This readme.txt file was generated on <20231222> by Recommended citation for the data: Sapes, G., Schroeder, L., Scott, A., Clark, I., Juzwik, J., Montgomery, R., Cavender-Bares, J. Mechanistic links between physiology and spectral reflectance enable pre-visual detection of oak wilt and drought stress. 2024. Proceedings of the National Academy of Sciences. In press. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data and Code for "Mechanistic links between physiology and spectral reflectance enable pre-visual detection of oak wilt and drought stress" 2. Author Information Principal Investigator Contact Information Name:Jeannine Cavender-Bares Institution: University of Minnesota Address: Email: cavender@umn.edu ORCID: https://orcid.org/0000-0003-3375-9630 Associate or Co-investigator Contact Information Name: Jennifer Juzwik Institution: University of Minnesota - USDA Address: Email: jennifer.juzwik@usda.gov ORCID: https://orcid.org/0000-0003-0577-7809 Associate or Co-investigator Contact Information Name: Rebecca Montgomery Institution: University of Minnesota Address: Email: rebeccam@umn.edu ORCID: https://orcid.org/0000-0002-4131-1847 3. Date published or finalized for release: TBD 4. Date of data collection (single date, range, approximate date) 20190301-20210931 5. Geographic location of data collection (where was data collected?): Cedar Creek Ecosystem Science Reserve and University of Minnesota Plant Growth Facilities 6. Information about funding sources that supported the collection of the data: Minnesota Invasive Terrestrial Plants and Pests Center (Legislative-Citizen Commission on Minnesota Resources, Project 00050727) NSF ASCEND Biology Integration Institute DBI: 2021898 NASA Biodiversity program Award number: 80NSSC21K1349 NSF Cedar Creek Long Term Ecological Research program DEB:1831944. 7. Overview of the data (abstract): Tree mortality due to global change-including range expansion of invasive pests and pathogens- is a paramount threat to forest ecosystems. Oak forests are among the most prevalent and valuable ecosystems both ecologically and economically in the United States. There is increasing interest in monitoring oak decline and death due to both drought and the oak wilt pathogen (Bretziella fagacearum). We combined anatomical and ecophysiological measurements with spectroscopy at leaf, canopy, and airborne levels to enable differentiation of oak wilt and drought, and detection prior to visible symptom appearance. We performed an outdoor potted experiment with Quercus rubra saplings subjected to drought stress and/or artificially inoculated with the pathogen to detect and distinguish both types of stressors. We also performed a field experiment where we validated the capacity of spectral reflectance models to predict physiological status and distinguish oak wilt from healthy trees. The data and code provided here address these goals. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: 2. Links to publications that cite or use the data: 3. Was data derived from another source? If yes, list source(s): 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/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- Root folder: Contains all the files needed to reproduce the manuscript. 1. File List A. Filename: DxOW_PNAS.R Short description: Code including data processing, analyses and figures. Data folder: Contains all the data needed to reproduce the manuscript. 1. File List A. Filename: Data_CC_2019 Short description: All the physiology and spectral reflectance data for the validation dataset from Cedar Creek is stored here into a single CSV file B. Filename: cedar_creek_seedling_experiment_2021_crowns_final Short description: Contains the multispectral reflectance data from the drone extracted from each pixel. Values are associated to tree IDs and timestamps C. Filename: cedar_creek_seedling_experiment_2021_fluorescence_meta Short description: Contains metadata to associate each fluorescence file number to their corresponding tree, treatment, sampling time, and leaf type D. Filename: cedar_creek_seedling_experiment_2021_physiology_data Short description: Contains all the leaf level physiology data associated to the corresponding