Data Package Metadata   View Summary

Multispectral absorbance and fluorescence analysis of dissolved organic carbon in water samples taken from the Upper Clark Fork River (Montana, USA) during water year 2019 (1 Oct 2018 - 30 Sep 2019)

General Information
Data Package:
Local Identifier:edi.1116.3
Title:Multispectral absorbance and fluorescence analysis of dissolved organic carbon in water samples taken from the Upper Clark Fork River (Montana, USA) during water year 2019 (1 Oct 2018 - 30 Sep 2019)
Alternate Identifier:DOI PLACE HOLDER
Abstract:

The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding likely to be extended through 2028. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are multispectral absorbance and fluorescence analyses of organic carbon dissolved in samples of well-mixed river thalweg water. Data include excitation-emission matrices, absorbance spectroscopy, as well as absorbance and fluorometric summary indices calculated at specific wavelengths of excitation and emission. Data are from the 2019 water year (1 Oct 2018 to 30 Sep 2019). Data were collected on the Upper Clark Fork River (USGS HUC 17010201) at 13 project sites distributed along the river from the vicinity of Anaconda to Missoula, Montana, USA.

Purpose:
Water quality in the Upper Clark Fork River (UCFR) suffers from a century-old mining legacy. Heavy metals and nitrogen enrichment associated with human activity influence aquatic communities and processes. A 200-million-dollar (USD) ecological remediation and restoration of the UCFR was initiated in 2013 and will continue for 20 years. Large-scale ecological restoration of the UCFR floodplain after removal of mine waste contamination is a component of the largest US EPA “superfund” project since implementation of the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) by the US government in 1980. Remediation of the uppermost 70 km of the UCFR is removing metal-contaminated sediments while restoration includes restructuring the floodplain and its vegetation while lowering its elevation to promote interaction with the river during high flows. Upgrades to wastewater treatment plants and changing hydrologic conditions will occur even as the State of Montana embarks upon a whole-scale restoration of the UCFR floodplain. Since the 1990s, state agencies and University of Montana (UM) researchers have gathered data on the benthic algae, river water chemistry, and sediment transformation of contaminants in water. UCFR LTREB funds starting in 2017 have continued support of baseline monitoring of metal contamination, carbon, biomass, nutrients, and metabolic activity. The motivation for extending the long-term dataset is to address changes in the character of subsidies and stressors for river productivity, algal blooms, and ecological integrity in a river being restored from long-term contamination problems. of generating the data product.
Publication Date:2024-07-15
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2018-10-11
End:
2019-09-17

People and Organizations
Contact:D'Andrilli, Juliana (University of North Texas) [  email ]
Creator:D'Andrilli, Juliana (University of North Texas)
Creator:Valett, H Maurice (University of Montana)
Creator:Utzman, Claire (University of Montana)
Associate:D'Andrilli, Juliana (University of North Texas, Funding Acquisition; Conceptualization; Supervision; Investigation; Methodology; Formal Analysis; Data curation)
Associate:Valett, H Maurice (University of Montana, Funding Acquisition; Conceptualization)
Associate:Utzman, Claire (University of Montana, Investigation)
Associate:Hurley, Patrick (University of Montana, Investigation)
Associate:Junker, James R (University of North Texas, Formal Analysis; Data curation)
Associate:Bayrd, Venice (Montana State University, Data curation)
Associate:Payn, Robert A (Montana State University, Funding Acquisition; Conceptualization; Data curation)
Associate:Peipoch, Marc (Stroud Water Research Center, Funding Acquisition; Conceptualization)
Associate:DeGrandpre, Michael D (University of Montana, Funding Acquisition; Conceptualization)

