Data Package Metadata   View Summary

Characterization of photosynthetic epilithic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 2019

General Information
Data Package:
Local Identifier:edi.1022.8
Title:Characterization of photosynthetic epilithic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 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 data in this product was to assess the response of the river algal community to the floodplain restoration. Data characterize epilithic biomass on the river bed including measurements of benthic standing stocks and abundance of pigments associated with primary producers. Metrics of characterization include areal density of chlorophyll a, areal density of phaeophytin, the ratio of carotenoid to chlorophyll absorbance, percent organic matter, areal density of organic matter, and category of biomass composition (filamentous algae vs. other epilithon). Samples were obtained from collecting and scrubbing five rocks at any given site. Biomass estimates were obtained from area-corrected ash free dry mass. Pigment concentrations were obtained through the use of extraction in acetone followed by spectroscopy. Data are from the 2019 algal growing season. Data were collected on the UCFR (USGS HUC 17010201) at seven 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 agency 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.
Publication Date:2023-04-14
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2019-07-09
End:
2019-10-04

People and Organizations
Contact:Valett, H Maurice (University of Montana) [  email ]
Creator:Valett, H Maurice (University of Montana)
Creator:Utzman, Claire (University of Montana)
Creator:Feijó de Lima, Rafael (University of Montana)
Associate:Valett, H Maurice (University of Montana, Funding Acquisition; Conceptualization; Supervision)
Associate:Utzman, Claire (University of Montana, Project administration; Investigation)
Associate:Feijó de Lima, Rafael (University of Montana, Conceptualization; Investigation; Methodology; 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:DeGrandpre, Michael D (University of Montana, Funding acquisition; Conceptualization)
Associate:Peipoch, Marc (Stroud Water Research Center, Funding acquisition; Conceptualization)
Associate:D'Andrilli, Juliana (Louisiana Universities Marine Consortium, Funding acquisition; Conceptualization)

Data Entities
Data Table Name:
Biomass_2019.csv
Description:
Analysis-ready characterization of epilithic biomass on rock samples taken from the river bed at study sites along the Upper Clark Fork River
Other Name:
Biomass_2019_meta.csv
Description:
Metadata describing the content of columns in the associated data table (comma delimited tabular text file)
Other Name:
Biomass_2019_vis.pdf
Description:
Summary visualization of the eplithic biomass data included in this product (postscript data file).
Other Name:
01_input.zip
Description:
Compressed data pipeline folder containing raw data files and 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.
Other Name:
readme.html
Description:
Notes from the processing of the metadata
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/6a6336c57d89f926d85071600d4da6f4
Name:Biomass_2019.csv
Description:Analysis-ready characterization of epilithic biomass on rock samples taken from the river bed at study sites along the Upper Clark Fork River
Number of Records:195
Number of Columns:9

