This README.md file was generated on 2025-08-14 by Daniel Hirmas

GENERAL INFORMATION

1. Title of Dataset: Predicting soil interpedal macroporosity and hydraulic conductivity dynamics: A model for integrating laser-scanned profile imagery with soil moisture sensor data [Dataset]

2. Author Information

   A. Researcher Information
   Name: Daniel R. Hirmas
   Institution: Texas Tech University
   Address: Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
   Email: dhirmas@ttu.edu

   Name: Hoori Ajami
   Institution: Universidy of California at Riverside
   Address: Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
   Email: hooria@ucr.edu

   Name: Matthew G. Sena
   Institution: University of Delaware
   Address: Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
   Email: senam@udel.edu

   Name: Xi Zhang
   Institution: Louisiana State University–Agricultural Center
   Address: Red River Research Station and School of Plant, Environment, and Soil Sciences, Louisiana State University–Agricultural Center, Bossier City, LA, 71112, USA
   Email: xizhang@agcenter.lsu.edu

   Name: Xiaoyang Cao
   Institution: Zaozhuang University
   Address: College of Tourism, Resources and Environment, Zaozhuang University, Zaoshuang, Shandong, China
   Email: xiaoyangcaoxyc@outlook.com

   Name: Bonan Li
   Institution: Oregon State University
   Address: College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, 97331, USA
   Email: libon@oregonstate.edu

   Name: Karla M. Jarecke
   Institution: University of Colorado Boulder
   Address: Department of Geography, University of Colorado Boulder, Boulder, CO, 80309, USA
   Email: Karla.Jarecke@colorado.edu

   Name: Sharon A. Billings
   Institution: University of Kansas
   Address: Department of Ecology and Evolutionary Biology and Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, KS, 66047, USA
   Email: sharon.billings@ku.edu

   Name: Julio C. Pachon
   Institution: University of Sydney
   Address: Sydney Institute of Agriculture, School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
   Email: julio.pachon@sydney.edu.au

   Name: Li Li
   Institution: Penn State University
   Address: Department of Civil and Environmental Engineering, Penn State University, University Park, PA, 16802, USA
   Email: lili@engr.psu.edu

   Name: Jesse B. Nippert
   Institution: Kansas State University
   Address: Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
   Email: nippert@ksu.edu

   Name: Lı́gia F.T. Souza
   Institution: Colorado State University
   Address: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
   Email: ligia.souza@colostate.edu

   Name: Alejandro N. Flores
   Institution: Boise State University
   Address: Department of Geosciences, Boise State University, Boise, ID, 83725, USA
   Email: lejoflores@boisestate.edu

   Name: Pamela L. Sullivan
   Institution: Oregon State University
   Address: College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, 97331, USA
   Email: sullipam@oregonstate.edu

3. Date of data collection: 2018-10 - 2021-08

4. Geographic location of data collection: Konza Prairie Biological Station, Manhattan, KS, USA

5. Information about funding sources that supported the collection of the data: National Science Foundation, Award: 2034214, 2034232, 2121760, 2121639, 2121621, 2121595, 2121694, 1656006 and US Department of Agriculture-National Institute of Food and Agriculture, Award: 2021-67019-34341, 2021-67019-34338, 2021-67019-34340

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.
2. Recommended citation for this dataset: Hirmas, Daniel R.; Ajami, Hoori; Sena, Matthew G. et al. 2025. Predicting soil interpedal macroporosity and hydraulic conductivity dynamics: A model for integrating laser-scanned profile imagery with soil moisture sensor data [Dataset]. Dryad. https://doi.org/10.5061/dryad.zs7h44jkn

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: Water Resources Research paper
2. Methods for processing the data: Water Resources Research paper
3. Instrument- or software-specific information needed to interpret the data: Latest versions of R available at https://cran.r-project.org/ and R Studio available at https://posit.co/download/rstudio-desktop/

DATA-SPECIFIC INFORMATION

1.     Data Analysis.zip  A Zipped folder. Contains six folders: Data, R Project, R Scripts, Functions, Output Files, and Plots.

1.1 Data A folder that contains the following files:

1.1.1 wchold.csv Comma Delimited Text File that holds the 10, 40, and 120 cm deep soil volumetric water content (v/v) for the Konza APT soil. Columns labeled "_5TM_1_VWC", "_5TM_2_VWC", and "_5TM_3_VWC" correspond measured water contents at the 10, 40, and 120 cm depths, respectively.

1.1.2 KONZA_APT_Ap1_0.18mmResolution_Analyze.csv Comma Delimited Text File that holds measured 2-D geometric information of each macropore in the MLT scanned data of the Ap1 horizon of the Konza APT soil processed through ImageJ. Meanings of column names can be found in the ImageJ Documentation (https://imagej.net/ij/docs/menus/analyze.html). All length units are in mm.

