This readme.txt file was generated on 20241123 by Laura Williams Recommended citation for the data: Williams, L.J., Kovach, K.R., Guzman Q., J.A., Stefanski, A., Bermudez, R., Butler, E.E., Glenn-Stone, C., Hajek, P., Klama, J., Moradi, A., Park, M.H., Scherer-Lorenzen, M., Townsend, P.A., Reich, P.B., Cavender-Bares, J., and Schuman, M.C. (YYYY) Data and code for spectral canopy transmittance in diverse tree communities. Retrieved from the Data Repository for the University of Minnesota (DRUM), ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data and code for spectral canopy transmittance in diverse tree communities 2. Author Information Principal Investigator Contact Information Name: Laura J. Williams Institution: Western Sydney University Address: Hawkesbury Institute for the Environment Science Road, Richmond, NSW 2753, Australia Email: laura.williams@westernsydney.edu.au ORCID: 0000-0003-3555-4778 Associate or Co-investigator Contact Information Name: Kyle Kovach Institution: University of Wisconsin-Madison Address: 1630 Linden Drive, Madison, WI 53706, USA Email: kyle.kovach@wisc.edu Associate or Co-investigator Contact Information Name: J. Antonio Guzmàn Q. Institution: Harvard University Address: 22 Divinity Avenue, Cambridge, MA 02138, USA Email: aguzman@fas.harvard.edu Associate or Co-investigator Contact Information Name: Artur Stefanski Institution: University of Wisconsin-Stevens Point Address: 2100 Main Street, Stevens Point, WI 54481, USA Email: astefans@uwsp.edu Associate or Co-investigator Contact Information Name: Raimundo Bermudez Institution: University of Minnesota Address: Green Hall, 1530 Cleveland Avenue N, St Paul, MN 55108, USA Email: bermu019@umn.edu Associate or Co-investigator Contact Information Name: Ethan Butler Institution: University of Minnesota Address: Green Hall, 1530 Cleveland Avenue N, St Paul, MN 55108, USA Associate or Co-investigator Contact Information Name: Catherine Glenn-Stone Institution: University of Minnesota Address: Green Hall, 1530 Cleveland Avenue N, St Paul, MN 55108 Email: glenn130@umn.edu Associate or Co-investigator Contact Information Name: Peter Hajek Institution: University of Freiburg Address: Schänzlestrausse 1, D-79104 Freiburg, Germany Email: peter.hajek@biologie.uni-freiburg.de Associate or Co-investigator Contact Information Name: Johanna Klama Institution: University of Freiburg Address: Schänzlestrausse 1, D-79104 Freiburg, Germany Associate or Co-investigator Contact Information Name: Aboubakr Moradi Institution: University of Zurich Address: Winterthurerstrasse 190, CH-8057 Zürich, Switzerland Associate or Co-investigator Contact Information Name: Maria Park Institution: Harvard University Address: 22 Divinity Avenue, Cambridge, MA 02138, USA Email: mariap@umn.edu Associate or Co-investigator Contact Information Name: Michael Scherer-Lorenzen Institution: University of Freiburg Address: Schänzlestrausse 1, D-79104 Freiburg, Germany Email: michael.scherer@biologie.uni-freiburg.de Associate or Co-investigator Contact Information Name: Philip Townsend Institution: University of Freiburg Address: 1630 Linden Drive, Madison, WI 53706, USA Email: ptownsend@wisc.edu Associate or Co-investigator Contact Information Name: Peter B. Reich Institution: University of Minnesota Address: Green Hall, 1530 Cleveland Ave. N, St Paul, MN 55108 Email: preich@umn.edu Associate or Co-investigator Contact Information Name: Jeannine Cavender-Bares Institution: Harvard University Address: 22 Divinity Avenue, Cambridge, MA 02138, USA Email: jcavender@fas.harvard.edu Associate or Co-investigator Contact Information Name: Meredith Schuman Institution: University of Zurich Address: Winterthurerstrasse 190, CH-8057 Zürich, Switzerland Email: meredithchristine.schuman@uzh.ch ORCID: 0000-0003-3159-3534 3. Date published or finalized for release: 4. Date of data collection (YYYYMMDD) 20210701 - 20210825 5. Geographic location of data collection (where was data collected?): Data was collected at the International Diversity Experiment Network with Trees (IDENT) sites at the Cloquet Forestry Center (Minnesota, USA, 46°40’46”N 92°31’12”W), Freiburg (Freiburg, Germany, 48°01’10” N, 7°49’37” E), and the Forests And Biodiversity experiment (FAB-1) at Cedar Creek Ecosystem Science Reserve (East Bethel, MN, USA, 45°24’17” N, 93°11’25” W). 