Data Entities
Data Table Name:
table_EEMSFiles_wy2019.csv
Description:
References to comma delimited text files with analysis-ready excitation-emission matrices (EEMS) from fluorometric analysis of dissolved organic carbon sampled in triplicate along the Upper Clark Fork River.
Data Table Name:
table_EEMS_excitation_wavelengths.csv
Description:
Wavelenths for excitation (columns left to right) in EEMS matrices
Data Table Name:
table_EEMS_emission_wavelengths.csv
Description:
Wavelenths for emissions (rows top to bottom) in EEMS matrices
Data Table Name:
table_absorbance_wy2019.csv
Description:
Absorbance for all excitation wavelengths from analysis with an Aqualog multispectral fluorometer
Data Table Name:
table_summary_metrics_wy2019.csv
Description:
Summary metrics of absorbance and fluorescence including the absorbace at 254nm, fluorescence index, and humification index
Other Name:
01_input.zip
Description:
Compressed data pipeline folder containing project default metadata, original data files, and code and notes for site-level preprocessing. 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.
Other Name:
matrices_EEMS_wy2019.zip
Description:
Compressed folder of comma-deliminted text files containing the excitation-emission matrices (EEMS) for this data product. File names indicate the sampling date, site ID, and replicate ID for the matrix in the file. Columns of matrices represent excitation wavelengths from 240 to 450 nm at 5 nm intervals. Rows of matrices represent emission wavelengths from 300 to 560 nm at 2 nm intervals (zip archive).
Other Name:
tableMeta_EEMSFiles_wy2019.csv
Description:
Metadata describing the content of columns in the associated table of references to EEMS matrices (comma delimited tabular text file)
Other Name:
tableMeta_EEMS_excitation_wavelengths.csv
Description:
Metadata describing the content of columns in the associated table of wavelengths for EEMS excitations (comma delimited tabular text file)
Other Name:
tableMeta_EEMS_emission_wavelengths.csv
Description:
Metadata describing the content of columns in the associated table of wavelengths for EEMS emissions (comma delimited tabular text file)
Other Name:
tableMeta_absorbance_wy2019.csv
Description:
Metadata describing the content of columns in the associated table of absorbances for fluorometric excitation wavelengths (comma delimited tabular text file)
Other Name:
tableMeta_summary_metrics_wy2019.csv
Description:
Metadata describing the content of columns in the associated table of summary fluorometric metrics known to characterize organic matter (comma delimited tabular text file)
Other Name:
dataVis_summary_metrics_wy2019.pdf
Description:
Summary visualization of the fluorescene and absorbance summary metrics (postcript data file, pdf)
Other Name:
readme.html
Description:
Detailed description of the data product
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/1cdff586076f7f0a863e877777b9a175
Name:table_EEMSFiles_wy2019.csv
Description:References to comma delimited text files with analysis-ready excitation-emission matrices (EEMS) from fluorometric analysis of dissolved organic carbon sampled in triplicate along the Upper Clark Fork River.
Number of Records:627
Number of Columns:4

Table Structure
Object Name:table_EEMSFiles_wy2019.csv
Size:43932 bytes
Authentication:5022448b31328844df4ffba30d25e9d8 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 
Column Name:dateString  
siteID  
repID  
eemsFile  
Definition:Summary: Date of sample collection using a Gregorian calendar in US Mountain time (America/Denver); Property: Time; Entity: Collection of a river water sample; Method: Field sample management protocolSummary: Identifier for site location; Property: Location; Entity: Upper Clark Fork River geography; Method: Field sample management protocolSummary: Identifier for replicate samples; Property: Replicate identifier; Entity: Sampling of river water; Method: Field sample management protocolSummary: Location of EEMS matrix file in accompanying zip file; Property: Location of excitation emission matrix file; Entity: Sample of filtered mixed thalweg river water; Method: Aqualog multispectral fluorometry
Storage Type:date  
string  
string  
string  
Measurement Type:dateTimenominalnominalnominal
Measurement Values Domain:
FormatYYYYMMDD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Code001
DefinitionProject site number 001
Source
Code Definition
Code002
DefinitionProject site number 002
Source
Code Definition
Code003
DefinitionProject site number 003
Source
Code Definition
Code004
DefinitionProject site number 004
Source
Code Definition
Code005
DefinitionProject site number 005
Source
Code Definition
Code006
DefinitionProject site number 006
Source
Code Definition
Code007
DefinitionProject site number 007
Source
Code Definition
Code008
DefinitionProject site number 008
Source
Code Definition
Code009
DefinitionProject site number 009
Source
Code Definition
Code010
DefinitionProject site number 010
Source
Code Definition
Code011
DefinitionProject site number 011
Source
Code Definition
Code012
DefinitionProject site number 012
Source
Code Definition
Code013
DefinitionProject site number 013
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeA
DefinitionReplicate sample A
Source
Code Definition
CodeB
DefinitionReplicate sample B
Source
Code Definition
CodeC
DefinitionReplicate sample C
Source
Code Definition
CodeD
DefinitionReplicate sample D
Source
DefinitionSummary: Location of EEMS matrix file in accompanying zip file; Property: Location of excitation emission matrix file; Entity: Sample of filtered mixed thalweg river water; Method: Aqualog multispectral fluorometry
Missing Value Code:
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
Accuracy Report:        
Accuracy Assessment:        
Coverage:        
Methods:        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/aca47c51d62de0ca85873496468a241c
Name:table_EEMS_excitation_wavelengths.csv
Description:Wavelenths for excitation (columns left to right) in EEMS matrices
Number of Records:43
Number of Columns:2