1.1.3 KONZA_APT_Bt_0.18mmResolution_Analyze.csv Comma Delimited Text File that holds measured 2-D geometric information of each macropore in the MLT scanned data of the Bt horizon of the Konza APT soil processed through ImageJ. Meanings of column names can be found in the ImageJ Documentation (https://imagej.net/ij/docs/menus/analyze.html). All length units are in mm.

1.1.4 KONZA_APT_Btkss2_0.18mmResolution_Analyze.csv Comma Delimited Text File that holds measured 2-D geometric information of each macropore in the MLT scanned data of the Btkss2 horizon of the Konza APT soil processed through ImageJ. Meanings of column names can be found in the ImageJ Documentation (https://imagej.net/ij/docs/menus/analyze.html). All length units are in mm.

1.1.5 20220312_KansasEPSCoR_KonzaAPT_SelectedData_aDRH.csv Comma Delimited Text File that holds the upper ("top", cm) and lower ("bot", cm) depths, measured field-capacity bulk denisty (reported on a dry basis; "rhofc", g/cm³), oven-dried bulk density ("rhood", g/cm³), total porosity ("phi"), coefficient of linear extensibility ("COLE"), field-capacity volumetric water content ("thetafc", v/v), wilting-point volumetric water content ("thetawp", v/v), and air-dried volumetric water content ("thetaad", v/v) data from the USDA-NRCS Kellogg Laboratory for the Ap1, Bt, and Btkss2 horizons of the Konza APT soil (Pedon ID: S2018KS161104; Lab Pedon No.: 19N0205; available from the USDA NCSS Lab Data Mart - https://ncsslabdatamart.sc.egov.usda.gov/). Volumetric water contents were converted from measured gravimetric water contents using the field-capacity bulk density for field-capacity water content and oven-dried bulk density for wilting-point and air-dried water contents. Total porosity was calculated using the field-capacity bulk density. The file also holds the area of the cross-section analyzed ("Axs", mm²), total area of the surface scan gaps ("Assg", mm²), total perimeter of the surface scan gaps ("Pssg", mm), and average macropore width measured at a dry state ("dds", mm) as well as ROSETTA (Schaap et al., 2001) [Schaap, M.G., F.J. Leij, and M.Th. van Genuchten. 2001. ROSETTA: A computer program for estimating soil hydraulic parameters with hierarchical pedotransfer functions. Journal of Hydrology 251:163-176. doi: 10.1016/S0022-1694(01)00466-8] pedotransfer function predicted residual ("thetar") and saturated ("thetas) volumetric water contents, the van Genuchten (1980) [van Genuchten, M.Th. 1980. A closed-form equation for predicting the hydraulic conductivity of unsaturated soils. Soil Science Society of America Journal 44:892-898. doi: 10.2136/sssaj1980.03615995004400050002x] water retention function fitting parameters ("alpha" given in units of 1/cm and "n"), and saturated hydraulic conductivity ("Ksm", cm/d).

1.1.6 20220319_EPSCoR_KonzaAPT_COLERod_RawData_aMS_eDRH.csv Comma Delimited Text File that holds coefficient of linear extensibility (COLE) data from a modified form of the COLE rod procedure described in the Water Resources Research paper. Data are from selected depths of four pedons in a larger Kansas EPSCoR project of which the Konza APT soil is a part. The other three pedons in this file are the Hays APT soil (Pedon ID: S2018KS051003; Lab Pedon No.: 19N0202; available from the USDA NCSS Lab Data Mart - https://ncsslabdatamart.sc.egov.usda.gov/), the Konza PPT soil (Pedon ID: S2018KS161103; Lab Pedon No.: 19N0204), and the Konza NPT soil (Pedon ID: S2018KS161102; Lab Pedon No.: 19N0203). The file holds the monolith ID ("tray"), upper ("top", cm) and lower ("bot", cm) depths of the sampled monoliths, the replicate number ("rep") sampled from the monolith, gravimetric water content ("gwc", g/g) for each determination time, and the rod length ("rodlength", mm), COLE rod value ("colerod", unitless), and standard COLE value ("cole", unitless) calculated following Schafer and Singer (1976) [Schafer, W.M., and M.J. Singer. 1976. New method of measuring shrink-swell potential using soil pastes. Soil Science Society of America Journal 40:805-806. doi: 10.2136/sssaj1976.03615995004000050050x] for each determination time. The numbers 1-5 in the column names refer to the initial, 2-hour, 4-hour, 8-hour, and 24-hour determinations, respectively. The "finalrodlength" and "finalgwc" correspond to the 48-hour rod length and gravimetric water content measurements, respectively. NA values refer to gravimetric water contents that were not measured in the analysis.