plant id, treatment, sampling time, and leaf type E. Filename: cedar_creek_seedling_experiment_2021_symptom_appearance Short description: Contains all the dates at which trees became symptomatic associated to the corresponding treatment and plant id F. Filename: oak_wilt_saplings_pgf_2021 Short description: Contains information on the stem diameter and tree height for each tree in the potted experiment G. Filename: Fluorescence folder Short description: Where all fluorescence data is stored. Subfolders M1-M13 contain each measurement campaign compiled into a single CSV file H. Filename: Spectra folder Short description: Whhere all reflectance spectra is stored. Subfolders M1-M13 within the "Rubra" folder contain each measurement campaign compiled into a single CSV file I. Filename: Xylem staining folder Short description: Where all xylem staining data is stored into a single CSV file Plots folder: Where plots generated in the code are saved 1. File List Empty Results folder: Where results can be saved if desired 1. File List Empty 2. Relationship between files: Files relate through the DXOW_PNAS.R code. #Code structure: There are a total of 15 collapsable sections. 1-####Libraries 2-####Custom functions 3-####setting directory and output folder for plots 4-####Loading data 5-####Data from Cedar Creek for validation 6-####Adding and Merging Fluorescence data 7-##### Loading reflectance point spectra data 8-####Scaling physiology to canopy level by proportion of leaf types 9-####Removing Outliers 10-####Leaf and canopy spectral wavelength differences 11-####Xylem staining 12-####Physiology since start of symptoms 13-####Drone spectra since start of experiment and since start of symptoms 14-####PLSR code 15-####Segmented regressions for previsual indicators Explanation of each section: 1- loads required libraries 2- includes custom built functions used for analyses, graphs, and plot themes 3- where the working directory is defined 4- All the data is loaded through this section and variables derived from the raw data are calculated 5- The validation dataset is loaded here 6- Fluorescence data is added here and merged with the rest of the data 7- Same as above but for leaf level reflectance data 8- All leaf-level variables are averaged based on the relative abundance of each leaf type within each tree to scale up to canopy level 9- Some outlier values are removed here. Most are from spectral indexes not used in the paper 10- A subset of wavelengths is selected here based on a custom-made function to study changes in reflectance over time 11- Differences in functional xylem and patterning among treatments are studied here 12- The progression of physiological parameters over time is analyzed here 13- Changes in standard deviation of RDVI within canopies are studied here 14- This section shows a representative code of our Partial Least Square Regression analyses. The dependent variable and number of components can be adjusted to reproduce the models for each of our physiological variables 15- This section runs bayesian segmented regressions based on the estimates of the PLSR models. The PLSR models must be ran first and the estimates need to be appended to the dataset before this section can run. ---------------------- R VERSION INFORMATION ---------------------- R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] coda_0.19-4 pillar_1.7.0 mcp_0.3.1 segmented_1.3-3 moments_0.14 [6] dplyr_1.0.2 Rmisc_1.5 plyr_1.8.6 chillR_0.72.2 caret_6.0-93 [11] lattice_0.20-41 pls_2.7-3 spectrolab_0.0.10 multcomp_1.4-15 TH.data_1.0-10 [16] MASS_7.3-53 survival_3.2-7 mvtnorm_1.1-1 ggpubr_0.4.0 ggsignif_0.6.0 [21] data.table_1.13.6 RColorBrewer_1.1-2 stringr_1.4.0 ggbeeswarm_0.7.2 ggplot2_3.3.5 loaded via a namespace (and not attached): [1] readxl_1.3.1 backports_1.2.0 spam_2.6-0 sp_1.4-7 [5] splines_4.0.3 listenv_0.8.0 GenSA_1.1.7 scattermore_0.8 [9] digest_0.6.27 foreach_1.5.1 htmltools_0.5.2 fansi_0.4.1 [13] magrittr_2.0.1 openxlsx_4.2.3 recipes_0.1.15 globals_0.14.0 [17] gower_0.2.2 matrixStats_0.57.0 Kendall_2.2 R.utils_2.10.1 [21] sandwich_3.0-0 prospectr_0.2.1 colorspace_2.0-0 haven_2.3.1 [25] crayon_1.3.4 RCurl_1.98-1.2 lme4_1.1-26 zoo_1.8-8 [29] iterators_1.0.13 glue_1.4.2 