Table Structure
Object Name:Biomass_2019.csv
Size:10124 bytes
Authentication:a4f7f64c82dbe743ac6c3da46c2008bc 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  
chla  
phaeo  
caroChlaRatio  
percentOM  
arealOM  
categoryBiomass  
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: Areal density of chlorophyll a in stream bed epilithon; Property: Areal density (mass per area) of chlorophyll a; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of suspension of sample from a measured surface area of stream bed substrateSummary: Areal density (mass per area) of phaeophytin in stream bed epilithon; Property: Areal density (mass per area) of phaeophytin; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of suspension of sample from a measured surface area of stream bed substrateSummary: Carotenoid to chlorophyll ratio in stream bed epilithon; Property: Carotenoid to chlorophyll ratio; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Spectrophotometric measurement of suspension of sample from a measured surface area of substrateSummary: Percent of epilithic sample; Property: Fraction ash-free dry mass; Entity: Top surface of sampled stone of stream bed substrate; Method: Ashing and reweighing of filtration residue from suspension of epilithon sample from a measured surface area of rockSummary: Areal density (mass per area) of organic matter in stream bed epilithon; Property: Areal density (mass per area) of organic matter; Entity: Epilithon from top surface of sampled stream bed substrate; Method: Ashing and reweighing of filtration residue from suspension of epilithon sample from a measured surface area of substrateSummary: High or low filamentous algae category assigned to biomass; Property: Category of abundance of filamentous algae; Entity: Top surface of sampled stone of stream bed substrate; Method: Field sample management protocol
Storage Type:date  
string  
string  
float  
float  
float  
float  
float  
string  
Measurement Type:dateTimenominalnominalratioratioratioratiorationominal
Measurement Values Domain:
FormatYYYYMMDD
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Code003
DefinitionProject site number 003
Source
Code Definition
Code004
DefinitionProject site number 004
Source
Code Definition
Code006
DefinitionProject site number 006
Source
Code Definition
Code008
DefinitionProject site number 008
Source
Code Definition
Code009
DefinitionProject site number 009
Source
Code Definition
Code011
DefinitionProject site number 011
Source
Code Definition
CodeJB
DefinitionProject site number JB
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Code1
DefinitionReplicate sample 1
Source
Code Definition
Code2
DefinitionReplicate sample 2
Source
Code Definition
Code3
DefinitionReplicate sample 3
Source
Code Definition
Code4
DefinitionReplicate sample 4
Source
Code Definition
Code5
DefinitionReplicate sample 5
Source
UnitmilligramsPerSquareMeter
Typereal
Min0.01 
Max200.05 
UnitmilligramsPerSquareMeter
Typereal
Min0.02 
Max118.01 
Unitdimensionless
Typereal
Min1.16 
Max2.57 
Unitdimensionless
Typereal
Min1.63 
Max97.29 
UnitgramsPerSquareMeter
Typereal
Min0.59 
Max175.95 
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeHigh
DefinitionHigh abundance of filamentous algae
Source
Code Definition
CodeLow
DefinitionLow abundance of filamntous algae, biomass dominated by other epilithon
Source
Missing Value Code:
CodeNA
ExplMissing value
CodeNA
ExplMissing value
CodeNA
ExplMissing value
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:Biomass_2019_meta.csv
Entity Type:unknown
Description:Metadata describing the content of columns in the associated data table (comma delimited tabular text file)
Physical Structure Description:
Object Name:Biomass_2019_meta.csv
Size:2899 bytes
Authentication:25c40b5a8b5ed2d15dce31cca636c46b Calculated By MD5
Externally Defined Format:
Format Name:text/csv
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/aa8ee320ebd93080d983cd8c21daf2ff

Non-Categorized Data Resource

Name:Biomass_2019_vis.pdf
Entity Type:unknown
Description:Summary visualization of the eplithic biomass data included in this product (postscript data file).
Physical Structure Description:
Object Name:Biomass_2019_vis.pdf
Size:54801 bytes
Authentication:a55f48256dc7f7c1024eb35f02bc106c Calculated By MD5
Externally Defined Format:
Format Name:application/pdf
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/5d92164a5adc2130ad4563182026d7b5

Non-Categorized Data Resource

Name:01_input.zip
Entity Type:unknown
Description:Compressed data pipeline folder containing raw data files and project default metadata. See methods for details.
Physical Structure Description:
Object Name:01_input.zip
Size:442412 bytes
Authentication:72ee21f66bd2747a0878903bed33e619 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/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:266108 bytes
Authentication:ee311b872a1386693180b712c5c65887 Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/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:9091717 bytes
Authentication:89c15338e9441e86b31ad205fc9c61eb Calculated By MD5
Externally Defined Format:
Format Name:application/zip
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/e269ff6c46d3c6c4aba7cbee117b8289

Non-Categorized Data Resource

Name:readme.html
Entity Type:unknown
Description:Notes from the processing of the metadata
Physical Structure Description:
Object Name:readme.html
Size:676323 bytes
Authentication:e2706769a52f4ca33b2f9910bace9d0a Calculated By MD5
Externally Defined Format:
Format Name:text/html
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1022/8/61a73fa3aa5fd7cba2bed0366aa8ec58

