Data Package Metadata   View Summary

2018 seasonal high frequency monitoring of Upper Clark Fork River (Montana, USA) dissolved carbon dioxide, dissolved oxygen, pH, and electrical conductivity

General Information
Data Package:
Local Identifier:edi.404.1
Title:2018 seasonal high frequency monitoring of Upper Clark Fork River (Montana, USA) dissolved carbon dioxide, dissolved oxygen, pH, and electrical conductivity
Alternate Identifier:DOI PLACE HOLDER
Abstract:

These data were collected by the University of Montana and Montana State University to support the Upper Clark Fork River restoration monitoring project supported by the US NSF Long Term Research in Environmental Biology (LTREB) program. The original analytical intent for these data was to assess the response of river metabolic regime to the floodplain restoration via inference of whole-ecosystem metabolism from the daily variation in carbon dioxide concentrations. Data are primarily measurements of dissolved carbon dioxide, dissolved oxygen, pH, electrical conductivity, and temperature in well-mixed river thalweg water. Additional miscellaneous data were collected from grab samples for quality assurance. Data are from late in the 2018 field season. Data were collected on the Upper Clark Fork River (USGS HUC 17010201) at the Galen and Racetrack sites northeast of Anaconda, Montana, USA. High frequency carbon dioxide, oxygen, and pH data were collected using field deployments SAMI sensors from Sunburst Sensors (Missoula, Montana, USA). Electrical conductivity and pressure data were collected with Hobo sensors from Onset Computer Corporation (Bourne, Massachusetts, USA).

Purpose:

These data were collected by the University of Montana and Montana State University to support the Upper Clark Fork River restoration monitoring project supported by the US NSF Long Term Research in Environmental Biology (LTREB) program. The original analytical intent for these data was to assess the response of river metabolic regime to the floodplain restoration via inference of whole-ecosystem metabolism from the daily variation in carbon dioxide concentrations.

Publication Date:2021-08-07

Time Period
Begin:
2018-08-29
End:
2018-10-17

People and Organizations
Contact:DeGrandpre, Michael D (University of Montana) [  email ]
Creator:DeGrandpre, Michael D (University of Montana)
Creator:Beatty, Cory M (University of Montana)
Associate:Bayrd, Venice (Montana State University, Data curation)
Associate:Payn, Robert A (Montana State University, Data curation and project PI at MSU)
Associate:Valett, H Maurice (University of Montana, Project PI at UM)
Associate:Peipoch, Marc (Stroud Water Research Center, Project co-PI)
Associate:D'Andrilli, Juliana (Louisiana University Marine Consortium, Project co-PI)

Data Entities
Data Table Name:
pCO2-DO_Galen_2018_SAMI_C22.csv
Description:
In situ measurements by SAMI CO2 probe at Galen site
Data Table Name:
pCO2-DO_Galen_2018_SAMI_C24.csv
Description:
In situ measurements by SAMI CO2 probe at Galen site. Joint deployment for QA.
Data Table Name:
pCO2-DO_Racetrack_2018_SAMI_C24.csv
Description:
In situ measurements by SAMI CO2 probe at Racetrack site
Data Table Name:
pH_Galen_2018_SAMI_P87.csv
Description:
In situ measurements by SAMI pH probe at Galen site
Data Table Name:
pH_Galen_2018_SAMI_P13.csv
Description:
In situ measurements by SAMI pH probe at Galen site. Joint deployment for QA.
Data Table Name:
pH_Racetrack_2018_SAMI_P13.csv
Description:
In situ measurements by SAMI pH probe at Racetrack site
Data Table Name:
ec_Galen_2018_Hobo_20200212.csv
Description:
In situ measurements by Hobo EC probe at Galen site
Data Table Name:
ec_Galen_2018_Hobo_204522395.csv
Description:
In situ measurements by Hobo EC probe at Galen site. Joint deployment for QA.
Data Table Name:
ec_Racetrack_2018_Hobo_204522395.csv
Description:
In situ measurements by Hobo EC probe at Racetrack site
Other Name:
01_input.zip
Description:
Compressed data pipeline folder containing raw data downloaded from instruments. See methods for details.
Other Name:
02_protocol.zip
Description:
Compressed data pipeline folder containing R markdown and R scripts for processing data and metadata. See methods for details.
Other Name:
03_incremental.zip
Description:
Compressed data pipeline folder containing detailed notes and incremental data associated with generation of the data product. See methods for details.
Detailed Metadata