gtable_0.3.0 ipred_0.9-9 [33] car_3.0-10 maps_3.3.0 abind_1.4-5 scales_1.1.1 [37] rstatix_0.6.0 Rcpp_1.0.8.3 xtable_1.8-4 foreign_0.8-80 [41] dotCall64_1.0-0 stats4_4.0.3 lava_1.6.8.1 prodlim_2019.11.13 [45] httr_1.4.2 ellipsis_0.3.2 pkgconfig_2.0.3 loo_2.4.1 [49] XML_3.99-0.5 R.methodsS3_1.8.1 farver_2.0.3 nnet_7.3-14 [53] utf8_1.1.4 tidyselect_1.1.0 labeling_0.4.2 rlang_1.1.1 [57] reshape2_1.4.4 later_1.1.0.1 munsell_0.5.0 cellranger_1.1.0 [61] tools_4.0.3 cli_3.6.1 generics_0.1.0 broom_0.7.3 [65] mathjaxr_1.0-1 fastmap_1.1.0 ModelMetrics_1.2.2.2 zip_2.1.1 [69] purrr_0.3.4 future_1.22.1 nlme_3.1-149 mime_0.9 [73] R.oo_1.24.0 compiler_4.0.3 rstudioapi_0.13 beeswarm_0.4.0 [77] curl_4.3 tibble_3.0.4 statmod_1.4.35 stringi_1.5.3 [81] forcats_0.5.0 fields_11.6 Matrix_1.2-18 nloptr_1.2.2.2 [85] shinyjs_2.0.0 vctrs_0.3.8 lifecycle_1.0.1 furrr_0.2.3 [89] cowplot_1.1.1 bitops_1.0-6 raster_3.5-15 httpuv_1.5.4 [93] patchwork_1.1.1 R6_2.5.0 promises_1.1.1 rio_0.5.16 [97] vipor_0.4.5 parallelly_1.28.1 codetools_0.2-16 boot_1.3-25 [101] withr_2.5.0 mgcv_1.8-33 parallel_4.0.3 hms_0.5.3 [105] terra_1.5-21 grid_4.0.3 rpart_4.1-15 timeDate_3043.102 [109] tidyr_1.1.2 class_7.3-17 minqa_1.2.4 carData_3.0-4 [113] pROC_1.16.2 shiny_1.7.2 lubridate_1.7.9.2 -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: 2. Methods for processing the data: 3. Instrument- or software-specific information needed to interpret the data: 4. Standards and calibration information, if appropriate: 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: Sapes, Gerard Schroeder, Lucy Scott, Allison Clark, Isaiah Juzwik, Jennifer Montgomery, Rebecca Cavender-Bares, Jeannine -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [cedar_creek_seedling_experiment_2021_crowns_final.csv] -------------------------------------------------------------------------------------- 1. Number of variables:28 2. Number of cases/rows: 167996 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: tif Description: Describes the name of the tif file from which data was extracted B. Name: shape Description: Lists the name of the polygon layer used to extract the data. There are four polygon layers for each tif image. One layer per treatment type. A. Name: date Description: The date at which the tif file was generated. Corresponds to the drone flying date. A. Name: id Description: The plant ID to which the data corresponds to. A. Name: Variables VI690 to CMS Description: A set of spectral indexes based on the different wavelengths that the drone can measure. See DxOW_PNAS.R Conde for more detailed descriptions of these indexes. Unitless. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [cedar_creek_seedling_experiment_2021_fluorescence_meta.csv] -------------------------------------------------------------------------------------- 1. Number of variables:13 2. Number of cases/rows: 566 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: _record_id Description: Internal unique ID from our lab. Ignore. B. Name: Title Description: Internal unique ID from our lab. Ignore. A. Name: _server_updated_at Description: Internal unique ID from our lab. Ignore. A. Name: _updated_by Description: Internal unique ID from our lab. Ignore. A. Name: _geometry Description: Internal unique ID from our lab. Ignore. A. Name: _latitude Description: The latitude of the record automatically taken by the phone GPS. A. Name: _longitude Description: The longitude of the record automatically taken by the phone GPS. A. Name: _plant_id Description: The plant ID to which the data corresponds to. A. Name: treatment Description: The treatment to which the data corresponds to. Can be Control (C), Drought(D), Oak wilt (OW), or both drought and oak wilt (DxOW). A. Name: sampling Description: The sampling event at which the data was recorded. A. Name: fluor_type Description: The type of fluorescence measurement taken as well as the status of the leaf when the measurement was taken. Can be dark- (Dark) or light-acclimated (Light) fluorescence in leaves that look either Healthy, Diseased, with brown tips, or totally dry (Crispy). A. Name: leaf_type Description: The status of the leaf when the measurement was taken. Can be leaves that look either Healthy, Diseased, with brown tips, or totally dry (Crispy). A. Name: file_name Description: The name of the file storing the fluorescence data. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [cedar_creek_seedling_experiment_2021_physiology_data.csv] -------------------------------------------------------------------------------------- 1. Number of variables:33 2. Number of cases/rows: 555 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: _record_id Description: Internal unique ID from our lab. Ignore. A. Name: _geometry Description: Internal unique ID from our lab. Ignore. A. Name: _latitude Description: The latitude of the record automatically taken by the phone GPS. A. Name: _longitude Description: The longitude of the record automatically taken by the phone GPS. A. Name: _plant_id Description: The plant ID to which the data corresponds to. A. Name: treatment Description: The treatment to which the data corresponds to. Can be Control (C), Drought(D), Oak wilt (OW), or both drought and oak wilt (DxOW). A. Name: sampling Description: The sampling event at which the data was recorded. A. Name: days_since_start Description: Number of days since the start of the experiment. A. Name: leaf_type Description: The status of the leaf when the measurement was taken. Can be leaves that look either Healthy, Diseased, with brown tips, or totally dry (Crispy). A. Name: healthy_ Description: The proportion of healthy looking leaves in the canopy in percentage. A. Name: diseased_ Description: The proportion of diseased looking leaves in the canopy in percentage. A. Name: brown_tips_ Description: The proportion of leaves with brown tips in the canopy in percentage. A. Name: crispy_ Description: The proportion of fully dry leaves in the canopy in percentage. A. Name: wp_predawn_mpa Description: The water potential at predawn in megapascals. A. Name: wp_leaf_mpa Description: The leaf water potential at midday in megapascals. A. Name: wp_stem_mpa Description: The stem water potential at midday based on an equilibrated leaf in megapascals. A. Name: fw_leaf_g Description: The fresh weight of the leaf in grams. A. Name: fw_stem_g Description: The fresh weight of a stem segment in grams. A. Name: fv_leaf_g Description: The fresh volume of displaced water by the leaf in grams. A. Name: fv_stem_g Description: The fresh volume of displaced water by a stem segment in grams. A. Name: sw_leaf_g Description: The saturated weight of the leaf in grams. A. Name: sw_stem_g Description: The saturated weight of a stem segment in grams. A. Name: dw_leaf_g Description: The dry weight of the leaf in grams. A. Name: dw_stem_g Description: The dry weight of a stem segment in grams. A. Name: control_conductivity_leaf_us Description: The electric conductivity of a leaf in microsiemens before starting the experiment. A. Name: control_conductivity_stem_us Description: The electric conductivity of a stem segment in microsiemens before starting the experiment. A. Name: fresh_conductivity_leaf_us Description: The electric conductivity of the leaf in microsiemens. A. Name: fresh_conductivity_stem_us Description: The electric conductivity of a stem segment in microsiemens. A. Name: autoclaved_conductivity_leaf_us Description: The electric conductivity of the leaf in microsiemens after autoclaving its tissue. A. Name: autoclaved_conductivity_stem_us Description: The electric conductivity of a stem segment in microsiemens after autoclaving its tissue. A. Name: notes Description: Any notes taken during sampling about the observation. A. Name: rwc_leaf_ Description: The relative water content of the leaf in percentage based on its fresh, saturated, and dry weight. A. Name: rwc_stem_ Description: The relative water content of a stem segment in percentage based on its fresh, saturated, and dry weight. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [cedar_creek_seedling_experiment_2021_symptom_appearance.csv] -------------------------------------------------------------------------------------- 1. Number of variables:7 2. Number of cases/rows: 55 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: _record_id Description: Internal unique ID from our lab. Ignore. A. Name: _geometry Description: Internal unique ID from our lab. Ignore. A. Name: _latitude Description: The latitude of the record automatically taken by the phone GPS. A. Name: _longitude Description: The longitude of the record automatically taken by the phone GPS. A. Name: _plant_id Description: The plant ID to which the data corresponds to. A. Name: treatment Description: The treatment to which the data corresponds to. Can be Control (C), Drought(D), Oak wilt (OW), or both drought and oak wilt (DxOW). A. Name: first_symptomatic_date Description: The date at which a symptomatic tree showed the virst visual symptoms. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [oak_wilt_saplings_pgf_2021.csv] -------------------------------------------------------------------------------------- 1. Number of variables:7 2. Number of cases/rows: 116 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: _record_id Description: Internal unique ID from our lab. Ignore. A. Name: _geometry Description: Internal unique ID from our lab. Ignore. A. Name: _latitude Description: The latitude of the record automatically taken by the phone GPS. A. Name: _longitude Description: The longitude of the record automatically taken by the phone GPS. A. Name: _plant_id Description: The plant ID to which the data corresponds to. A. Name: stem_basal_perimeter_cm Description: The perimeter of the tree stem at the base of the stem in centimeters. A. Name: height_cm Description: The height of the tree in centimeters. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [Stained_sector_count.csv] -------------------------------------------------------------------------------------- 1. Number of variables:33 2. Number of cases/rows: 118 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: _plant_id Description: The plant ID to which the data corresponds to. A. Name: treatment Description: The treatment to which the data corresponds to. Can be Control (C), Drought(D), Oak wilt (OW), or both drought and oak wilt (DxOW). A. Name: sampling Description: The sampling event at which the data was recorded. A. Name: dry_wet Description: Whether the sample was dry or wet when measured. A. Name: flushed_notflushed Description: Whether the sample was flushed or not before measured. A. Name: Date_stained Description: The date at which we stained the sample. A. Name: Red_pixels Description: The number of pixels stained in red in the sample. A. Name: NonRed_pixels Description: The number of pixels not stained in red in the sample. A. Name: Total_pixels Description: The total number of pixels in the sample. A. Name: Red_vessel_pixels Description: A failed attempt at quantifying stained pixels specifically inside vessels. Please ignore. A. Name: NonRed_vessel_pixels Description: A failed attempt at quantifying non-stained pixels specifically inside vessels. Please ignore. A. Name: Total_vessel_pixels Description: A failed attempt at quantifying the number of pixels specifically inside vessels. Please ignore. A. Name: Red_ratio Description: The percent of pixels stained. A. Name: Red_vessel_ratio Description: A failed attempt at quantifying the percent of pixels stained specifically inside vessels. Please ignore. A. Name: Notes Description: Any notes taken during the collection of the observation. A. Name: stained_1 to stained_16 Description: Each variable corresponds to a radial sector within the stem circunference. If the sector had stained pixels, the value is 1. If not, the value is 0. A. Name: total_functional Description: The amount of sectors that are functional. A. Name: total_clogged Description: The amount of sectors that are clogged and cannnot transport water. ------------------------------------------------------------------------------------ DATA-SPECIFIC INFORMATION FOR: [Spectra_PGF_2021_M1.csv to Spectra_PGF_2021_M1 M13.csv] -------------------------------------------------------------------------------------- 1. Number of variables:2016 2. Number of cases/rows: Varies by file 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: Full_file_name Description: The name of the spectral file containing the raw data. A. Name: X_record_id Description: Internal unique ID from our lab. Ignore. A. Name: X_geometry Description: Internal