6. Information about funding sources that supported the collection of the data: This research was supported by the NSF Biology Integration Institute ASCEND (Advancing Spectral Biology in Changing Environments to understand Diversity; NSF-DBI- 2021898). Additional funding sources included NSF Macrosystems Biology and NEON-Enabled Science (MSB-NES) award DEB 1638720, University of Freiburg (Innovationsfonds Forschung), Long-Term Ecological Research program at Cedar Creek Ecosystem Science Reserve (NSF LTER 1831944), the NOMIS foundation grant Remotely Sensing Ecological Genomics. 7. Overview of the data (abstract): Light may shape forest function not only as a source of energy or a cause of stress but also as a context cue: plant photoreceptors can detect specific wavelengths of light, and plants use this information to assess their neighborhoods and adjust their patterns of growth and allocation. Here, we examined how the spectral profile of light (350-2200 nm) transmitted through tree canopies differs among communities within three tree diversity experiments on two continents (200 plots each planted with one to 12 tree species). This repository includes data and metadata on canopy transmittance and leaf area index (LAI) measured on these plots as well as leaf-level transmittance measured for each species in monoculture plots. Data processing and analysis code is also provided. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: http://creativecommons.org/licenses/by-sa/4.0/ 2. Links to publications that cite or use the data: Williams, L.J., Kovach, K.R., Guzman Q., J.A., Stefanski, A., Bermudez, R., Butler, E.E., Coq--Etchegaray, D., Glenn-Stone, C., Hajek, P., Klama, J., Medlyn, B.E., Messier, C., Moradi, A., Paquette, A., Park, M.H., Scherer-Lorenzen, M., Townsend, P.A., Reich, P.B., Cavender-Bares, J., Schuman, M.C. (accepted) Tree diversity shapes the spectral signature of light transmittance in developing forests. Ecology. 3. Was data derived from another source? No 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- This dataset comprises a series of folders and sub-folders that contain the following: (1) data files (in the folder: Data), (2) example R code to process raw spectrometer files (Code/R_processing), (3) example R code for data analysis (Code/R_analysis), and (4) supplementary figures used to assess data processing and outlier identification (Figures_data-processing). 1. Folder: Data Short description: This folder contains data files. 1.1. File List A. Filename: FAB1_transmittance_svc-asd_outliers-identified.csv Short description: Individual measurements of canopy transmittance at the FAB-1 experiment. B. Filename: IDENT-Cloquet_transmittance_svc-asd_outliers-identified.csv Short description: Individual measurements of canopy transmittance at the IDENT-Cloquet experiment. C. Filename: IDENT-Freiburg_transmittance_svc-asd_outliers-identified.csv Short description: Individual measurements of canopy transmittance at the IDENT-Freiburg experiment. D. Filename: LAI.csv Short description: Leaf area index (LAI) measurements at the FAB-1, IDENT-Cloquet and IDENT-Freiburg experiments. E. Filename: Leaf_transmittance_monoculture_means.csv Short description: Measurements of leaf-level transmittance from the FAB-1, IDENT-Cloquet and IDENT-Freiburg experiments. F. Filename: Leaf_transmittance_CWM.csv Short description: Community-weighted mean (CWM) values of leaf-level transmittance for forest plots at the FAB-1, IDENT-Cloquet and IDENT-Freiburg experiments. This was the dataframe of leaf-level transmtitance used in data analyses. G. Filename: Plot-composition-diversity-lookup.csv Short description: The species composition and diversity of forest plots at the FAB-1, IDENT-Cloquet and IDENT-Freiburg experiments. H. Filename: Species_BA_proportions_Cloquet_2021.csv Short description: Matrix of the proportion of live basal area per species in forest plots at the IDENT-Cloquet experiment; measured at the end of the growing season in 2021. I. Filename: Species_BA_proportions_FAB1_2021.csv Short description: Matrix of the proportion of live basal area per species in forest plots at the FAB-1 experiment; measured at the end of the growing season in 2021. J. Filename: Species_BA_proportions_Freiburg_2021.csv Short description: Matrix of the proportion of live basal area per species in forest plots at the IDENT-Freiburg experiment; measured at the end of the growing season in 2021. K. Filename: Species_planted_proportions_Cloquet.csv Short description: Matrix of the proportion of trees of each species initially planted in forest plots at the IDENT-Cloquet experiment. L. Filename: Species_planted_proportions_FAB1.csv Short description: Matrix of the proportion of trees of each species initially