intraspecific competition coefficient generated from the yield-density model of the focal species in the MS biculture and the focal species' monoculture intra_MH: intraspecific competition coefficient generated from the yield-density model of the focal species in the MH biculture and the focal species' monoculture intra_MC: intraspecific competition coefficient generated from the yield-density model of the focal species in the MC biculture and the focal species' monoculture intra_SH: intraspecific competition coefficient generated from the yield-density model of the focal species in the SH biculture and the focal species' monoculture intra_SC: intraspecific competition coefficient generated from the yield-density model of the focal species in the SC biculture and the focal species' monoculture intra_HC: intraspecific competition coefficient generated from the yield-density model of the focal species in the HC biculture and the focal species' monoculture inter_MS: interspecific competition coefficient generated from the yield-density model of the focal species in the MS biculture and the focal species' monoculture inter_MH: interspecific competition coefficient generated from the yield-density model of the focal species in the MH biculture and the focal species' monoculture inter_MC: interspecific competition coefficient generated from the yield-density model of the focal species in the MC biculture and the focal species' monoculture inter_SH: interspecific competition coefficient generated from the yield-density model of the focal species in the SH biculture and the focal species' monoculture inter_SC: interspecific competition coefficient generated from the yield-density model of the focal species in the SC biculture and the focal species' monoculture inter_HC: interspecific competition coefficient generated from the yield-density model of the focal species in the HC biculture and the focal species' monoculture 4. Missing data codes: Cells were left blank if species were not present. No observations were missing except for 0.6M. ------------------------------------- DATA-SPECIFIC INFORMATION FOR: [observedandseededdensity.csv] This dataset was used to calculate the figures describing the differences of seeded density per sq meter and the density that was observed. Each row is a species in a mixture. It is a subset of the testspp.csv dataset made long paired with intended seeded density. Observations missing information were excluded (0.6M was excluded from dataset as it was missing density.) 1. Number of variables: 11 2. Number of cases/rows: 208 (including headers) 3. Variable List: plot: plot number, seen on plot map key2: seed treatments, decimal in front relates to the proportion (p) of recommended seeding rate and letter denotes species included. Replicates of 3 and 4 species mixtures are not differentiated. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. mix: describes the species present in each plot and is similar to key2, except that seed proportions are not specified. spp: focal species of the mix. richness: number of species in the plot den_obs: the observed number of plants per square meter of the focal species in the plot den_seeding: the intended number of seeds planted per square meter that was seeded of the focal species in the plot dC: density, the observed number of C plants per square meter observed in the plot dM: density, the observed number of M plants per square meter observed in the plot dS: density, the observed number of S plants per square meter observed in the plot dH: density, the observed number of H plants per square meter observed in the plot ------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [seed_costs.csv] This dataset was used to calculate seed costs for different seeding rate combinations. Each row is a different species and provides general information about seeding rate costs. 1. Number of variables: 6 2. Number of cases/rows: 5 (including headers) 3. Variable List: species: M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. germination_rate: germination rate of seed found on seed tags for 2014. It is used to calculate the adjusted seeding rate so that plots per planted on pure live seed basis. adjkg_per_ha: seeding rate kilograms per hectare of the recommended monoculture rate adjusted on a pure live seed basis seeds_per_m2: number of seeds per square meter dollar_per_kg: cost in USD of seed in 2014 by kilogram dollar_per_seed: cost in USD of one seed ------------------------------------------ ------------------------------------------ VALIDATION DATA ------------------------------------------ DATA-SPECIFIC INFORMATION FOR: [safe9_h2_poly_long.csv] This dataset was used to validate the competition coefficients determined in the main experiment. The dataset structure takes a similar format to tricoefflong.csv but the density and biomass data are from a related set of experiments that used the same species, seeding rates, and sampling protocols and the competition coefficients and intercept estimates were added. Each row in the dataset represents a focal species in a 3- or 4-species mixture across 9 site-years. The validation experiment was conducted in 2013 and 2014 at (i) the Cornell Musgrave Research Farm (Aur)--the same as the main experiment of this repository entry; (ii) the Cornell Willsboro Research Farm (Wil) in Willsboro, NY (44°21’ N, 73°23’ W); and (iii) the USDA–ARS Beltsville Agricultural Research Center (Bel) in Beltsville, MD (39°02’ N, 76°54’ W). The Bel location included two different field sites in 2013, and the Aur and Wil locations included two different field sites in 2014. Different field sites within a location were planted a month apart, as indicated by “E” (for early) and “L” (for late). Thus, the validation experiment had nine site-years. A randomized complete block design was used (except for the BelL13 site-year) with four to five blocks per site-year for a total of 199 plots. using the same protocol described above. More details about the validation experiment can be found in Functional Diversity in Summer Annual Grass and Legume Intercrops in the Northeastern United States: doi: 10.2135/cropsci2016.01.0046. 