Data Entities


Data Table

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Number of Columns:4

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temp  
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Data Table

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Name:pH_Galen_2018_SAMI_P87.csv
Description:In situ measurements by SAMI pH probe at Galen site
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temp  
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Description:In situ measurements by SAMI pH probe at Galen site. Joint deployment for QA.
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Name:pH_Racetrack_2018_SAMI_P13.csv
Description:In situ measurements by SAMI pH probe at Racetrack site
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temp  
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Data Package Usage Rights

Intellectual rights to the data of this data package are treated separately to the code; please read carefully below.

It is considered professional etiquette to provide attribution of the original work if this data package is shared in whole or by individual components. A generic citation is provided for this data package on the website https://portal.edirepository.org (herein "website") in the summary metadata page. Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. This data package (and its components) is made available "as is" and with no warranty of accuracy or fitness for use. The creators of this data package and the website shall not be liable for any damages resulting from misinterpretation or misuse of the data package or its components. Periodic updates of this data package may be available from the website. Thank you.

- BEGIN CODE LICENSE STATEMENT -

Copyright 2021 - Robert Payn

The code files presented here are available under the MIT License. The full Legal Code text is available below, and also here: https://opensource.org/licenses/MIT. Specific files released under this license include:

02_protocol.zip/.Rprofile; 02_protocol.zip/02_galen_tables.Rmd; 02_protocol.zip/02_galen_tables_compile.R; 02_protocol.zip/03_racetrack_tables.Rmd; 02_protocol.zip/03_racetrack_tables_compile.R; 02_protocol.zip/10_metadata.Rmd; 02_protocol.zip/10_metadata_compile.R; 02_protocol.zip/99_runall.R; 02_protocol.zip/base.R; 02_protocol.zip/RStudioProject.Rproj

-- Begin Legal Code Text - MIT License -- Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

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-- End Legal Code Text - MIT License --

- END CODE LICENSE STATEMENT -

- BEGIN DATA RIGHTS STATEMENT -

The data presented here, as well as their selection and arrangement; documentation; and metadata are available under CC0 1.0 Universal Public Domain Dedication. The full Legal Code text is available below, and also here: https://creativecommons.org/publicdomain/zero/1.0/legalcode. Specific files included in the public domain dedication include:

EC_003_Galen_2017_Hobo.csv; EC_004_Racetrack_2017_Hobo.csv; pCO2_003_Galen_2017_SAMI_S5u.csv; pCO2_004_Racetrack_2017_SAMI_S53.csv; pH_003_Galen_2017_SAMI_P87.csv; pH_004_Racetrack_2017_SAMI_S13u.csv; pressure_003_Galen_2017_Hobo.csv; pressure_004_Racetrack_2017_Hobo.csv; QAsamples_003_Galen_2017.csv; QAsamples_004_Racetrack_2017.csv; 01_input.zip (all files, recursively); 02_protocol.zip/supplemental/CO2sys_Freshwater_2020.xlsm (already public domain; produced by a US government entity); 02_protocol.zip/00_deployment_notes.docx; 03_incremental.zip (all files, recursively); edi.x.x.xml (where "x" in ".x." may be replaced by any number); edi.x.x.txt (where "x" in ".x." may be replaced by any number)

-- Begin Legal Code Text - CC0 1.0 Universal Public Domain Dedication --

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Keywords

By Thesaurus:
(No thesaurus)Upper Clark Fork River restoration, NSF DEB LTREB 1655197, Montana, Northwestern United States, Northwestern Forested Mountains Ecoregion
NALTriver water, pH, dissolved carbon dioxide
LTER Controlled Vocabularydissolved oxygen, electrical conductivity