planted in forest plots at the FAB-1 experiment. M. Filename: Species_planted_proportions_Freiburg.csv Short description: Matrix of the proportion of trees of each species initially planted in forest plots at the IDENT-Freiburg experiment. N. Filename: Canopy_transmittance.txt Short description: The mean canopy transmittance measured on each forest plot at the IDENT-Cloquet, IDENT-Freiburg and FAB-1 experiments. This was the dataframe of canopy transmittance used in data analyses. O. Filename: NBE_canopy_transmittance.txt Short description: The net biodiversity effect on canopy transmittance on each mixed-species forest plot at the IDENT-Cloquet, IDENT-Freiburg and FAB-1 experiments. This was the dataframe of net biodiversity effects on canopy transmittance used in data analyses. 1.2. Relationship between files: Files 'A', 'B' and 'C' contain individual canopy transmittance measurements with identified erroneous readings and outliers flagged. These flagged readings were removed and measurements averaged to give a mean canopy transmittance value for each canopy height on each forest plot; these mean values are given in File 'N'. File 'E' contains leaf-level transmittance for each species in monoculture; these values are combined with the species composition of forest plots to give the community-weighted mean leaf transmittance values presented in File 'F'. Files 'G', 'H' , 'I', 'J', 'K', 'L' and 'M' give information on the species composition of forest plots. 3. Folder: Code/R_processing Short description: This folder contains R scripts to process raw data files from spectrometers and subsequently calculate canopy transmittance and leaf-level transmittance. 3.1. File List A. Filename: 01-interpolate_coefficients.R Short description: R script to interpolate correction coefficients through time. B. Filename: 01-IntSph_read-process.R Short description: R script to read and process measurements of leaf-level transmittance from integrating sphere measurements. C. Filename: 01-matching_files.R Short description: R script to match several data frames by date and time. D. Filename: 01-read_spectrometer.R Short description: R script to read and process files from ASD and SVC spectrometers. E. Filename: 02-nearest_record.R Short description: R script to take output from 'C' (01-matching_files.R) and search for the nearest record between sensors. F. Filename: 03-get_coefficients.R Short description: R script to compute the coefficients of difference between sensors. G. Filename: 03-get_transmittance.R Short description: R script to take indices of nearest record between sensors (output from 'E' '02-nearest_record.R') and estimate the canopy transmittance spectra from target and reference spectrometers. H. Filename: 03-visual_assessment.R Short description: R script to produce several plots of transmittance to visually assess the quality of the measurement. I. Filename: asd_files.R Short description: R function to extract information of .asd files. J. Filename: matching.R Short description: R function to match file frames by date and time. K. Filename: read_asd.R Short description: R function to extract information of .asd files. L. Filename: read_svc.R Short description: R function to extract information of .sig files. M. Filename: sig_files.R Short description: R function to extract information of .sig files from integrating sphere. N. Filename: svc_files.R Short description: R function to extract information of .sig files. 2.2. Relationship between files: Some R scripts depend on output or functions contained within others; these are called upon ('sourced') when needed. For example, Files 'I' to 'N' are R scripts with functions that are variously called upon in the preceding R scripts (Files 'A' to 'H'). 3. Folder: Code/R_analysis Short description: R scripts for data analysis and graphing. 3.1. File List A. Filename: A1.1_calculating-mean-canopy-transmittance.R Short description: R script to take raw canopy transmittance values, calculate a mean canopy transmittance value per plot and canopy height, and combine with LAI data (i.e., creates file 1.1.N 'Canopy_transmittance.txt' from files 1.1.A, 1.1.B, 1.1.C, 1.1.D) B. Filename: A1.2_calculating-NBE-canopy-transmittance.R Short description: R script to take mean canopy transmittance values per plot (file 1.1.N 'Canopy_transmittance.txt') and species' planted abundances (files 1.1.K, 1.1.L, 1.1.M) to calculate the net biodiversity effect on canopy transmittance (i.e., creates file 1.1.O 'NBE_canopy_transmittance.txt') C. Filename: A2.1_initial-plots.R Short description: R script to create plots of canopy transmittance spectra (Figure 2a-f in associated paper). D. Filename: A2.2_initial-plots-NBE.R Short description: R script to create plots of the net biodiversity effect on canopy transmittance (Figure 2g-i in associated paper). E. Filename: A3.1_linear-models.R Short description: R script with examples of linear models reported in associated paper. 