Data Package Usage Rights

Intellectual rights to the data of this data package are treated separately from those that apply 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 2023 - 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. This license applies to any code files released in the following compressed directory or it's subdirectories. - *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, epilithon
LTER Controlled Vocabularyorganic matter, algae, biomass, benthos

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 columns in full metadata for Data Tables under the Data Entities heading. More detail on the many of the methods summarized here are available in Hauer and Lamberti (2017). ### *Field sample management protocol* At each sampling site, 5 rocks (with repID numbered 1-5) were selected haphazardly in an attempt to approximate a random sample (true random sampling was impractical). Each rock was subjectively designated with either "high" filamentous biomass and processed by sampling filamentous algae from a measured surface area of the rock or "low" filamentous biomass and processed with conventional scrubbing and rinsing of epilithon from a measured surface area of the rock (Hauer and Lamberti 2017). Epilithon was sampled by scrubbing the rock with an iron brush where detached material was washed into a collection tray using river water. Resulting samples were bagged in the field and kept in a dark cooler for transport to the lab, where they were stored at 4 degrees Celsius until analysis. ### *Spectrophotometric measurement of suspension of epilithon sample from a measured surface area of rock* Pigment standing stocks were obtained from the residue of filtering a known volume of sample onto a 0.7-micron GFF filter or from a 1-2 gram subsample of a bulk sample of filamentous algal biomass collected from a measured surface area of the rock. Pigments were extracted from samples for 24h in a 90% buffered acetone solution. Absorbance of light at specific wavelengths was measured pre- and post- acidification of extracts for turbidity-corrected chlorophyll and phaeophytin quantification (664, 665, and 750nm, Hauer and Lamberti 2017) and carotenoids estimation (430nm). ### *Ashing and reweighing of filtration residue from suspension of epilithon sample from a measured surface area of rock* Organic matter standing stocks were obtained through a gravimetric approach based on residue from filtering a known volume of sample through a 0.7-micron GFF filter or a 1-2 gram subsample of a bulk sample of filamentous algal biomass collected from a measured surface area of the rock. The residue or subsample were dried until reaching a constant mass, combusted in a muffle furnace, and then reweighed to determine the mass of remaining ash. Ash-free dry mass was determined by subtracting the mass of inorganic ash from the dry weight that includes combustible organic matter (Hauer and Lamberti 2017). ## 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. Where 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 - *people.xlsx* - Excel file with tabular data on people associated with the project used for metadata generation. - *sites\_main.xlsx* - Microsoft Excel file with authoritative project site list at the time of publication of these data. - *2019\_Biomass\_AFDM\_Running\_QAQC.xlsx* - Spreadsheet with summary of AFDM calculations - *2019\_Biomass\_PIGMENTS\_Running\_QAQC.xlsx* - Spreadsheet with spectrophotometric data processing - *LTREB\_AFDM\_Chl a Rock Scrapings.zip* - Collection of spreadsheets with calculations for AFDM and spectrophotometric metrics for each sample and each sampling campaign. Zip file contains an MS Excel spreadsheet for each sampling campaign. ### *Contents of 02\_protocol.zip* - *pkgs/* - Folder with locally installed R packages for customized features - *.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 in the product (readme.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. R code in the protocol depends on external R packages: knitr, readxl, rmarkdown, purrr, xml2, EMLassemblyline, and shiny. 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. ### *Contents of 03\_incremental.zip* - *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) - *LTREB\_BIOMASS\_PIGMENTS\_2019\_DICTIONARY.xlsx* - Original metadata for 2019 data (for reference only, not all entries verified) - *LTREB\_BIOMASS\_PIGMENTS\_2019\_EDI\_METADATA.docx* - Original metadata for 2019 data (for reference only, not all entries verified) - *LTREB\_BIOMASS\_PIGMENTS\_2019\_ISF.csv* - Original internal data file for 2019 - *LTREB\_BIOMASS\_PIGMENTS\_2019\_ISF\_RFL\_2021\_10\_04.csv* - Updated original internal data file for 2019 - *processing\_notes.html* - Metadata regarding the processing of the raw data files to the product's data tables and basic visualizations. 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. ## References Hauer, F.R. and Lamberti, G. eds. 2017. Methods in stream ecology: Volume 1: Ecosystem structure. Academic Press. ## Data product development history - 2022 July 29: Original draft - Inquiry regarding Jens Bridge site ID - 2023 March 7 - Fixed Jens Bridge site info - Updated current practice on readme file and using CRediT taxonomy on personnel - 2023 April 2 - Finalizing for publication