1.1.7 AWE012.csv Comma Delimited Text File that holds daily meteorological data between 1982 and 2020 from the Konza Prairie Biological Station headquarters weather station. The year, month, day is given in the columns "RECYEAR", "RECDAY", and "RECDAY" and the Julian day is given as "DAYOFYEAR". Maximum, minimum, and average temperature (C) is provided in columns labeled "TMAX", "TMIN", and "TAVE", respectively. Daily average relative humidity (%), total solar radiation (MJ/m²), precipitation (mm), maximum, minimum, and average soil temperature (C) at 25 cm, and average wind speed (m/s) are in the columns labeled "DHUMID", "DSRAD", "DPPT", "SMAX", "SMIN", "S_AVE", and "WAVE", repsectively; "." values refer to data that were missing or were not measured. Data were obtained from Nippert (2024) [Nippert, J. 2024. AWE01 Meteorological data from the Konza Prairie headquarters weather station. Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/910469efbf1f7e8d54c2b1ca864edec9].

1.2 R Project A folder that contains the following file:

1.2.1 PredictingMacroporosityandConductivityDynamics.RProj R Studio File that holds the R Studio project file used to process the data.

1.3 R Scripts A folder that contains the following files:

1.3.1 20250614_PredictingMacroporosityandConductivityDynamics_RScript.R R Text File that holds the master script for conducting the analyses and generating the figures for the Water Resources Research paper. After the R Studio project file is opened to launch R Studio, this R text file should be navigated to and opened through the Files tab within R Studio. The script in this file should be executed to change the appropriate working directories to match the 6-folder stucture within the Data Analysis folder, and to call the following R scripts in the appropriate order.

1.3.2 20250614_PredictingMacroporosityandConductivityDynamics_PartitionScript.R R Text File that holds the script called by the master script file to partition the sensor water content into macropore and matrix water contents.

1.3.3 20250614_PredictingMacroporosityandConductivityDynamics_WRCParameterScript.R R Text File that holds the script called by the master script file to develop a model to predict the water retention parameters of the macropore (structural) domain for any matrix water content.

1.3.4 20250614_PredictingMacroporosityandConductivityDynamics_PoreResponseScript.R R Text File that holds the script called by the master script file to use the calculated matrix water content values to examine the effect on pore metrics.

1.3.5 20250614_PredictingMacroporosityandConductivityDynamics_KSurfacePlotScript.R R Text File that holds the script called by the master script file to plot the unsaturated hydraulic conductivity surface for any matrix and macropore water contents.

1.3.6 20250614_PredictingMacroporosityandConductivityDynamics_ValidationScript.R R Text File that holds the script called by the master script file to validate the Ks predictions from this theory against the transient Ks calculated using the theory from Stewart et al. (2016) [Stewart, R.D., M.R. Abou Najm, D.E. Rupp, and J.S. Selker. 2016. Modeling multidomain hydraulic properties of shrink-swell soils. Water Resources Research 52:7911-7930. doi: 10.1002/2016WR019336].

1.3.7 20250614_PredictingMacroporosityandConductivityDynamics_SensitivityScript.R R Text File that holds the script called by the master script file to evaluate the sensitivity of the model to variation in the input parameters: Ap, P, and dds.

1.4 Functions A folder that contains the following file:

1.4.1 20250614_PredictingMacroporosityandConductivityDynamics_RFunctions.R R Text File that holds a script with R functions developed for the Water Resources Research paper and called by the master script.

1.5 Output Files A folder that is used by the master script to place output tables from the analysis with the current date. This folder contains the following files:

1.5.1 20250614_PredictingMacroporosityandConductivityDynamics_KonzaAPT_PredictionCoefficientsforalpha2andn2.csv Comma Delimited Text File that holds the model output shown in Table 1 of the Water Resources Research paper.

1.5.2 20250614_PredictingMacroporosityandConductivityDynamics_KonzaAPT_MatrixAbsorptionCoeficients.csv Comma Delimited Text File that holds the model output shown in Table 2 of the Water Resources Research paper.

1.5.3 20250614_PredictingMacroporosityandConductivityDynamics_KonzaAPT_SoilShrinkageCurveParameters.csv Comma Delimited Text File that holds the soil shrinkage curve model output shown in Table 5 of the Water Resources Research paper.

1.6 Plots A folder that contains no files but is used by the master script to place the plots generated from the analysis with the current date.