4. Folder: Figures_data-processing Short description: This folder includes figures of canopy transmittance spectra to illustrate which transmittance spectra were included or excluded from analysis. 4.1 File List A. Filename: Cloquet_plots_mean-transmittance.pdf Short description: Plots of canopy transmittance measured on forest plots at the IDENT-Cloquet experiment, showing included and excluded spectra. B. Filename: FAB1_plots_mean-transmittance.pdf Short description: Plots of canopy transmittance measured on forest plots at the FAB-1 experiment, showing included and excluded spectra. C. Filename: Freiburg_plots_mean-transmittance.pdf Short description: Plots of canopy transmittance measured on forest plots at the IDENT-Freiburg experiment, showing included and excluded spectra. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Methods are documented in the following publication: Williams et al. Tree diversity shapes the spectral signature of light transmittance in developing forests. Ecology. 2. Methods for processing the data: See publication above and R scripts listed above (3. Code/R_processing) 3. Instrument- or software-specific information needed to interpret the data: N/A 4. Standards and calibration information, if appropriate: See publication above. 5. Environmental/experimental conditions: See publication above. 6. Describe any quality-assurance procedures performed on the data: See publication above. 7. People involved with sample collection, processing, analysis and/or submission: Kyle Kovach, Artur Stefanski, Laura Williams, Raimundo Bermudez, Maria Park, Catherine Glenn-Stone, Ethan Butler and Lauren Latter collected data in the field at FAB-1. Kyle Kovach, Artur Stefanski, Laura Williams, Raimundo Bermudez, and Catherine Glenn-Stone, with assistance from B4WarmED interns, collected data in the field at IDENT-Cloquet. Jeannine Cavender-Bares, Meredith Schuman, Johanna Klama, Peter Hajek, Aboubakr Moradi, and Michael Scherer-Lorenzen, with assistance from Cheng Li and Nemish Murawat, collected data in the field at IDENT-Freiburg. J. Antonio Guzman Q. wrote R scripts for data processing. Laura Williams wrote R scripts for data analysis with input from the other data contributors. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 A FAB1_transmittance_svc-asd_outliers-identified.csv ----------------------------------------- 1. Number of variables: 2161 2. Number of cases/rows: 211 3. Missing data codes: N/A 4. Variable List A. Name: target_file Description: File name of the target spectrometer reading. B. Name: ID Description: Identification code for the location of measurement, as follows: experiment (FAB1), plot (number), species composition (four-letter species codes, as listed below) and canopy height (b = below canopy [c. 0.5 m above ground], m = mid-canopy [c. 2 m above ground]). Species codes: ACNE = Acer negundo ACRU = Acer rubrum BEPA = Betula papyrifera JUVI = Juniperus virginiana PIBA = Pinus banksiana PIRE = Pinus resinosa PIST = Pinus strobus QUAL = Quercus alba QUEL = Quercus ellipsoidalis QUMA = Quercus macrocarpa QURU = Quercus rubra TIAM = Tilia americana C. Name: Date_manual Description: Date of measurement (YYYYMMDD) recorded manually. D. Name: date Description: Date of measurement (DD/M/YYYY) recorded by the target spectrometer. E. Name: time Description: Time of measurement recorded by the target spectrometer. F. Name: target Description: File index of the target spectrometer reading. G. Name: reference Description: File index of the reference spectrometer reading. H. Name: time difference Description: Time difference between the target spectrometer reading and the reference spectrometer reading in seconds. I. Name: reference_file Description: File name of the target spectrometer reading. J-CEB. Names: X350 to X2500 Description: Fraction of irradiance of a given wavelength transmitted through the canopy (e.g., X350 = transmittance at 350 nm) CEC. Name: Excluded Description: Canopy transmittance spectrum identified as erroneous and to be excluded. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 B IDENT-Cloquet_transmittance_svc-asd_outliers-identified.csv ----------------------------------------- 1. Number of variables: 2161 2. Number of cases/rows: 942 3. Missing data codes: N/A 4. Variable List A. Name: target_file Description: File name of the target spectrometer reading. B. Name: ID Description: Identification code for the location of measurement, as follows: block (letter code), plot (letter-number code), species composition (four-letter species codes, as listed below) and canopy height (b = below canopy [c. 0.5 m above ground], m = mid-canopy [c. 2 m above ground]). Species codes: ACPL = Acer platanoides ACSA = Acer saccharum BEPA = Betula papyrifera BEPE = Betula pendula LADE = Larix decidua LALA = Larix laricina PIAB = Picea abies PIGL = Picea glauca PIST = Pinus strobus PISY = Pinus sylvestris QURO = Quercus robur QURU = Quercus rubra C. Name: Date_manual Description: Date of measurement (YYYYMMDD) recorded manually. D. Name: date Description: Date of measurement (DD/M/YYYY) recorded by the target spectrometer. E. Name: time Description: Time of measurement recorded by the target spectrometer. F. Name: target Description: File index of the target spectrometer reading. G. Name: reference Description: File index of the reference spectrometer reading. H. Name: time difference Description: Time difference between the target spectrometer reading and the reference spectrometer reading in seconds. I. Name: reference_file Description: File name of the target spectrometer reading. J-CEB. Names: X350 to X2500 Description: Fraction of irradiance of a given wavelength transmitted through the canopy (e.g., X350 = transmittance at 350 nm) CEC. Name: Excluded Description: Canopy transmittance spectrum identified as erroneous and to be excluded. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 C IDENT-Freiburg_transmittance_svc-asd_outliers-identified.csv ----------------------------------------- 1. Number of variables: 2161 2. Number of cases/rows: 479 3. Missing data codes: N/A 4. Variable List A. Name: target_file Description: File name of the target spectrometer reading. B. Name: ID Description: Identification code for the location of measurement, as follows: block (letter code), plot (letter-number code), species composition (four-letter species codes, as listed below) and canopy height (b = below canopy [c. 0.5 m above ground], m = mid-canopy [c. 2 m above ground]). Species codes: ACPL = Acer platanoides ACSA = Acer saccharum BEPA = Betula papyrifera BEPE = Betula pendula LADE = Larix decidua LALA = Larix laricina PIAB = Picea abies PIGL = Picea pungens var. glauca PIST = Pinus strobus PISY = Pinus sylvestris QURO = Quercus robur QURU = Quercus rubra C. Name: Date_manual Description: Date of measurement (YYYYMMDD) recorded manually. D. Name: date Description: Date of measurement (DD/M/YYYY) recorded by the target spectrometer. E. Name: time Description: Time of measurement recorded by the target spectrometer. F. Name: target Description: File index of the target spectrometer reading. G. Name: reference Description: File index of the reference spectrometer reading. H. Name: time difference Description: Time difference between the target spectrometer reading and the reference spectrometer reading in seconds. I. Name: reference_file Description: File name of the target spectrometer reading. J-CEB. Names: X350 to X2500 Description: Fraction of irradiance of a given wavelength transmitted through the canopy (e.g., X350 = transmittance at 350 nm) CEC. Name: Excluded Description: Canopy transmittance spectrum identified as erroneous and to be excluded. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 D LAI.csv ----------------------------------------- ID LAI_allloc LAI_specloc LAI_allloc_corrected LAI_specloc_corrected 1. Number of variables: 5 2. Number of cases/rows: 400 3. Missing data codes: N/A 4. Variable List A. Name: ID Description: Identification code for the location of measurement (matches 'ID' variable in other data files) B. Name: LAI_allloc Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., "LAI-effective"). One value is given per canopy height and plot, these values are the average of measurements taken at four or five locations per plot and canopy height (for details see associated publication, Appendix S1: Figure S1). C. Name: LAI_specloc Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., "LAI-effective"). One value is given per canopy height and plot, this is the value measured at the same location as the canopy transmittance measurement (for details see associated publication, Appendix S1: Figure