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:
## 1. Measurement methods Each description below is cross-referenced with the brief methods caption provided in the descriptions of the table columns. ### 1.1 Sensor deployments The following summarizes the methods for deployed sensors. Sensors were cleaned at approximately the same time as quality assurance samples were collected (see below). _Deployed SAMI CO<sub>2</sub> probe_: A Submersible Autonomous Moored Instrument (SAMI) CO<sub>2</sub> probe (Sunburst Sensors, Missoula, Montana, USA) was deployed directly in the channel thalweg and measured the partial pressure of dissolved CO<sub>2</sub> in river water. The pH of the indicator fluid measured by colorimetric absorbance can then be calibrated to the influence of dissolved carbon dioxide gas on the buffering system of the indicator. Calibrations were carried out in the DeGrandpre lab at University of Montana. The probe also records the water temperature and time of measurements. The SAMIs included a couplded Aanderaa dissolved oxygen optode sensor, and dissolved oxygen data were collected with the carbon dioxide and temperature data on the SAMI data logger. _Adjusted deployed SAMI CO<sub>2</sub> probe_: Measurements were made as described for deployed SAMI CO<sub>2</sub> probe, above. The pCO<sub>2</sub> measurements were then adjusted downward by 37 microatmospheres for the SAMI serial C24 because it read higher than the SAMI serial C22 and the grab samples matched the SAMI serial C22 data. _Deployed SAMI pH probe_: A Submersible Autonomous Moored Instrument (SAMI) pH probe (Sunburst Sensors, Missoula, Montana, USA) was deployed directly in the channel thalweg and measured pH in the river water. Samples of river water are automatically pumped into the SAMI and are passively mixed with indicator dye. A spectrophotometric measurement of the mixture provides a value for pH. The probe also records the water temperature and time of measurements. _Deployed Hobo EC probe_: An Onset Hobo electrical conductivity probe (Onset Computer Corporation, Bourne, Massachusetts, USA) was deployed directly in the channel thalweg and measured the temperature-corrected electrical conductivity in river water. The electrical conductivity is measured by applying a voltage across leads with a specific geometry of connection with river water and measuring the resistance between those leads to conducting an electrical current. The probe also records the water temperature and time of measurements. The software from the manufacturer of the probe (Hobo Onset) provides a post-processor that performs the temperature-correction of the conductivity to 25 degrees Celsius. The factory calibration was used on the instrument. _Deployed Hobo pressure probe_: An Onset Hobo pressure transducer (Onset Computer Corporation, Bourne, Massachusetts, USA) was deployed with the SAMI CO<sub>2</sub> probe to track the relative variation in river depth during the deployment. The pressure transducers derives absolute pressure by measuring the deformation of a ceramic diaphragm. The probe also records the water temperature and time of measurements. ### 1.2 Quality assurance sampling The following methods apply to data collected for quality assurance. Sensor deployment data have not been altered based on these measurements, and they are provided for information to users of these data. _Colorimetry with indicator dye_: For quality assurance purposes, pH of discrete river water samples was measured in a laboratory setting following the procedures in Lai et al. (2016). Briefly, indicator dyes were added to river samples stored in a 10-cm cylindrical optical cell. Values of pH for the samples were obtained by monitoring the spectrum of the dye-sample mixture via a Cary 300 spectrophotometer (Varian, Inc.). Measurements are routinely performed at ~20 degrees Celsius and corrected to in situ temperature (i.e. temperature when samples were taken) using the CO2Sys Excel spreadsheet model for the inorganic carbon system (Pierrot et al., 2006). _Gran titration_: Alkalinity samples were measured by acidimetric open-cell titration (Gran 1952). Alkalinity is inferred from non-linear regression analysis from a titration curve between pH values of 3.5 and 3.0. Results of Gran titration are presented as molarity and can be interpreted as the molarity of hydrogen ions neutralized by proton accepting compounds dissolved in the water. _CO2Sys calculated from alkalinity and pH_: The CO2Sys model (Pierrot et al., 2006) was used to calculate the partial pressure of carbon dioxide in sampled river water from the measured alkalinity and pH. Partial pressure of carbon dioxide was calculated for both bottle temperature at time of lab analysis and in situ river water temperature at the time of sample collection. ## 2. Data processing methods This data product is designed to provide the provenance of final tables in a pipeline format, to the degree that provenance is available. Raw data files from instruments and manufacturer software are available in the 01\_input.zip file. The coding used to process the data is available in the 02\_protocol.zip file. In this case, final processing was carried out with R scripts and R markdown files. Incremental files created for the purpose of data processing are available in the 03\_incremental.zip file. Ready-to-use analytical data are available at the data package's root level (on the dataset landing page under the "Resources" section) and are described in the full metadata. ### 2.1. Contents of 01\_input.zip * _003\_UCFR\_Hobo\_Cond\_20200212\_LTREB\_082918\_101718.hobo_ - Binary file for Onset Hobo electrical conductivity sensor serial number 20200212 * _003\_UCFR\_Hobo\_Depth\_20183501\_2018.hobo_ - Comma delimited export of data for Onset Hobo pressure sensor serial number 20183501 * _003\_UCFR\_SAMI-CO2\_C22u\_171018.txt_ - Raw file for SAMI CO<sub>2</sub> sensor serial number C22 * _003\_UCFR\_SAMI-pH\_P87\_171018.txt_ - Raw file for SAMI pH sensor serial number P87 * _004\_UCFR\_Hobo\_Cond\_20422395\_LTREB\_082918\_101718.hobo_ - Binary file for Onset Hobo electrical conductivity sensor serial number 20422395 * _004\_UCFR\_Hobo\_Depth\_20183502\_2018.hobo_ - Comma delimited export of data for Onset Hobo pressure sensor serial number 20183502 * _004\_UCFR\_SAMI-CO2\_C24u\_171018(QC).txt_ - Raw file for SAMI CO<sub>2</sub> sensor serial number C24 * _004\_UCFR\_SAMI-pH\_P13u\_171018(QC).txt_ - Raw file for SAMI pH sensor serial number P13 * _meta/_ - Directory with project templates for metadata * _meta/2021 Site Table.xlsx_ - Microsoft Excel file with authoritative project site list at the time of publication of these data. * _attributes.xlsx_ - Excel file with commonly used table column attributes in the project * _people.xlsx_ - Excel file with tabular data on people associated with the project used for metadata generation. ### 2.2. Contents of 02\_protocol.zip R code in the protocol depends on R packages: tidyr, readtext, knitr, readxl, EMLassemblyline, and xml2. Code also makes system calls to the zip command using arguments compatible with Info-Zip implementation 3.0, which appear to be mostly consistent with linux zip arguments. * _.RProfile_ - An R profile file with R code that establishes the appropriate working directory for the R project used to generate this data product. * _00\_deployment\_notes.docx_ - Microsoft Word document for generating the deployment notes PDF file * _01\_processing.Rmd_ - R markdown defining the quality assurance visualizations, tables, and table metadata. * _01\_processing\_compile.R_ - R script that compiles the processing R markdown to a PDF document (03\_incremental.zip - processing\_notes.pdf) * _10\_metadata.Rmd_ - R markdown defining the generation of the metadata file and the EML file based on EDI EML assembly line. * _10\_metadata\_compile.R_ - R script that compiles the metadata R markdown to an HTML document (metadata_summary.html) and an EML file in the product directory. * _99\_runall.R_ - Convenience R script for fully regenerating the data product. * _RStudioProject.Rproj_ - An RStudio project file provided for convenience in working with the code generating this data product with the appropriate working directory. * _supplemental/_ - Directory with supplemental protocol provenance data * _CO2sys\_Freshwater\_2020.xlsm_ - Version 2.1 (18 September 2012) of the CO2Sys spreadsheet (Pierrot et al., 2006) used to adjust the pH measured in the lab to ambient river temperatures at the time of sampling. (Data are not in this spreadsheet. It is provided for convenience.) ### 2.3. Contents of 03\_incremental.zip * _2018_UCFR\_Sensor\_Deployment\_Data.xlsx_ - Microsoft Excel file with the final compiled data tables. * _metadata\_summary.html_ - Summary of metadata and the process of archiving the workflow pipeline and compiling the associated metadata into EML * _processing\_notes.html_ - Notes on generating data tables and table metadata * _meta/_ - Directory with narrative metadata elements incorporated into metadata summary and EML * _abstract.md_ - A markdown file sourcing the data abstract. * _intellectual\_rights.txt_ - A text file sourcing the license for data use. * _methods.md_ - A markdown file sourcing the description of methods. * _purpose.txt_ - A text file sourcing the description of purpose. ## 3. References: Gran, G. 1952. Determination of the equivalence point in potentiometric titrations. Part II. Analyst 77: 661-671. doi: 10.1039/AN9527700661 Lai C.-Z., M. D. DeGrandpre, B. D. Wasser, T. A. Brandon, D. S. Clucas, E. J. Jaqueth, Z. D. Benson, C. M. Beatty, and R. S. Spauldin. 2016. Spectrophotometric measurement of freshwater pH with purified meta-cresol purple and phenol red. Limnology and Oceanography: Methods 14(12) 864-873. doi: 10.1002/lom3.10137. Pierrot, D. E. Lewis,and D. W. R. Wallace. 2006. MS Excel Program Developed for CO<sub>2</sub> System Calculations. ORNL/CDIAC-105a. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee. doi: 10.3334/CDIAC/otg.CO2SYS\_XLS\_CDIAC105a ## 4. Data product development history * 2021 August 7: Preparing initial version * Check on pH processing. Did 0.1 unit correction happen? * Update file lists in license statement and methods. * Check QA methods

