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Selection of supportive data sets and representative outputs of the three dimensional hyporheic model of the River Bure, UK.

Authors: Cagri Gokdemir Alberto Bellin Catherine M. Heppell Daniele Tonina
Owners: Cagri Gokdemir
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Created: Apr 28, 2018 at 9:41 a.m.
Last updated: Apr 28, 2018 at 5:24 p.m. by Cagri Gokdemir
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The combined effect of stream morphology, water discharge and heterogeneity of the hydraulic conductivity of stream-bed sediments on hyporheic exchange processes was aimed to be revealed. Hyporheic flow dynamics and their effects on dissolved oxygen were investigated in an heterogeneous and morphologically complex low-gradient sub-reach of River Bure, UK. The work was applied by combining field measurements with detailed numerical simulations. The data provided in this contribution contains: (1) Field data; Stream Water Discharge, stream velocity, floodplain water table, stratigrafic data for the sediment, and topographic data with surface and subsurface water dissolved oxygen concentrations, (2) Some part of Model data; particle set data from simulations, imposed water surface elevation boundaries for subsurface model, and supportive codes for data visualization and analysis (see details on README file).

Resource Level Coverage


Coordinate System/Geographic Projection:
WGS 84 EPSG:4326
Coordinate Units:
Decimal degrees
Place/Area Name: River Bure study site
North Latitude
East Longitude
South Latitude
West Longitude


Start Date:
End Date:



Paper: A three dimensional hyporheic model of River Bure: The role of streambed
heterogeneity and estimation of Oxic/Anoxic zones. Water Resources Research

Authors: Cagri Gokdemir, Alberto Bellin, Catherine M. Heppell, Daniele Tonina


This README file describes the data package accompanying the above publication in coherent fashion as introduced on the text of manuscript. 

Folders and Files: Enumerated lines of the list are the folders, lines designated by letters are the files. 

Data: Main Folder
	1. Field
		1.1. Biogeochemical_data
			a. BioGeo.txt: Porewater Dissolved Oxygen concentrations (mg/L) with coordinates and sample IDs.
		1.2. Hydrological_data
			a. Discharge.txt: Results of cross-sectional discharge calculations.
			b. Velocity.txt: Velocity values with coordinates both for discharge calculations on cross-sections and streamflow model inputs.
			c. WaterSurfaceElevation.txt: Coordinates and elevation of water surface at 4m intervals through sections, same local coordinate system as the streambed elevation.
			d. GW Measurements: Corrected groundwater levels between 7 September 2013 to 16 February 2014 with hourly intervals. Each file represents a groundwater monitoring wells with pressure transducers.
			f. RiverBure_levellogger_Feb_2014.pptx: Explanatory document of groundwater wells with their locations and manual measurement values on diagrams.  
		1.3. Stratigrafic_data
			a. Core_4kind_Bure.txt: Digitized sediment types with local coordinate system same as the streambed elevation, and specific depths of sediment types from sediment cores. Used as 			an input to TPROGS in order to create realizations conditional to core data.  
			b. CoreSample_SedimentStat.xlsx: Statistics for the sediment core samples and texture definitions.  
		1.4. Topographic_data
			a. Elevation_Raw.txt: Scalar elevation data of streambad and bank-lines. 
			b. Elevation_Interpolated.txt: Interpolated elevation data prior to streamflow modeling.  
	2. Model
		2.1. ResidenceTimes
			a. Particle Set informations: Contains 19 files start with section (Meander, Plain, Pool), followed by subsurface filling of three realizations that is introduced in the above 			paper (Heterogeneous:het1,het2,het3, homogeneous:hom) and discharge conditions (0.2,0.5,0.8 cubic meter per second). All heterogeneous formations are include 0.5 discharge. Each 			file has Particle Index, for each particle path; coordinates of each particle interval and total residence times in minutes. 
			Ex. Meander_het1: Particle info. of meander section for heterogeneous realization1. 
		2.2. WaterSurfaceElevations: Generated water surface elevations of three discharge conditions. Imposed as head boundaries to subsurface flow domain. 
			a. WSE_02.txt
			b. WSE_05.txt
			c. WSE_08.txt
		2.3. Codes: Includes 4 folders with set of Matlab (R2017a) codes 
			2.3.1. Biogeochemical
				a. biogeotime.m: The function is written in order to replicate porewater sampling for each heterogeneous case. Function is designed as a recursive to calculate ensamble 				average of local DO of all sample points. Used to create Figure 12 on the manuscript. Input files: BioGeo.txt and any single/multiple particle set file.    
				b. mean_curve.m: Estimates mean DO values from pdfs of DO distributions (ensemble mean)
				c. pdf_arrange.m: Creates visaully aranged PDF print of the Figure. 
			2.3.2. CDF
				a. find_max_time_multiple.m: Calculates and prints Cummulative Distribution Functions (CDF) of particle sets.
				b. call_multiple_base.m: Call function for multiple particle sets files to creat overlapping CDFs (CDFs of Figure 9, Figure 10, and Figure 11)
			2.3.3. Metrics
				a. metrics_hz.m: Calculates spatiotemporal metrics of hyporheic zone based on particle set data. 
				b. compute_multiple_metrics.m: Call function to calculate spatiotemporal metrics from multiple particle set data. 
				c. logmean.m and logstd.m: Side functions for logaritmic mean and logarithmic standard deviations of given data sets respectively.
			2.3.4. Visualization: Two scripts couple visualizations of modpath particles with streambed elevations.
				a. Modpath2Matlab.m: Converts particle sets into visual particle paths and couples with streambed elevation data with eldata.m script (Path visualization of Figure 9 and Figure 11)


Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
Education, Audiovisual and Culture Executive Agency of the European Commission Erasmus Mundus Fellowship


People or organizations that contributed technically, materially, financially, or provided general support for the creation of the resource's content but are not considered authors.

Name Organization Address Phone Author Identifiers
Nadim K. Copty Bogazici University, Turkey Istanbul, Turkey

How to Cite

Gokdemir, C., A. Bellin, C. M. Heppell, D. Tonina (2018). Selection of supportive data sets and representative outputs of the three dimensional hyporheic model of the River Bure, UK., HydroShare, http://www.hydroshare.org/resource/162cc421f46e428b8a93837da8d32349

This resource is shared under the Creative Commons Attribution CC BY.



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