S1). D. Name: LAI_allloc_corrected Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) corrected for within-shoot clumping (i.e., our best estimate of the true LAI). One value is given per canopy height and plot, these values are the average of measurements taken at four or five locations per plot and canopy height (for details see associated publication, Appendix S1: Figure S1). E. Name: LAI_specloc_corrected Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., our best estimate of the true LAI). One value is given per canopy height and plot, this is the value measured at the same location as the canopy transmittance measurement (for details see associated publication, Appendix S1: Figure S1). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 E Leaf_transmittance_monoculture_means.csv ----------------------------------------- 1. Number of variables: 2154 2. Number of cases/rows: 36 3. Missing data codes: N/A 0 denotes no transmittance 4. Variable List A. Name: Site Description: Experimental site Cloquet = IDENT-Cloquet FAB1 = FAB-1 Freiburg = IDENT-Freiburg B. Name: Species Description: Four-letter species code: ACNE = Acer negundo ACPL = Acer platanoides ACRU = Acer rubrum ACSA = Acer saccharum BEPA = Betula papyrifera BEPE = Betula pendula JUVI = Juniperus virginiana LADE = Larix decidua LALA = Larix laricina PIAB = Picea abies PIBA = Pinus banksiana PIGL = Picea glauca (or Picea pungens var. glauca at IDENT-Freiburg) PIRE = Pinus resinosa PIST = Pinus strobus PISY = Pinus sylvestris QUAL = Quercus alba QUEL = Quercus ellipsoidalis QUMA = Quercus macrocarpa QURO = Quercus robur QURU = Quercus rubra TIAM = Tilia americana C. Name: X350 to X2500 Description: Proportional leaf transmittance at a given wavelength (e.g., X350 = transmittance at 350 nm). These values are the mean leaf-level transmittance per species from leaves collected at the top, mid and bottom of the crown of trees of each species growing in monoculture plots. C. Name: RtoFR Description: The ratio of red to far-red leaf-level transmittance (i.e., 660 nm / 730 nm). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 F Leaf_transmittance_CWM.csv ----------------------------------------- 1. Number of variables: 2154 2. Number of cases/rows: 754 3. Missing data codes: N/A 0 denotes no transmittance 4. Variable List A. Name: Site_names Description: Experimental site Cloquet = IDENT-Cloquet FAB1 = FAB-1 Freiburg = IDENT-Freiburg B. Name: Plot Description: Unique plot code (see Plot-composition-diversity-lookup.csv for details) C. Name: X350 to X2500 Description: Community-weighted mean values of leaf transmittance at a given wavelength (e.g., X350 = transmittance at 350 nm). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 G Plot-composition-diversity-lookup.csv ----------------------------------------- 1. Number of variables: 7 2. Number of cases/rows: 1128 3. Missing data codes: N/A 4. Variable List A. Name: ID Description: Identification code (concatenation of Plot and Mix; Site, Plot and Mix for the FAB-1 experiment) B. Name: Site Description: Experimental site Cloquet = IDENT-Cloquet Freiburg = IDENT-Freiburg FAB1 = FAB-1 C. Name: Plot Description: Plot code, unique for each experimental site D. Name: Mix Description: Four-letter species codes indicating the species planted on the forest plot. See above for species codes. 6 NA = 6 North American species (ACSA, BEPA, LALA, PIGL, PIST, QURU) 6 EU = 6 European species (ACPL, BEPE, LADE, PIAB, PISY, QURO) 6 angio = 6 angiosperm species (ACPL, ACSA, BEPA, BEPE, QURO, QURU) 6 gymno = 6 gymnosperm species (LADE, LALA, PIAB, PIGL, PIST, PISY) NAangioEUgymno = 6 species (ACSA, BEPA, QURU, LADE, PIAB, PISY) NAgymnoEUangio = 6 species (ACPL, BEPE, QURO, LALA, PIGL, PIST) E. Name: SR Description: Species richness (number of species planted on the forest plot). F. Name: AngioGymnoMix Description: Whether trees on the forest plot are angiosperm species, gymnosperm species or a mixture of angiosperm and gymnosperm species. A = angiosperm species G = gymnosperm species M = mixture of angiosperm and gymnosperm species G. Name: CWM_shtol_pa Description: Community weighted mean of shade tolerance (from Niinemets Ü, Valladares F. 2006. Tolerance to Shade, Drought, and Waterlogging of Temperate Northern Hemisphere Trees and Shrubs. Ecological Monographs 76: 521–547) based on the proportion of trees planted per species on the forest plot. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 H Species_BA_proportions_Cloquet_2021.