Data Package Metadata   View Summary

Multispectral absorbance and fluorometric analysis of dissolved organic carbon in water samples taken from the Upper Clark Fork River (Montana, USA) during water year 2018 (1 Oct 2017 - 30 Sep 2018)

General Information
Data Package:
Local Identifier:edi.410.6
Title:Multispectral absorbance and fluorometric analysis of dissolved organic carbon in water samples taken from the Upper Clark Fork River (Montana, USA) during water year 2018 (1 Oct 2017 - 30 Sep 2018)
Alternate Identifier:DOI PLACE HOLDER
Abstract:

These data were collected to support monitoring of the Upper Clark Fork River restoration, and data collection was funded by the US NSF Long Term Research in Environmental Biology (LTREB) program and the US NSF EPSCoR funded Montana Consortium for Research on Environmental Water Systems. The LTREB monitoring project consists of monthly or bi-weekly water quality monitoring across a 200-km restoration gradient contaminated by historic mining practices to monitor inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and heavy metal contamination. The original analytical intent for these data was to assess the response of river dissolved organic carbon to the floodplain restoration. Data are multispectral fluorometric analyses of organic carbon dissolved in samples of well-mixed river thalweg water. Data include excitation-emission matrices as well as fluorometric summary indices calculated from specific wavelengths of excitation and emission. Data are from the 2018 water year (1 Oct 2017 to 30 Sep 2018). Data were collected on the Upper Clark Fork River (USGS HUC 17010201) at 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 N 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 and restoration of the uppermost 70 km of the UCFR are removing metal-contaminated sediments and lowering the floodplain to promote river-floodplain interaction 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) PIs from this project have gathered data on the benthic algae, river water chemistry, and sediment transformation of contaminants in water. UCFR LTREB funds support 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.
Publication Date:2022-02-13
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2017-10-26
End:
2018-09-27

People and Organizations
Contact:D'Andrilli, Juliana (Louisiana Universities Marine Consortium) [  email ]
Creator:D'Andrilli, Juliana (Louisiana Universities Marine Consortium)
Creator:Valett, H Maurice (University of Montana)
Creator:Utzman, Claire (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, Lead PI and Project PI at UM)
Associate:Peipoch, Marc (Stroud Water Research Center, Project co-PI)
Associate:DeGrandpre, Michael D (University of Montana, Project co-PI)
Associate:D'Andrilli, Juliana (Louisiana Universities Marine Consortium, Project co-PI)

Data Entities
Data Table Name:
EEMS_wy2018_Aqualog.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:
EEMS_excitation_wavelengths.csv
Description:
Wavelenths for excitation (columns left to right) in EEMS matrices
Data Table Name:
EEMS_emission_wavelengths.csv
Description:
Wavelenths for emissions (rows top to bottom) in EEMS matrices
Data Table Name:
Absorbance_wy2018_Aqualog.csv
Description:
Absorbance for all excitation wavelengths from analysis with an Aqualog multispectral fluorometer
Data Table Name:
Summary_metrics_wy2018.csv
Description:
Summary metrics of absorbance and fluorescence including the absorbace at 254nm, fluorescence index, and humification index
Other Name:
EEMS_wy2018_Aqualog_matrices.zip
Description:
Compressed zip file with fluorometric excitation-emission matrices. Matrix columns represent excitation wavelengths and matrix rows represent emission wavelengths (see Methods for details). Files are indexed by sampling date, site ID, and replicate ID in the table EEMS_wy2018_Aqualog.csv.
Other Name:
01_input.zip
Description:
Compressed data pipeline folder containing project default metadata. 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

Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/36fb7bf73713f245a6adc46525e2f03a
Name:EEMS_wy2018_Aqualog.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:657
Number of Columns:4

Table Structure
Object Name:EEMS_wy2018_Aqualog.csv
Size:45375 bytes
Authentication:3134f23383e50c0b71ab92addf55ced6 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: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 protocol.Identifier for site location. Property: Location. Entity: Upper Clark Fork River geography. Method: Project sampling map.Identifier for replicate samples. Property: Replicate identifier. Entity: Sampling of river water. Method: Field sample management protocol.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
DefinitionLocation 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
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
Accuracy Report:        
Accuracy Assessment:        
Coverage:        
Methods:        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/b2d7dd3f29cfc44e654ada3b3c6b0273
Name:EEMS_excitation_wavelengths.csv
Description:Wavelenths for excitation (columns left to right) in EEMS matrices
Number of Records:41
Number of Columns:2