Table Structure
Object Name:table_EEMS_excitation_wavelengths.csv
Size:360 bytes
Authentication:031784c44cec550967ee50db853c3a64 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 
Column Name:colNum  
ExWavelength  
Definition:Summary: Column number of a matrix; Property: Index; Entity: Matrix column dimension; Method: CountSummary: Fluorometric excitation wavelength; Property: Wavelength; Entity: Instrument radiation excitation; Method: Aqualog multispectral fluorometry
Storage Type:float  
float  
Measurement Type:ratioratio
Measurement Values Domain:
Unitdimensionless
Typenatural
Min
Max43 
Unitnanometer
Typenatural
Min240 
Max450 
Missing Value Code:
CodeNA
ExplNot Available
CodeNA
ExplNot Available
Accuracy Report:    
Accuracy Assessment:    
Coverage:    
Methods:    

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/ab69582c34c9a33ae74d48ad45f24500
Name:table_EEMS_emission_wavelengths.csv
Description:Wavelenths for emissions (rows top to bottom) in EEMS matrices
Number of Records:131
Number of Columns:2

Table Structure
Object Name:table_EEMS_emission_wavelengths.csv
Size:1096 bytes
Authentication:ec2daad030eb11b66fdd945373a912d6 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 
Column Name:rowNum  
EmWavelength  
Definition:Summary: Row number of a matrix; Property: Index; Entity: Matrix row dimension; Method: CountSummary: Fluorometric emission wavelength; Property: Wavelength; Entity: Sample radiation emission; Method: Aqualog multispectral fluorometry
Storage Type:float  
float  
Measurement Type:ratioratio
Measurement Values Domain:
Unitdimensionless
Typenatural
Min
Max131 
Unitnanometer
Typenatural
Min300 
Max560 
Missing Value Code:
CodeNA
ExplNot Available
CodeNA
ExplNot Available
Accuracy Report:    
Accuracy Assessment:    
Coverage:    
Methods:    

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/9532796f587bc990b95f3f604e06fee7
Name:table_absorbance_wy2019.csv
Description:Absorbance for all excitation wavelengths from analysis with an Aqualog multispectral fluorometer
Number of Records:201267
Number of Columns:5

Table Structure
Object Name:table_absorbance_wy2019.csv
Size:7054980 bytes
Authentication:7eba5ac8e00779548647a8823295b3d7 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 
Column Name:dateString  
siteID  
repID  
wavelength  
absorbance  
Definition:Summary: Date of sample collection using a Gregorian calendar in US Mountain time (America/Denver); Property: Time; Entity: Collection of a river water sample; Method: Field sample management protocolSummary: Identifier for site location; Property: Location; Entity: Upper Clark Fork River geography; Method: Field sample management protocolSummary: Identifier for replicate samples; Property: Replicate identifier; Entity: Sampling of river water; Method: Field sample management protocolSummary: Fluorometric excitation wavelength; Property: Wavelength; Entity: Instrument radiation excitation; Method: Aqualog multispectral fluorometrySummary: Absorbance of radiation for a sample of river water; Property: Absorbance of radiation; Entity: Sample of filtered mixed thalweg river water; Method: Aqualog multispectral fluorometry
Storage Type:date  
string  
string  
float  
float  
Measurement Type:dateTimenominalnominalratioratio
Measurement Values Domain:
FormatYYYYMMDD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Code001
DefinitionProject site number 001
Source
Code Definition
Code002
DefinitionProject site number 002
Source
Code Definition
Code003
DefinitionProject site number 003
Source
Code Definition
Code004
DefinitionProject site number 004
Source
Code Definition
Code005
DefinitionProject site number 005
Source
Code Definition
Code006
DefinitionProject site number 006
Source
Code Definition
Code007
DefinitionProject site number 007
Source
Code Definition
Code008
DefinitionProject site number 008
Source
Code Definition
Code009
DefinitionProject site number 009
Source
Code Definition
Code010
DefinitionProject site number 010
Source
Code Definition
Code011
DefinitionProject site number 011
Source
Code Definition
Code012
DefinitionProject site number 012
Source
Code Definition
Code013
DefinitionProject site number 013
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeA
DefinitionReplicate sample A
Source
Code Definition
CodeB
DefinitionReplicate sample B
Source
Code Definition
CodeC
DefinitionReplicate sample C
Source
Code Definition
CodeD
DefinitionReplicate sample D
Source
Unitnanometer
Typenatural
Min240 
Max560 
Unitdimensionless
Typereal
Min-0.076822 
Max0.188304 
Missing Value Code:
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
Accuracy Report:          
Accuracy Assessment:          
Coverage:          
Methods:          

