Data from: Cross-scale regulation of seasonal microclimate by vegetation and snow in the Arctic tundra

ReadMe for cleaned datasets used in analyses

Associated publication:
von Oppen, J., Assmann, J.J., Bjorkman, A.D., Treier, U.A., Elberling, B., Nabe-Nielsen, J., & Normand, S. (2022) Cross-scale regulation of seasonal microclimate by vegetation and snow in the Arctic tundra. Global Change Biology

Description

The files contain data used in the analyses for von Oppen et al. (2022) Global Change Biology. See also the ReadMe in the root directory (ReadMe.Rmd), as well as scripts/data_cleaning.R and scripts/analyses.R for data cleaning and analysis workflows, respectively. Access through the R project file provided in the root directory (e.g. with RStudio) is recommended for seamless running of the code. Please see the paper (link in the zenodo archive) for methodological details, results and discussion.

Files

This directory data/plot_data/processed contains several datasets that share a similar structure and many of the same variables, yet are aggregated at different temporal resolution:

  • microclim_plot_data_complete.csv: data at plot level at study period resolution, i.e. one observation per study plot. Temperature values are aggregated across the whole available time period (e.g., growing season for TMS data) or as specified in the variable names
  • microclim_plot_data_complete_season19/ndjfm1920.csv: data at plot level at daily resolution, i.e. one observation per day per study plot. Temperature values are aggregated daily (according to WGST time zone)

Variables

Variable name [format]

  • plot_id [chr]
  • date [Date, YYYY-MM-DD]
  • tms/hobo_id [int]: logger identifier
  • lat/lon [num]: plot coordinates in WGS84
  • elevation [num]: plot elevation in masl
  • sector [chr]: mountain slope (= region; east = e / west = w) + elevation band (elev_band; 1-5) of the respective plot location
  • aspect/slope [int]: plot exposition / slope inclination in °
  • sri_daily/season19/ndjfm1920 [num]: Solar Radiation Index (Keating et al. 2007) for each date / integrated over growing season / winter season, respectively
  • *topo_prim(_num)/topo_sec* [chr/int]: topography/landform classification of the study plot location. 1 = snowbed, 2 = depression, 3 = flat, 4 = slope, 5 = ridge (num = numeric)
  • tms_moist_vol_mean/min/max/amp_scaled [num]: growing-season mean daily mean/minimum/maximum/amplitude of soil moisture. Raw readings were calibrated based on in situ soil particle size samples (see *scripts/data_cleaning.R). Before calculating seasonal means, daily values were scaled between 0 and 1 to conserve relative differences between plots while avoiding negative values due to suboptimal calibration in single plots
  • ndays_snowcover_ndjfm [int]: no. snow-covered days as inferred from soil temperature measurements
  • soil_depth_avg [num]: soil depth in cm, averaged from four vertical probing measurements taken at 50 cm distance from the plot centre in semi-cardinal directions
  • peg_height [num]: maximum vertical height of the peg marking the plot centre
  • tms_shield_height_avg [num]: height of the top shield of the TMS logger, averaged from four vertical measurements taken at all cardinal directions
  • tms_substrate [chr]: subjective classification of the substrate the TMS logger was located in
  • cover_tms/hobo_top/low/ground [num]: vegetation cover estimate in %, within a circle of 5 cm radius at the location of the TMS/HOBO logger, at height of the top and bottom TMS shield and at the ground surface, respectively
  • veg_height_avg/max_tms/hobo [num]: average/maximum vegetation height at the TMS/HOBO logger, measured vertically four times across cardinal directions
  • date_setup/survey/tms_/hobo_retrieval [POSIXct, YYYY-MM-DD hh:mm:ss]: date of plot establishment, vegetation survey, TMS or HOBO logger retrieval, respectively, in UTC (2am = 12am in WGST)
  • researcher/photo_id/comment_setup/survey/retrieval
  • time_tms/hobo_retrieval [num, hh:mm:ss]: specific time of TMS/HOBO logger retrieval
  • tms/hobo_logger_make/model [chr]: manufacturer/model of loggers
  • tms_T1/2/3/hobo_depth/height [int]: depth/height of logger sensors in cm relative to ground surface level
  • cov_{type}_{radius} [num]: % cover estimates for the following plant functional types/cover categories across the different sample plot sizes: shrubs, forbs, graminoids, bryophytes, sphagnum moss, lichen, cyanobacteria/biocrust, rocks (>2 cm diameter), bare ground/soil (<2 cm), litter, vascular plants (= shrubs + forbs + graminoids), open surface (= rocks + bare ground)
  • veg_height_avg_{radius} [num]: average vegetation height across the different sample plot sizes
  • plant_div_{radius} [int]: number of plant species found in the different sample plot sizes
  • plot-level temperature and soil moisture variables: see below
  • min_diff_station [chr]: ID of automated weather station with least elevational difference to each study plot (= paired station)