Table Structure
Object Name:EEMS_excitation_wavelengths.csv
Size:344 bytes
Authentication:736155084b76fae98ee023b544f18581 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:Column number of a matrix. Property: Index. Entity: Matrix column dimension. Method: Count.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
Max41 
Unitnanometer
Typenatural
Min250 
Max450 
Missing Value Code:
CodeNA
ExplMissing value
CodeNA
ExplMissing value
Accuracy Report:    
Accuracy Assessment:    
Coverage:    
Methods:    

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/b82ae99807105d94d24edd3b44f88c96
Name: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: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:Row number of a matrix. Property: Index. Entity: Matrix row dimension. Method: Count.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
ExplMissing value
CodeNA
ExplMissing value
Accuracy Report:    
Accuracy Assessment:    
Coverage:    
Methods:    

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/d27f58c57912746219f6146838a6a986
Name:Absorbance_wy2018_Aqualog.csv
Description:Absorbance for all excitation wavelengths from analysis with an Aqualog multispectral fluorometer
Number of Records:210897
Number of Columns:5

Table Structure
Object Name:Absorbance_wy2018_Aqualog.csv
Size:7391743 bytes
Authentication:572e6b6d3a26f70adfda1b3513ea76e4 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: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 protocol.Identifier for site location. Property: Location. Entity: Upper Clark Fork River geography. Method: Project sampling map.Identifier for replicate samples. Property: Replicate identifier. Entity: Sampling of river water. Method: Field sample management protocol.Fluorometric excitation wavelength. Property: Wavelength. Entity: Instrument radiation excitation. Method: Aqualog multispectral fluorometry.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
Unitnanometer
Typenatural
Min240 
Max560 
Unitdimensionless
Typereal
Min-0.039824 
Max0.418811 
Missing Value Code:
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
Accuracy Report:          
Accuracy Assessment:          
Coverage:          
Methods:          

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/2f61893f6ad6f401731ba4fc8059be9f
Name:Summary_metrics_wy2018.csv
Description:Summary metrics of absorbance and fluorescence including the absorbace at 254nm, fluorescence index, and humification index
Number of Records:641
Number of Columns:6

Table Structure
Object Name:Summary_metrics_wy2018.csv
Size:47786 bytes
Authentication:aba28a9461bd2e63012e54ca04f324a6 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_254nm  
FI  
HIX  
Definition: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 protocol.Identifier for site location. Property: Location. Entity: Upper Clark Fork River geography. Method: Project sampling map.Identifier for replicate samples. Property: Replicate identifier. Entity: Sampling of river water. Method: Field sample management protocol.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 fluorometry.Fluorescence index of river water. Property: Fluorescence Index. Entity: Sample of filtered mixed thalweg river water. Method: Fluorescence index derivation.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
Unitdimensionless
Typereal
Min0.0233757656014137 
Max0.358993627320717 
Unitdimensionless
Typereal
Min1.40528859823713 
Max2.31538453689248 
Unitdimensionless
Typereal
Min0.888173878924306 
Max12.7809350266267 
Missing Value Code:
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
Accuracy Report:            
Accuracy Assessment:            
Coverage:            
Methods:            

Non-Categorized Data Resource

Name:EEMS_wy2018_Aqualog_matrices.zip
Entity Type:unknown
Description:Compressed zip file with fluorometric excitation-emission matrices. Matrix columns represent excitation wavelengths and matrix rows represent emission wavelengths (see Methods for details). Files are indexed by sampling date, site ID, and replicate ID in the table EEMS_wy2018_Aqualog.csv.
Physical Structure Description:
Object Name:EEMS_wy2018_Aqualog_matrices.zip
Size:11930075 bytes
Authentication:78a77ab87618088a4cb44dd8e836d2e9 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/4f738147ef5566b2cbd21745e4bd5818