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/3d83ea1c2c09c0ae547385cea7e95282
Name:table_summary_metrics_wy2019.csv
Description:Summary metrics of absorbance and fluorescence including the absorbace at 254nm, fluorescence index, and humification index
Number of Records:627
Number of Columns:6

Table Structure
Object Name:table_summary_metrics_wy2019.csv
Size:46747 bytes
Authentication:bc1ecf173fb9b224e350fe620d990b87 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 
Column Name:dateString  
siteID  
repID  
abs_254  
FI  
HIX  
Definition:Summary: Date of sample collection using a Gregorian calendar in US Mountain time (America/Denver); Property: Time; Entity: Collection of a river water sample; Method: Field sample management protocolSummary: Identifier for site location; Property: Location; Entity: Upper Clark Fork River geography; Method: Field sample management protocolSummary: Identifier for replicate samples; Property: Replicate identifier; Entity: Sampling of river water; Method: Field sample management protocolSummary: Absorbance of radiation at 254 nm for a sample of river water; Property: Absorbance of 254 nm radiation; Entity: Sample of filtered mixed thalweg river water; Method: Aqualog multispectral fluorometrySummary: Fluorescence index of river water; Property: Fluorescence Index; Entity: Sample of filtered mixed thalweg river water; Method: Fluorescence index derivationSummary: Humification index of river water; Property: Humification Index; Entity: Sample of filtered mixed thalweg river water; Method: Humification index derivation
Storage Type:date  
string  
string  
float  
float  
float  
Measurement Type:dateTimenominalnominalratioratioratio
Measurement Values Domain:
FormatYYYYMMDD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Code001
DefinitionProject site number 001
Source
Code Definition
Code002
DefinitionProject site number 002
Source
Code Definition
Code003
DefinitionProject site number 003
Source
Code Definition
Code004
DefinitionProject site number 004
Source
Code Definition
Code005
DefinitionProject site number 005
Source
Code Definition
Code006
DefinitionProject site number 006
Source
Code Definition
Code007
DefinitionProject site number 007
Source
Code Definition
Code008
DefinitionProject site number 008
Source
Code Definition
Code009
DefinitionProject site number 009
Source
Code Definition
Code010
DefinitionProject site number 010
Source
Code Definition
Code011
DefinitionProject site number 011
Source
Code Definition
Code012
DefinitionProject site number 012
Source
Code Definition
Code013
DefinitionProject site number 013
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeA
DefinitionReplicate sample A
Source
Code Definition
CodeB
DefinitionReplicate sample B
Source
Code Definition
CodeC
DefinitionReplicate sample C
Source
Code Definition
CodeD
DefinitionReplicate sample D
Source
Unitdimensionless
Typereal
Min0.0253343603643397 
Max0.159811993240917 
Unitdimensionless
Typereal
Min1.40831459471035 
Max4.72869931542917 
Unitdimensionless
Typereal
Min0.0607827953440882 
Max495.297296663619 
Missing Value Code:
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
CodeNA
ExplNot Available
Accuracy Report:            
Accuracy Assessment:            
Coverage:            
Methods:            

Non-Categorized Data Resource

Name:01_input.zip
Entity Type:unknown
Description:Compressed data pipeline folder containing project default metadata, original data files, and code and notes for site-level preprocessing. See methods for details.
Physical Structure Description:
Object Name:01_input.zip
Size:5063748 bytes
Authentication:5b436070bbd05e7afdf5be7d24c70245 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/ea878d31f456aaa1c1b82d3fb7927a42

Non-Categorized Data Resource

Name:02_protocol.zip
Entity Type:unknown
Description:Compressed data pipeline folder containing R markdown and R scripts for processing data and metadata. See methods for details.
Physical Structure Description:
Object Name:02_protocol.zip
Size:13433 bytes
Authentication:d294e6344410628692bfb0d84887aa5d Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/d4ac7e8b52aed4b7c17dc83de280ac54