Daily temperature and soil moisture variables

Daily temperature amd soil moisture variables available differ between study periods, due to different deployment periods (TMS only during growing season).

In microclim_plot_data_complete_ndjfm1920.csv (winter season):

  • hobo_temp_mean/min/max [num]: daily mean/minimum/maximum soil temperatures for HOBO sensors across the winter season (November – March)
  • station_pair_daily_mean/min/max_tamp [num]: daily mean/minimum/maximum free-air temperature from paired automated weather station (to calculate vertical temperature differences)
  • station_base_daily_mean/min/max_tamp [num]: daily mean/minimum/maximum free-air temperature from lowest automated weather station (for macroclimate reference temperatures)
  • hobo_dT4hobo_mean/min/max [num]: difference in daily mean/minimum/maximum temperatures between soil (HOBO) and paired free-air weather station (‘T4’) sensors. Differences are calculated as lower – higher layer. Example: dT4hobo_mean = daily mean soil – daily mean free-air temperature

In microclim_plot_data_complete_season19.csv (growing season):

  • tms_T1/2/3_mean/min/max [num]: daily mean/minimum/maximum temperatures for TMS sensors in soil (T1), at near-surface (T2) and canopy height(T3) level, across the growing season
  • hobo_temp_mean/min/max [num]: daily mean/minimum/maximum soil temperatures for HOBO sensors across the growing season
  • station_pair_daily_mean/min/max_tamp [num]: daily mean/minimum/maximum free-air temperature from paired automated weather station (to calculate vertical temperature differences)
  • station_base_daily_mean/min/max_tamp [num]: daily mean/minimum/maximum free-air temperature from lowest automated weather station (for macroclimate reference temperatures)
  • tms_d{sensor comparison pair}_mean/min/max [num]: difference in daily mean/minimum/maximum temperatures between two sensors (T1 = TMS soil, T2 = TMS near-surface, T3 = TMS canopy-layer, T4 = weather station free-air, hobo = HOBO). Differences are calculated as lower – higher layer. Example: dT3T1_mean = daily mean soil – daily mean canopy-layer temperature; dT4T3_max = daily maximum canopy-layer – daily maximum free-air temperature
  • soil_class_TOMST [chr]: soil class used for calibration of soil moisture curves. Soil classes and calibration curves were provided by the manufacturer – see Appendix A in Wild et al. (2019) for available soil types and calibration curves
  • *tms_moist_vol_daily_mean/min/max/amp(_scaled)* [num]: original and scaled calibrated daily mean/minimum/maximum/amplitude of volumetric soil moisture

Contact

The data are being made openly available upon publication of the study. However, we kindly ask you to contact us before using the data:

Jonathan von Oppen, Department of Biology, Aarhus University, Denmark. jonathan.vonoppen@bio.au.dk

Dataset owner and manager: Signe Normand, Department of Biology, Aarhus University, Denmark. signe.normand@bio.au.dk