Non-Categorized Data Resource

Name:01_input.zip
Entity Type:unknown
Description:Compressed data pipeline folder containing project default metadata. See methods for details.
Physical Structure Description:
Object Name:01_input.zip
Size:34333 bytes
Authentication:5f820a9463062314441f1ffb9c23f48e Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/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:11222 bytes
Authentication:f085156de66c519a9fea39478b33acb5 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/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:4543159 bytes
Authentication:a65c0940339acb0635d7e2f271adcc2e Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/410/6/e269ff6c46d3c6c4aba7cbee117b8289

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 2022 - 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_; * _01\_processing.Rmd;_ * _01\_processing\_compile.R;_ * _05\_ui\_narrative.R;_ * _05\_ui\_people.R;_ * _10\_metadata.Rmd;_ * _10\_metadata\_compile.R;_ * _99\_runall.R;_ * _RStudioProject.Rproj_ ### 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, Fluorometric Excitation-Emission Matrix
NALTriver water
LTER Controlled Vocabularydissolved organic carbon, fluorescence

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 W.A. Franke College of Forestry & Conservation Ecosystems Lab (directed by Ben Coleman) at the University of Montana 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 (5 nanometer resolution). Excitation wavelengths correspond to the columns of the excitation-emission matrices provided in this data product. The fluorometric intensity of the emission wavelengths are measured from 300 to 560 nanometers (2 nanometer resolution). Emission wavelengths correspond to the columns of the excitation-emission matrices provided in this data product. Values provided in the excitation-emission matrices 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 commonly used absorbance wavelengths like 254 nm. Note that absorbances above 450 nm are not valid data because there is no excitation above this wavelength. ### _Fluorescence index derivation_: After fluorometric excitation at a wavelength of 370 nm, the fluorescence index is calculated as the ratio of the fluorescent emission intensity at 450 nm divided by the fluorescent emission intensity at 500 nm (McKnight et al. 2001). ### _Humification index derivation_: FIXME ## 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 * _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. ### Contents of 02\_protocol.zip R code in the protocol depends on R packages: tidyr, readtext, knitr, 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. * _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) * _05\_ui\_narrative.R_ - shiny R app for managing narrative metadata (requires external package) * _05\_ui\_people.R_ - shiny R app for managing people metadata (requires external package) * _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). * _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. ### 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. * _LTREB\_OpticalProp\_Aqualog\_WY\_2018\_FINAL.csv_ - Original data file for summary metrics. * _metadata\_summary.html_ - Summary of metadata and the process of archiving the workflow pipeline and compiling the associated metadata into EML. * _processing\_notes.html_ - Metadata regarding the processing of the raw data files to the product's data tables and basic visualizations. * _meta/_ - Directory with narrative metadata elements incorporated into metadata summary and EML * _metadata\_narrative.RData_ - R data file with narrative metadata (created by Shiny R app) * _metadata\_people.RData_ - R data file with people metadata (created by Shiny R app) ## 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. ## Data product development history * 2022 February 12: Added the 254 absorbance, fluorescence index, and humification index data * Added Shiny tools for narrative and people * 2021 October 30: Incorporated content and feedback * Added sampling protocol info from Claire * Incorporated edits from Venice and Juliana * 2021 October 24: Updated with some detail from Juliana * Updated creator list to include Maury and Claire * Updated methods, need more detail on sampling from Claire * 2021 October 17: Updated with some of the new code and template updates * Added some information about matrices, including tables with wavelengths * 2021 August 15: Drafting first version of product * Checking on site IDs

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Juliana D'Andrilli
Organization:Louisiana Universities Marine Consortium
Email Address:
jdandrilli@lumcon.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:Louisiana Universities Marine Consortium
Email Address:
jdandrilli@lumcon.edu
Id:https://orcid.org/0000-0002-3352-2564
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:Lead PI and 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: Michael D DeGrandpre
Organization:University of Montana
Email Address:
michael.degrandpre@mso.umt.edu
Id:https://orcid.org/0000-0003-1969-6709
Role:Project co-PI
Individual: Juliana D'Andrilli
Organization:Louisiana Universities 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:
2017-10-26
End:
2018-09-27
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: DL park on frontage Rd north of bridge, samples taken via (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: bridge on McFarland Rd - Bonita (site name: Bonita)
Site Coordinates:
Longitude (degree): -113.589177777778Latitude (degree): 46.7177666666667
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: Madison)
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

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

UNM logo UW-M logo