Non-Categorized Data Resource

Name:03_incremental.zip
Entity Type:unknown
Description:Compressed data pipeline folder containing detailed notes and incremental data associated with generation of the data product. See methods for details.
Physical Structure Description:
Object Name:03_incremental.zip
Size:372868 bytes
Authentication:be13bb7df2d0366db030d75c4af36382 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/e269ff6c46d3c6c4aba7cbee117b8289

Non-Categorized Data Resource

Name:matrices_EEMS_wy2019.zip
Entity Type:unknown
Description:Compressed folder of comma-deliminted text files containing the excitation-emission matrices (EEMS) for this data product. File names indicate the sampling date, site ID, and replicate ID for the matrix in the file. Columns of matrices represent excitation wavelengths from 240 to 450 nm at 5 nm intervals. Rows of matrices represent emission wavelengths from 300 to 560 nm at 2 nm intervals (zip archive).
Physical Structure Description:
Object Name:matrices_EEMS_wy2019.zip
Size:11686568 bytes
Authentication:6c49a6437aba9939a0f33988e67add04 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/28d580ab52cfc088dd1b3fae53aa6468

Non-Categorized Data Resource

Name:tableMeta_EEMSFiles_wy2019.csv
Entity Type:unknown
Description:Metadata describing the content of columns in the associated table of references to EEMS matrices (comma delimited tabular text file)
Physical Structure Description:
Object Name:tableMeta_EEMSFiles_wy2019.csv
Size:1132 bytes
Authentication:db285e31f25eec1962b683f09b072ab8 Calculated By MD5
Externally Defined Format:
Format Name:text/csv
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/647fad6eb25bf06ff8f3dce26a984c1b

Non-Categorized Data Resource

Name:tableMeta_EEMS_excitation_wavelengths.csv
Entity Type:unknown
Description:Metadata describing the content of columns in the associated table of wavelengths for EEMS excitations (comma delimited tabular text file)
Physical Structure Description:
Object Name:tableMeta_EEMS_excitation_wavelengths.csv
Size:528 bytes
Authentication:3dec885c82a4b577d53945a99a0d1223 Calculated By MD5
Externally Defined Format:
Format Name:text/csv
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/d903872e5c453817f7d261b68a0b1ca9

Non-Categorized Data Resource

Name:tableMeta_EEMS_emission_wavelengths.csv
Entity Type:unknown
Description:Metadata describing the content of columns in the associated table of wavelengths for EEMS emissions (comma delimited tabular text file)
Physical Structure Description:
Object Name:tableMeta_EEMS_emission_wavelengths.csv
Size:512 bytes
Authentication:84a5aa67d4e426898334115f356d2fe3 Calculated By MD5
Externally Defined Format:
Format Name:text/csv
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/f0876afabafd38bb68dc117bba01477f

Non-Categorized Data Resource

Name:tableMeta_absorbance_wy2019.csv
Entity Type:unknown
Description:Metadata describing the content of columns in the associated table of absorbances for fluorometric excitation wavelengths (comma delimited tabular text file)
Physical Structure Description:
Object Name:tableMeta_absorbance_wy2019.csv
Size:1357 bytes
Authentication:4a39907f594b196996208a37cbc242b6 Calculated By MD5
Externally Defined Format:
Format Name:text/csv
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/42afa84ba319a8ef9ae4d891d407c14f

Non-Categorized Data Resource

Name:tableMeta_summary_metrics_wy2019.csv
Entity Type:unknown
Description:Metadata describing the content of columns in the associated table of summary fluorometric metrics known to characterize organic matter (comma delimited tabular text file)
Physical Structure Description:
Object Name:tableMeta_summary_metrics_wy2019.csv
Size:1604 bytes
Authentication:93ff239be0f78062343db7f46b06783b Calculated By MD5
Externally Defined Format:
Format Name:text/csv
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/4fac0fcc7efe305712a731030a2ccbdc

Non-Categorized Data Resource

Name:dataVis_summary_metrics_wy2019.pdf
Entity Type:unknown
Description:Summary visualization of the fluorescene and absorbance summary metrics (postcript data file, pdf)
Physical Structure Description:
Object Name:dataVis_summary_metrics_wy2019.pdf
Size:94686 bytes
Authentication:de5502fd7277184206ae724f507136bd Calculated By MD5
Externally Defined Format:
Format Name:application/pdf
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/51711cdcc12abadaf6bb789b8be6e586

Non-Categorized Data Resource

Name:readme.html
Entity Type:unknown
Description:Detailed description of the data product
Physical Structure Description:
Object Name:readme.html
Size:1076675 bytes
Authentication:8f621093b397b48db01514f4115c2392 Calculated By MD5
Externally Defined Format:
Format Name:text/html
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1116/3/61a73fa3aa5fd7cba2bed0366aa8ec58