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: 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
Individual: Rafael Feijó de Lima
Organization:University of Montana
Email Address:
rafael.feijo@mso.umt.edu
Id:https://orcid.org/0000-0001-8514-2195
Contacts:
Individual: H Maurice Valett
Organization:University of Montana
Email Address:
Maury.Valett@mso.umt.edu
Id:https://orcid.org/0000-0001-7146-6420
Associated Parties:
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; Supervision
Individual: Claire Utzman
Organization:University of Montana
Email Address:
claire.utzman@mso.umt.edu
Id:https://orcid.org/0000-0002-3228-8470
Role:Project administration; Investigation
Individual: Rafael Feijó de Lima
Organization:University of Montana
Email Address:
rafael.feijo@mso.umt.edu
Id:https://orcid.org/0000-0001-8514-2195
Role:Conceptualization; Investigation; Methodology; 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: 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
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: Juliana D'Andrilli
Organization:Louisiana Universities Marine Consortium
Email Address:
jdandrilli@lumcon.edu
Id:https://orcid.org/0000-0002-3352-2564
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:
2019-07-09
End:
2019-10-04
Sampling Site: 
Description:Site ID: 003; Common site name: Galen; Restoration project reach: A; Description: bridge on Galen Road
Site Coordinates:
Longitude (degree): -112.753194444444Latitude (degree): 46.2373
Sampling Site: 
Description:Site ID: 004; Common site name: Racetrack; Restoration project reach: A; Description: bridge on corner of W River Road and Gembeck Road, upstream of of Racetrack exit
Site Coordinates:
Longitude (degree): -112.744577777778Latitude (degree): 46.2654055555556
Sampling Site: 
Description:Site ID: 006; Common site name: Deer Lodge; Restoration project reach: A; Description: DL park on frontage Rd north of bridge
Site Coordinates:
Longitude (degree): -112.738411111111Latitude (degree): 46.3829861111111
Sampling Site: 
Description:Site ID: 008; Common site name: Garrison; Restoration project reach: A; Description: Above LBf River- river access from the fishing access road off the Beck Hill exit before the fishing loop from the road
Site Coordinates:
Longitude (degree): -112.739544444444Latitude (degree): 46.4985388888889
Sampling Site: 
Description:Site ID: 009; Common site name: Gold Creek; Restoration project reach: B; Description: below bridge on Gold Cr road, access is downstream, river right
Site Coordinates:
Longitude (degree): -112.928541666667Latitude (degree): 46.5901027777778
Sampling Site: 
Description:Site ID: 011; Common site name: Bonita; Restoration project reach: B; Description: Downstream from the bridge for Gillespie-Sliderock Road
Site Coordinates:
Longitude (degree): -113.5724Latitude (degree): 46.7217694444444
Sampling Site: 
Description:Site ID: JB; Common site name: Jens Bridge; Restoration project reach: B; Description: Near the bridge for Jens Road downstream from Goldcreek
Site Coordinates:
Longitude (degree): -113.012865Latitude (degree): 46.594844

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 '3.5.4'
        |     |     |___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