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 192 3. Missing data codes: N/A 4. Variable List A. Name: Plot Description: Unique plot code B. Name: Four letter codes of species names (ACPL, ACSA, BEPA, BEPE, LADE, LALA, PIAB, PIGL, PIST, PISY, QURO, QURU) Description: The proportion of live basal area on a plot that belongs to each species. Basal area measured at the end of the growing season in 2021. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 I Species_BA_proportions_FAB1_2021.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 140 3. Missing data codes: N/A 4. Variable List A. Name: Plot Description: Unique plot code B. Name: Four letter codes of species names (ACNE, ACRU, BEPA, JUVI, PIBA, PIRE, PIST, QUAL, QUEL, QUMA, QURU, TIAM) Description: The proportion of live basal area on a plot that belongs to each species. Basal area measured at the end of the growing season in 2021. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 J Species_BA_proportions_Freiburg_2021.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 415 3. Missing data codes: N/A 4. Variable List A. Name: Plot Description: Unique plot code. B. Name: Four letter codes of species names (ACPL, ACSA, BEPA, BEPE, LADE, LALA, PIAB, PIGL, PIST, PISY, QURO, QURU) Description: The proportion of live basal area on a plot that belongs to each species. Basal area measured at the end of the growing season in 2021. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 K Species_planted_proportions_Cloquet.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 192 3. Missing data codes: N/A 4. Variable List A. Name: Plot Description: Unique plot code. B. Name: Four letter codes of species names (ACPL, ACSA, BEPA, BEPE, LADE, LALA, PIAB, PIGL, PIST, PISY, QURO, QURU) Description: For each plot, the proportion of trees planted of each species. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 L Species_planted_proportions_FAB1.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 140 3. Missing data codes: N/A 4. Variable List A. Name: Plot Description: Unique plot code. B. Name: Four letter codes of species names (ACNE, ACRU, BEPA, JUVI, PIBA, PIRE, PIST, QUAL, QUEL, QUMA, QURU, TIAM) Description: For each plot, the proportion of trees planted of each species. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 M Species_planted_proportions_Freiburg.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 415 3. Missing data codes: N/A 4. Variable List A. Name: Plot Description: Unique plot code. B. Name: Four letter codes of species names (ACPL, ACSA, BEPA, BEPE, LADE, LALA, PIAB, PIGL, PIST, PISY, QURO, QURU) Description: For each plot, the proportion of trees planted of each species. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 N Canopy_transmittance.txt ----------------------------------------- 1. Number of variables: 1584 2. Number of cases/rows: 400 3. Missing data codes: N/A 4. Variable List A. Name: ID Description: Identification code for the location of measurement (matches 'ID' variable in other data files). B. Name: Site Description: Experimental site. Cloquet = IDENT-Cloquet FAB1 = FAB-1 Freiburg = IDENT-Freiburg C. Name: Plot Description: Unique plot code D. Name: Mix Description: Four-letter species codes indicating the species planted on the forest plot. See above for species codes. 6 NA = 6 North American species (ACSA, BEPA, LALA, PIGL, PIST, QURU) 6 EU = 6 European species (ACPL, BEPE, LADE, PIAB, PISY, QURO) 6 angio = 6 angiosperm species (ACPL, ACSA, BEPA, BEPE, QURO, QURU) 6 gymno = 6 gymnosperm species (LADE, LALA, PIAB, PIGL, PIST, PISY) E. Name: CanopyHt Description: Canopy height b = below canopy (c. 0.5 m above ground) m = mid-canopy (c. 2 m above ground) F. Name: BlMix Description: Unique code for each plot, concatenation of the experimental Block (or plot) and Mix G. Name: LAI_allloc Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., "LAI-effective"). One value is given per canopy height and plot, these values are the average of measurements taken at four or five locations per plot and canopy height (for details see associated publication, Appendix S1: Figure S1). H. Name: LAI_specloc Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., "LAI-effective"). One value is given per canopy height and plot, this is the value measured at the same location as the canopy transmittance measurement (for details see associated publication, Appendix S1: Figure S1). I. Name: LAI_allloc_corrected Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) corrected for within-shoot clumping (i.e., our best estimate of the true LAI). One