Data Package Usage Rights

Intellectual rights to the data of this data package are treated separately to the code; please read carefully below. Professional etiquette dictates 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. ## CODE LICENSE STATEMENT Copyright 2024 - 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. Files released under this license include any code in the folder *02\_protocol.zip*. ### 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ## DATA RIGHTS STATEMENT The data selection and arrangement; documentation; metadata; and all data in this product not explicitly listed in the code license specified above 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. ### Legal Code Text **CC0 1.0 Universal Public Domain Dedication** Statement of Purpose The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others. For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights. 1. Copyright and Related Rights. A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following: 1. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work; 2. moral rights retained by the original author(s) and/or performer(s); 3. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work; 4. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below; 5. rights protecting the extraction, dissemination, use and reuse of data in a Work; 6. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and 7. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof. 2. Waiver. To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose. 3. Public License Fallback. Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose. 4. Limitations and Disclaimers. 1. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document. 2. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law. 3. Affirmer disclaims responsibility for clearing rights of other persons that may apply to the Work or any use thereof, including without limitation any person's Copyright and Related Rights in the Work. Further, Affirmer disclaims responsibility for obtaining any necessary consents, permissions or other rights required for any use of the Work. 4. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work.

Keywords

By Thesaurus:
(No thesaurus)Upper Clark Fork River restoration, NSF DEB LTREB 1655197, Montana, Northwestern United States, Northwestern Forested Mountains Ecoregion, excitation-emission matrix
NALTriver water, fluorescence, absorbance, spectroscopy
LTER Controlled Vocabularydissolved organic carbon