unique ID from our lab. Ignore. A. Name: X_latitude Description: The latitude of the record automatically taken by the phone GPS. A. Name: X_longitude Description: The longitude of the record automatically taken by the phone GPS. A. Name: _plant_id Description: The plant ID to which the data corresponds to. A. Name: treatment Description: The treatment to which the data corresponds to. Can be Control (C), Drought(D), Oak wilt (OW), or both drought and oak wilt (DxOW). A. Name: sampling Description: The sampling event at which the data was recorded. A. Name: spectra_type Description: The type of spectral reflectance measurement taken. Can be whole canopy (Canopy) or leaf level. In the latter case, it's reported as Healthy, Diseased, Brown_tips, or Crispy depending on the status of the measured leaf. A. Name: file_name Description: The name of the file storing the spectral reflectance data. A. Name: healthy_ Description: The proportion of healthy looking leaves in the canopy in percentage. A. Name: diseased_ Description: The proportion of diseased looking leaves in the canopy in percentage. A. Name: brown_tips_ Description: The proportion of leaves with brown tips in the canopy in percentage. A. Name: crispy_ Description: The proportion of fully dry leaves in the canopy in percentage. A. Name: normalization_magnitude Description: The value used to vector normalize the spectral reflectance across all the wavelenghts . A. Name: 400 to 2400 Description: The normalized spectral reflectance at each wavelength starting from wavelength 400 nm and ending on wavelength 2400 nm. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [PGF_FvFm_M1.csv to PGF_FvFm_M13.csv] -------------------------------------------------------------------------------------- 1. Number of variables:7 2. Number of cases/rows: varies by file 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: File # Description: The file name containing the raw fluorescence data. A. Name: Date Description: The date of data collection in dd/mm/yyy format. A. Name: Time Description: The time of data collection in 24h format. A. Name: Fo Description: The minimal level of fluorescence. A. Name: Fm Description: The maximum level of fluorescence when exposed to a saturating light intensity. A. Name: Fv Description: The difference between Fm and Fo. A. Name: Fv/Fm Description: The maximum efficiency of Photosystem II. -------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION FOR: [data_plsr_CC_2.csv] -------------------------------------------------------------------------------------- 1. Number of variables:2052 2. Number of cases/rows: 69 3. Missing data codes: NA No data 4. Variable List A. Name: Description: Observation number. A. Name: plant_ID Description: The plant ID to which the data corresponds to. A. Name: Treatment Description: The treatment to which the data corresponds to. Can be Control (C), Drought(D), Oak wilt (OW), or both drought and oak wilt (DxOW). A. Name: Sampling Description: The sampling event at which the data was recorded. A. Name: Leaf_type Description: The status of the leaf when the measurement was taken. Can be leaves that look either Healthy, Diseased, with brown tips, or totally dry (Crispy). A. Name: Species Description: Empty as they are all a mixture of Quercus rubra and ellipsoidalis including hybrids difficult to classify. A. Name: Days_since_start Description: Number of days since the start of the experiment. A. Name: Healthy_. Description: The proportion of healthy looking leaves in the canopy in percentage. A. Name: Diseased_. Description: The proportion of diseased looking leaves in the canopy in percentage. A. Name: Brown_tips_. Description: The proportion of leaves with brown tips in the canopy in percentage. A. Name: Crispy_. Description: The proportion of fully dry leaves in the canopy in percentage. A. Name: Plant_height_cm Description: Empty. A. Name: Stem_diam_mm Description: Empty. A. Name: Browning_. Description: Empty. A. Name: VWC_soil Description: Empty. A. Name: WP_predawn_Mpa Description: Empty. A. Name: WP_leaf_Mpa Description: The leaf water potential at midday. A. Name: WP_stem_Mpa Description: The stem water potential at midday based on an