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Creators:
Individual: Michael D DeGrandpre
Organization:University of Montana
Email Address:
michael.degrandpre@mso.umt.edu
Id:https://orcid.org/0000-0003-1969-6709
Individual: Cory M Beatty
Organization:University of Montana
Email Address:
cory.beatty@mso.umt.edu
Id:https://orcid.org/0000-0001-7868-2257
Contacts:
Individual: Michael D DeGrandpre
Organization:University of Montana
Email Address:
michael.degrandpre@mso.umt.edu
Id:https://orcid.org/0000-0003-1969-6709
Associated Parties:
Individual: Venice Bayrd
Organization:Montana State University
Email Address:
venice.bayrd@montana.edu
Id:https://orcid.org/0000-0002-5814-9380
Role:Data curation
Individual: Robert A Payn
Organization:Montana State University
Email Address:
rpayn@montana.edu
Id:https://orcid.org/0000-0001-8421-525X
Role:Data curation and project PI at MSU
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Role:Project PI at UM
Individual: Marc Peipoch
Organization:Stroud Water Research Center
Email Address:
mpeipoch@stroudcenter.org
Id:https://orcid.org/0000-0002-5943-831X
Role:Project co-PI
Individual: Juliana D'Andrilli
Organization:Louisiana University Marine Consortium
Email Address:
jdandrilli@lumcon.edu
Id:https://orcid.org/0000-0002-3352-2564
Role:Project co-PI