value is given per canopy height and plot, these values are the average of measurements taken at four or five locations per plot and canopy height (for details see associated publication, Appendix S1: Figure S1). J. Name: LAI_specloc_corrected Description: Leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., our best estimate of the true LAI). One value is given per canopy height and plot, this is the value measured at the same location as the canopy transmittance measurement (for details see associated publication, Appendix S1: Figure S1). K. Name: Wavelength (X350 to X2200) Description: Fraction of irradiance of a given wavelength transmitted through the canopy (e.g., X350 = transmittance at 350 nm) L. Name: transm_par Description: Fraction of photosynthetically active radiation (PAR, 400-700 nm) transmitted through the canopy. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 1.1 O NBE_canopy_transmittance.txt ----------------------------------------- 1. Number of variables: 1587 2. Number of cases/rows: 250 3. Missing data codes: N/A ID Site Plot Mix CanopyHt BlMix NBE_LAI_allloc NBE_LAI_specloc NBE_LAI_allloc_corrected NBE_LAI_specloc_corrected X350 NBE_transm_par NBE_RtoFR SR AngioGymnoMix 4. Variable List A. Name: ID Description: Identification code for the location of measurement (matches 'ID' variable in other data files). B. Name: Site Description: Experimental site. Cloquet = IDENT-Cloquet FAB1 = FAB-1 Freiburg = IDENT-Freiburg C. Name: Plot Description: Unique plot code D. Name: Mix Description: Four-letter species codes indicating the species planted on the forest plot. See above for species codes. 6 NA = 6 North American species (ACSA, BEPA, LALA, PIGL, PIST, QURU) 6 EU = 6 European species (ACPL, BEPE, LADE, PIAB, PISY, QURO) 6 angio = 6 angiosperm species (ACPL, ACSA, BEPA, BEPE, QURO, QURU) 6 gymno = 6 gymnosperm species (LADE, LALA, PIAB, PIGL, PIST, PISY) E. Name: CanopyHt Description: Canopy height b = below canopy (c. 0.5 m above ground) m = mid-canopy (c. 2 m above ground) F. Name: BlMix Description: Unique code for each plot, concatenation of the experimental Block (or plot) and Mix G. Name: NBE_LAI_allloc Description: Net biodiversity effect on leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., "LAI-effective"). One value is given per canopy height and plot, these values are the average of measurements taken at four or five locations per plot and canopy height (for details see associated publication, Appendix S1: Figure S1). H. Name: LAI_specloc Description: Net biodiversity effect on leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., "LAI-effective"). One value is given per canopy height and plot, this is the value measured at the same location as the canopy transmittance measurement (for details see associated publication, Appendix S1: Figure S1). I. Name: LAI_allloc_corrected Description: Net biodiversity effect on leaf area index (LAI, m^2 of leaf per m^2 of ground) corrected for within-shoot clumping (i.e., our best estimate of the true LAI). One value is given per canopy height and plot, these values are the average of measurements taken at four or five locations per plot and canopy height (for details see associated publication, Appendix S1: Figure S1). J. Name: LAI_specloc_corrected Description: Net biodiversity effect on leaf area index (LAI, m^2 of leaf per m^2 of ground) not corrected for within-shoot clumping (i.e., our best estimate of the true LAI). One value is given per canopy height and plot, this is the value measured at the same location as the canopy transmittance measurement (for details see associated publication, Appendix S1: Figure S1). K. Name: Wavelength (X350 to X2200) Description: Net biodiversity effect on the fraction of irradiance of a given wavelength transmitted through the canopy (e.g., X350 = the net biodiversity effect on transmittance at 350 nm) L. Name: NBE_transm_par Description: Net biodiversity effect on the fraction of photosynthetically active radiation (PAR, 400-700 nm) transmitted through the canopy. M. Name: NBE_RtoFR Description: Net biodiversity effect on the ratio of red to far-red radiation transmitted through the canopy (i.e., 660 nm / 730 nm). N. Name: Name: SR Description: Species richness (number of species planted on the forest plot). O. Name: AngioGymnoMix Description: Whether trees on the forest plot are angiosperm species, gymnosperm species or a mixture of angiosperm and gymnosperm species. A = angiosperm species G = gymnosperm species M = mixture of angiosperm and gymnosperm species