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:
## Measurement methods Where more details are available, each description below is cross-referenced with the brief methods caption provided in the descriptions of the table columns. ### *Field sample management protocol* Water samples were collected from the thalweg using a 4-L HDPE bottle. Filtration was conducted with an apparatus that included a Millipore filter holder with a filtrate collection vessel, Whatman glass fiber filters (pore size 0.7 micron), and a 12-V Thomas vacuum pump. Before sampling, filters were combusted at 500 degrees Celsius for one hour. Filtered water from this unit was placed into a 20-milliliter borosilicate amber glass vial, which before sampling was acid-washed and combusted at 425 degrees Celsius for 4 hours. Filtered water was used to rinse the vials before being filled. Vials were capped with a lid containing a Teflon disc. Samples were stored on ice in a cooler in the dark in transport to the lab and subsequently stored in a refrigerator at ca. 4 degrees Celsius before analysis. ### *Aqualog multispectral fluorometry* Fluorescence of aqueous samples was measured in the Environmental Analytical Laboratory (directed by Dr. Stephanie Ewing) in the Department of Land Resources and Environmental Sciences (LRES) in the College of Agriculture at Montana State University using an Aqualog Multispectral Fluorometer (Horiba, Kyoto, Japan). Filtered samples of river water are exposed to radiation at excitation wavelengths from 240 to 450 nanometers at a 5-nanometer resolution. Excitation wavelengths correspond to the columns of the excitation-emission matrices (EEMS) provided in this data product. The fluorometric intensity of the emission wavelengths are measured from 300 to 560 nanometers at a 2-nanometer resolution. Emission wavelengths correspond to the rows of the EEMS provided in this data product. Values provided in the EEMS are thus fluorometric intensities of emission at a given pairing of excitation and emission wavelengths as indicated by the column and row in the matrix. All data were generated in signal/reference mode to normalize the emission signal relative to the excitation light intensity. EEMS were corrected using Aqualog-specific protocols outlined in Cory et al. (2010). Spectra were corrected against purified water (Milli-Q) field blanks that were exposed to the same sampling protocol as stated in the field sample management protocol above. One blank sample was collected per sampling day. UV-Vis absorbance spectra from each scan were used to correct the EEMS for the inner filter effects and scattering corrections were applied for the Rayleigh-Tyndall effect and Raman scattering peaks. The fraction of the excitation radiation absorbed by the sample at each wavelength is also measured by the fluorometer. Absorbance was interpolated from the 5-nm excitation resolution to a 1-nm resolution of absorbance values. This interpolation is necessary to estimate absorbance values at wavelengths commonly used for summarizing organic matter quality, such as 254 nm. ### *Fluorescence index derivation* After fluorometric excitation at a wavelength of 370 nm, the fluorescence index (FI) is calculated as the ratio of the fluorescence emission intensity at 450 nm divided by the fluorescence emission intensity at 500 nm (McKnight et al. 2001). ### *Humification index derivation* After fluorometric excitation at a wavelength of 254 nm, the humification index (HIX) is calculated by dividing the sum of fluorescence intensities between emission wavelengths 435 and 480 nm by the sum of fluorescence intensities between emission wavelengths 300 and 345 nm (Ohno, 2002). Numbers reported are relative to the corresponding absorbance of a blank sample, such that negative numbers indicate an absorbance less than that of the blank. ## 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. ### *Contents of 01\_input.zip* - *meta/* - Directory with project templates for metadata - *attributes.xlsx* - Excel file with commonly used table column attributes in the project - *narr\_abstract.md* - Markdown text file source for abstract - *narr\_methods.md* - Markdown text file source for methods - *narr\_purpose.md* - Markdown text file source for purpose statement - *narr\_rights.md* - Markdown text file source for intellectual rights - *narr\_title.txt* - Text file source for title - *people.xlsx* - Excel file with tabular data on people associated with the project used for metadata generation. - *ppl\_contact.csv* - Comma delimited text file source for contact information - *ppl\_creators.csv* - Comma delimited text file source for list of creators - *ppl\_funding.csv* - Comma delimited text file source for list of funders - *ppl\_others.csv* - Comma delimited text file source for list of other contributors - *sites_main.xlsx* - Microsoft Excel file with authoritative project site list at the time of publication of these data. - *absorbance.zip* - Raw files from the Aqualog ### *Contents of 02\_protocol.zip* R code in this folder depends on external R packages: knitr, readxl, rmarkdown, xml2, and EMLassemblyline. 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. - *01\_processing.Rmd* - R markdown creating the data tables and associated metadata. - *01\_processing\_compile.R* - R script that compiles the processing R markdown to an HTML document (*03\_incremental.zip/processing\_notes.html*) - *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.html) and an EML file (eml.xml). - *RStudioProject.Rproj* - An RStudio project file provided for convenience in working with the code generating this data product with the appropriate working directory. ### *Contents of 03\_incremental.zip* R code included in this product will generate temporary files in the ./03\_incremental/.temp folder. These temporary files contain no unique data or metadata and thus are not archived in the corresponding zip file. - *absFilenames.RData* - RData file with the incremental copy of the sorted Absorbance file names - *eemsFilenames.RData* - RData file with the incremental copy of the sorted EEMS file names for generating the cross-reference table - *LTREB\_OpticalProp\_Aqualog\_WY\_2019\_FINAL.csv* - Original data file for summary metrics. - *metadata.RData* - Incremental metadata generated by the data processing R markdown - *processing\_notes.html* - Metadata regarding the processing of the raw data files to the product's data tables and basic visualizations. ## References Cory, R. M., M. P. Miller, D. M. McKnight, J. J. Guerard, and P. L. Miller. 2010. Effect of instrument-specific response on the analysis of fulvic acid fluorescence spectra. Limnology and Oceanography-Methods 8(2) 67-78. McKnight, D. M., E. W. Boyer, P. K. Westerhoff, P. T. Doran, T. Kulbe, and D. T. Andersen. 2001. Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity. Limnology and Oceanography 46(1) 38-48. Ohno, T. 2002. Fluorescence inner-filtering correction for determining the humification index of dissolved organic matter. Environmental Science and Technology, 36, 742-746.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Juliana D'Andrilli
Organization:University of North Texas
Email Address:
Juliana.D'andrilli@unt.edu
Id:https://orcid.org/0000-0002-3352-2564
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Individual: Claire Utzman
Organization:University of Montana
Email Address:
claire.utzman@mso.umt.edu
Id:https://orcid.org/0000-0002-3228-8470
Contacts:
Individual: Juliana D'Andrilli
Organization:University of North Texas
Email Address:
Juliana.D'andrilli@unt.edu
Id:https://orcid.org/0000-0002-3352-2564
Associated Parties:
Individual: Juliana D'Andrilli
Organization:University of North Texas
Email Address:
Juliana.D'andrilli@unt.edu
Id:https://orcid.org/0000-0002-3352-2564
Role:Funding Acquisition; Conceptualization; Supervision; Investigation; Methodology; Formal Analysis; Data curation
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Role:Funding Acquisition; Conceptualization
Individual: Claire Utzman
Organization:University of Montana
Email Address:
claire.utzman@mso.umt.edu
Id:https://orcid.org/0000-0002-3228-8470
Role:Investigation
Individual: Patrick Hurley
Organization:University of Montana
Email Address:
patrick.hurley@umontana.edu
Role:Investigation
Individual: James R Junker
Organization:University of North Texas
Email Address:
James.Junker@unt.edu
Id:https://orcid.org/0000-0001-9713-2330
Role:Formal Analysis; Data curation
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:Funding Acquisition; Conceptualization; Data curation
Individual: Marc Peipoch
Organization:Stroud Water Research Center
Email Address:
mpeipoch@stroudcenter.org
Id:https://orcid.org/0000-0002-5943-831X
Role:Funding Acquisition; Conceptualization
Individual: Michael D DeGrandpre
Organization:University of Montana
Email Address:
michael.degrandpre@mso.umt.edu
Id:https://orcid.org/0000-0003-1969-6709
Role:Funding Acquisition; Conceptualization