equilibrated leaf in megapascals. A. Name: FW_leaf_g Description: The fresh weight of the leaf in grams. A. Name: FV_leaf_g Description: The fresh volume of displaced water by the leaf in grams. A. Name: SW_leaf_g Description: The saturated weight of the leaf in grams. A. Name: DW_leaf_g Description: The dry weight of the leaf in grams. A. Name: FW_stem_g Description: The fresh weight of a stem segment in grams. A. Name: FV_stem_g Description: The fresh volume of displaced water by a stem segment in grams. A. Name: SW_stem_g Description: The saturated weight of a stem segment in grams. A. Name: Sinker Description: The amount of water displaced by the sinker in grams used to measure volume displacement. RWC_leaf_. RWC_stem_. VWC_leaf_. VWC_stem_. Notes TxLTxM SWC_leaf SWC_stem PLRC_leaf_. PLRC_stem_. OSM_leaf_Mpa PP_leaf_Mpa Fo Fm Fv Fv.Fm Fs Fm. X.S2 ETR ETR_real NPQ qN TxLT TxM A. Name: RWC_leaf_. Description: The relative water content of the leaf in percentage based on its fresh, saturated, and dry weight. A. Name: RWC_stem_. Description: The relative water content of a stem segment in percentage based on its fresh, saturated, and dry weight. A. Name: VWC_leaf_. Description: The volumetric water content of the leaf in percentage based on its fresh weight, dry weight and its fresh volume. A. Name: VWC_stem_. Description: The relative water content of a stem segment in percentage based on its fresh weight, dry weight and its fresh volume. A. Name: Notes Description: Any notes taken during sampling about the observation. A. Name: TxLTxM Description: A factor describing the treatment level AND leaf type AND sampling time by combining th erespective variables. A. Name: SWC_leaf Description: The saturated water content of the leaf in grams of water per gram of tissue. A. Name: SWC_stem Description: The saturated water content of a stem segment in grams of water per gram of tissue. A. Name: PLRC_leaf_. Description: The loss of recovery capacity of the leaf in percentage. A. Name: PLRC_stem_. Description: The loss of recovery capacity of a stemsegment in percentage. A. Name: OSM_leaf_Mpa Description: The osmotic potential of the leaf in megapascals. Uncertain values as leaves dry. A. Name: PP_leaf_Mpa Description: The pressure potential of the leaf in megapascals based on the water potential and the osmotic potential. Uncertain values as leaves dry. A. Name: Fo Description: The minimal level of fluorescence. A. Name: Fm Description: The maximum level of fluorescence when exposed to a saturating light intensity. A. Name: Fv Description: The difference between Fm and Fo. A. Name: Fv.Fm Description: The maximum efficiency of Photosystem II. A. Name: Fs Description: The minimal level of fluorescence in light-acclimated conditions. Light-acclimated values might be innacurate. We recommend not using them. A. Name: Fm. Description: The fluorescence level when exposed to a saturating light intensity in light-acclimated conditions. Light-acclimated values might be innacurate. We recommend not using them. A. Name: X.S2 Description: The efficiency of Photosystem II in light-acclimated conditions. Light-acclimated values might be innacurate. We recommend not using them. A. Name: ETR Description: The electron transport rate calculated by the fluorometer. Wrong PAR amount. Do not use. A. Name: ETR_real Description: The electron transport rate calculated based on the observed PAR amount. Light-acclimated values might be innacurate. We recommend not using them. A. Name: NPQ Description: The nonphotochemical quenching. Light-acclimated values might be innacurate. We recommend not using them. A. Name: qN Description: The nonphotochemical quenching of both regulated and unregulated heat dissipation based on the puddle model. Light-acclimated values might be innacurate. We recommend not using them. A. Name: TxLT Description: A factor describing the treatment level AND leaf type by combining the respective variables. A. Name: TxM Description: A factor describing the treatment level AND sampling time by combining the respective variables. A. Name: 400-2400 Description: The normalized spectral reflectance at each wavelength starting from wavelength 400 nm and ending on wavelength 2400 nm.