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2018-08-29
End:
2018-10-17
Sampling Site: 
Description:Site ID 003, restoration project reach A: bridge on Galen Road (site name: Galen)
Site Coordinates:
Longitude (degree): -112.753194444444Latitude (degree): 46.2373
Sampling Site: 
Description:Site ID 004, restoration project reach A: bridge on corner of W River Road and Gembeck Road, upstream of of Racetrack exit (site name: Racetrack)
Site Coordinates:
Longitude (degree): -112.744577777778Latitude (degree): 46.2654055555556

Project

Parent Project Information:

Title:LTREB: Collaborative research - River ecosystem responses to floodplain restoration
Personnel:
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Role:Principal Investigator
Funding: US National Science Foundation 1655197
Related Project:
Title:LTREB: Collaborative research - River ecosystem responses to floodplain restoration
Personnel:
Individual: Robert A Payn
Organization:Montana State University
Email Address:
rpayn@montana.edu
Id:https://orcid.org/0000-0001-8421-525X
Role:Principal Investigator
Funding: US National Science Foundation 1655198

Maintenance

Maintenance:
Description:Completed: Updates to these data are not expected
Frequency:
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'microatmospheres'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.101325'
        |     |     |     |  \___attribute 'name' = 'microatmospheres'
        |     |     |     |  \___attribute 'parentSI' = 'pascal'
        |     |     |     |  \___attribute 'unitType' = 'pressure'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'microatmospheres'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'micromolesPerLiter'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.000001'
        |     |     |     |  \___attribute 'name' = 'micromolesPerLiter'
        |     |     |     |  \___attribute 'parentSI' = 'molesPerLiter'
        |     |     |     |  \___attribute 'unitType' = 'concentration'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'micromoles of solute per liter of solution'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'microsiemensPerCentimeter'
        |     |     |     |  \___attribute 'multiplierToSI' = '0.00000001'
        |     |     |     |  \___attribute 'name' = 'microsiemensPerCentimeter'
        |     |     |     |  \___attribute 'parentSI' = 'siemensPerMeter'
        |     |     |     |  \___attribute 'unitType' = 'conductance'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'microSiemens per centimeter'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

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