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
2018-10-11
End:
2019-09-17
Sampling Site: 
Description:Site ID 001, restoration project reach A: bridge on Garnet Way (site name: Warm Springs)
Site Coordinates:
Longitude (degree): -112.770111111111Latitude (degree): 46.1870222222222
Sampling Site: 
Description:Site ID 002, restoration project reach A: bridge on Perkins Rd from frontage access, location of Galen USGS gauge 12323800 (site name: Perkins)
Site Coordinates:
Longitude (degree): -112.767502777778Latitude (degree): 46.2084666666667
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
Sampling Site: 
Description:Site ID 005, restoration project reach A: bridge on Sager Lane (site name: Sager)
Site Coordinates:
Longitude (degree): -112.736238888889Latitude (degree): 46.3172666666667
Sampling Site: 
Description:Site ID 006, restoration project reach A: Deer Lodge Arrow Stone park on frontage Rd north of bridge (site name: Deer Lodge)
Site Coordinates:
Longitude (degree): -112.738411111111Latitude (degree): 46.3829861111111
Sampling Site: 
Description:Site ID 007, restoration project reach A: bridge on Rock Creek Cattle Rd (site name: Cattle Rd)
Site Coordinates:
Longitude (degree): -112.72825Latitude (degree): 46.4727722222222
Sampling Site: 
Description:Site ID 008, restoration project reach A: Above LBF River- river access from the fishing access road off the Beck Hill exit before the fishing loop from the road (site name: Garrison)
Site Coordinates:
Longitude (degree): -112.739544444444Latitude (degree): 46.4985388888889
Sampling Site: 
Description:Site ID 009, restoration project reach B: below bridge on Gold Cr road, access is downstream, river right (site name: Gold Creek)
Site Coordinates:
Longitude (degree): -112.928541666667Latitude (degree): 46.5901027777778
Sampling Site: 
Description:Site ID 010, restoration project reach B: Bear Mouth rest stop on I90 W, upstream end of parking lot, just downstream of lone pine on bank (site name: Bear Gulch)
Site Coordinates:
Longitude (degree): -113.345752777778Latitude (degree): 46.7037916666667
Sampling Site: 
Description:Site ID 011, restoration project reach B: Downstream from the bridge for Gillespie-Sliderock Road (site name: Bonita)
Site Coordinates:
Longitude (degree): -113.5724Latitude (degree): 46.7217694444444
Sampling Site: 
Description:Site ID 012, restoration project reach C: bridge on Turah Rd (site name: Turah)
Site Coordinates:
Longitude (degree): -113.813647222222Latitude (degree): 46.8262416666667
Sampling Site: 
Description:Site ID 013, restoration project reach Middle Fork: foot bridge on Madison, UM (site name: Missoula)
Site Coordinates:
Longitude (degree): -113.983116666667Latitude (degree): 46.8674388888889

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
Related Project:
Title:RII Track-1 Consortium for Research on Environmental Water Systems
Personnel:
Individual: Ragan M Callaway
Organization:University of Montana
Email Address:
Ray.Callaway@mso.umt.edu
Id:https://orcid.org/0000-0001-7342-4312
Role:Principal Investigator
Funding: US National Science Foundation OIA-1757351

Maintenance

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

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |     |___text '\n            '
        |     |     |___element 'app'
        |     |     |     |___text 'EMLassemblyline'
        |     |     |___text '\n            '
        |     |     |___element 'release'
        |     |     |     |___text '3.5.5'
        |     |     |___text '\n         '
        |     |___text '\n      '
        |___text '\n   '

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

UNM logo UW-M logo