1. Number of variables: 38 2. Number of cases/rows: 638 (including headers) 3. Variable List: id:a unique identifier for each plot which combines the siteharvest, block, and plot site:indicates site-years Cornell Musgrave Research Farm (Aur); (ii) the Cornell Willsboro Research Farm (Wil) in Willsboro, NY (44°21’ N, 73°23’ W); and (iii) the USDA–ARS Beltsville Agricultural Research Center (Bel) in Beltsville, MD (39°02’ N, 76°54’ W). The Bel location included two different field sites in 2013, and the Aur and Wil locations included two different field sites in 2014. Different field sites within a location were planted a month apart, as indicated by “E” (for early) and “L” (for late). siteharvest: site with the harvest number. The second harvest (2) of the related set of experiments was most similar to the growing length of the main experiment so this was the data was used for validation. sitenspecies: identifier combines the site with the focal species year: year when experiment was planted and biomass was sampled dap: days after planting indicating when biomass was sampled block: treatments were repeated across blocks that represent replicates. The BelL13 site-year was unblocked plot: plot number, depending on the site-year plot number might be unique or repeated per block treatment: describes the species present in each plot. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea species:the focal species of the mix. M is pearl millet, S is sorghum sudangrass, H is sunn hemp, C is cowpea. density: the observed number of plants per square meter of the focal species in the plot dC: density, the observed number of C plants per square meter observed in the plot dM: density, the observed number of M plants per square meter observed in the plot dS: density, the observed number of S plants per square meter observed in the plot dH: density, the observed number of H plants per square meter observed in the plot biomass: the dry matter biomass per square meter of the focal species observed in the plot wb: dry matter biomass per square meter of the weeds observed in the plot tb: total dry matter biomass per square meter of all crop species observed in the plot a0_mono: intercept generated in the main experiment from the yield-density model of the focal species in monoculture a0_MS: intercept generated in the main experiment from the yield-density model of the focal species in the MS biculture and the focal species' monoculture a0_MH: intercept generated in the main experiment from the yield-density model of the focal species in the MH biculture and the focal species' monoculture a0_MC: intercept generated in the main experiment from the yield-density model of the focal species in the MC biculture and the focal species' monoculture a0_SH: intercept generated in the main experiment from the yield-density model of the focal species in the SH biculture and the focal species' monoculture a0_SC: intercept generated in the main experiment from the yield-density model of the focal species in the SC biculture and the focal species' monoculture a0_HC: intercept generated in the main experiment from the yield-density model of the focal species in the HC biculture and the focal species' monoculture i_mono: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in monoculture intra_MS: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the MS biculture and the focal species' monoculture intra_MH: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the MH biculture and the focal species' monoculture intra_MC: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the MC biculture and the focal species' monoculture intra_SH: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the SH biculture and the focal species' monoculture intra_SC: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the SC biculture and the focal species' monoculture intra_HC: intraspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the HC biculture and the focal species' monoculture inter_MS: interspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the MS biculture and the focal species' monoculture inter_MH: interspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the MH biculture and the focal species' monoculture inter_MC: interspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the MC biculture and the focal species' monoculture inter_SH: interspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the SH biculture and the focal species' monoculture inter_SC: interspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the SC biculture and the focal species' monoculture inter_HC: interspecific competition coefficient generated in the main experiment from the yield-density model of the focal species in the HC biculture and the focal species' monoculture