﻿This DATSETNAMEreadme.txt file was generated on 2022-02-14 by SARAH JOVAN
<help text is included in angle brackets, and can be deleted before saving>


GENERAL INFORMATION

1. Title of Dataset: Measurements of heavy metals in the moss Orthotrichum lyellii collected using community science in the Duwamish Valley, Seattle, Washington, U.S.A.

2. Author Information
	A. Principal Investigator Contact Information
		Name: Sarah Jovan
		Institution: U.S. Forest Service Pacific Northwest Research Station
		Address: 
		Email: sarah.jovan@usda.gov

	B. Associate or Co-investigator Contact Information
		Name: Christopher Zuidema
		Institution: University of Washington
		Address: 
		Email: czuidema@uw.edu

	C. Alternate Contact Information
		Name: Paulina Lopez
		Institution: Duwamish River Community Coalition
		Address: 
		Email: paulina@drcc.org

***This document focuses on the main moss dataset collected in the Duwamish Valley by local youth. Our analysis included boxplots comparing the youth's data with two 'reference' moss datasets. We include the reference datasets in our submitted data tables and summarize their contents in DATA-SPECIFIC INFORMATION below. There we provide links to more specific information on methodology used, etc.

3. Date of data collection (single date, range, approximate date) <suggested format YYYY-MM-DD>:2019-05-25 to 2019-06-13

4. Geographic location of data collection <latitude, longiute, or city/region, State, Country, as appropriate>: Duwamish Valley Region of Seattle, Washington, U.S.A

5. Information about funding sources that supported the collection of the data: University of Washington’s Biostatistics, Epidemiology, and Bioinformatics Training in Environmental Health (BEBTEH), grant number T32ES015459;USDA Forest Service Voluntary Agreement 20-VI-11261985-0001; Community Engagement Core of the University of Washington Interdisciplinary Center for Exposures, Diseases, Genomics and Environment, NIEHS grant number P30ES007033; State and Private Forestry Cooperative Agreement #18-CA-11062765-744, and Pacific Northwest Research Station Joint Venture Agreement #19-JV-11261985-072; Project funding was also provided by the City of Seattle, Office of Sustainability & Environment, and the Urban Waters Federal Partnership, Green Duwamish designation through Street Sounds Ecology, LLC. 


SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: none

2. Links to publications that cite or use the data: 
Derrien, M. M., Zuidema, C., Jovan, S., Bidwell, A., Brinkley, W., López, P., Barnhill, R., Blahna, D. J. 2020. Toward environmental justice in civic science: Youth performance and experience measuring air pollution using moss as a bio-indicator in industrial-adjacent neighborhoods. International Journal of Environmental Research and Public Health. 17(19): 7278.

Jovan, S. E., Zuidema, C., Derrien, M., Bidwell, A. L., Brinkley, W., Smith, R. J., Blahna, D. J., Barnhill, R., Gould, L., Rodríguez, A. J., Amacher, M. C., Abel, T. D., and López, P. (in revision for Ecosphere). Heavy metals in moss guide environmental justice investigation: a case study using community science in Seattle, WA, USA.

Kondo, M. C., Moran, H., Zuidema, C., Jovan, S., Derrien, M., Brinkley, W., De Roos, A. J, Tabb, L. P. (in press foor Science of the Total Environment). Spatial predictors of heavy metal concentrations in epiphytic moss samples in Seattle, WA.

3. Links to other publicly accessible locations of the data: 

4. Links/relationships to ancillary data sets: 

5. Was data derived from another source? yes/no NO
	A. If yes, list source(s): 

6. Recommended citation for this dataset: 


DATA & FILE OVERVIEW

1. File List: 
<list all files (or folders, as appropriate for dataset organization) contained in the dataset, with a brief description> 

Unaveraged_data_all_metals_June8.csv: raw dataset used for statistical analyses. Contains raw values of heavy metals measured in all moss samples along with basic information for each sample, including collector (expert vs youth), collection date, lat and long of sampled tree. 

Final_forMAPSV3: dataset used for mapping. Derived from Unaveraged_data_all_metals_June8.csv. Includes only youth-collected data. Metals concentrations in youth-collected replicate samples were averaged to one value although the dataset still includes a row for both the original and replicate sample (so, both have the same values)

01-duwamish-pca.R: R-code for running the Principal Components Analysis and Procrustes Analysis. 

manuscript_code.R: R-code for generating all other analyses in the paper. 

Portland_fulldataset: 'reference dataset' compared with main dataset. Contains raw values of five heavy metals measured in moss collected in Portland, OR. These and additional elemental data are available from https://usfs.maps.arcgis.com/apps/webappviewer/index.html?id=14766acdb73e4eb194ba3ada0ce8539d

seattleparks: 'reference dataset' compared with main dataset. Contains raw values of five heavy metals measured in moss collected from Seattle City Parks. 

2. Relationship between files, if important: stated above

3. Additional related data collected that was not included in the current data package: 

4. Are there multiple versions of the dataset? yes/no NO
	A. If yes, name of file(s) that was updated: 
		i. Why was the file updated? 
		ii. When was the file updated? 


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 

Moss sampling protocols were adapted from prior studies using the widespread epiphytic (i.e. “tree-dwelling”) moss species Orthotrichum lyellii (Donovan et al. 2016, Gatziolis et al. 2016). The Duwamish Valley Youth Corps (DVYC) and adult study partners collected the moss from a 250×250-m grid across two industrial-adjacent neighborhoods in Seattle's Duwamish Valley (Georgetown and South Park) with longstanding air pollution concerns. Moss was collected at the suitable tree nearest the centroid of each grid cell. The DVYC led moss sampling excursions on four warm, dry days in 2019 (May 25th, June 1st, 4th, and 8th). Participants met the following week in a local high school science laboratory to harvest the upper 2/3rds of living moss stems for heavy metals analysis (Gatziolis et al. 2016). To assess sampling precision, the youth-led teams immediately collected a replicate moss sample at 18 sites where ample moss was available. Their final analytical dataset had 79 samples from 61 grid cells. To check sampling accuracy, experts re-sampled 19 grid cells although this occurred about 2 weeks later on June 13, 2019 due to scheduling difficulties.

LAB METHOD

All moss samples were sealed and mailed to the US Forest Service Grand Rapids, MN laboratory where they underwent the same treatment. Samples were prepared for heavy metals analysis by oven drying at 40 °C for 24 h and homogenizing by grinding to a fine powder (IKA tube-mill, 1 min grinding time for each sample at 15,000 rpm). A 0.500-g subsample of each moss sample was processed using a modified microwave-assisted digestion with 10 mL concentrated HNO3 + 2 mL 30% H2O2 + 2 mL concentrated HCl (CEM, 2019). An overnight pre-digestion of the samples with added reagents was done at room temperature. Following the microwave-assisted digestion cycle, digests were transferred by rinsing with deionized water to 50 mL volumetric flasks, diluted to volume with deionized water, and filtered through 0.45-um membrane filters into plastic storage bottles prior to analysis. Concentrations of 25 elements in total were measured by inductively coupled plasma optical emission spectrophotometry (Thermo 7000 series dual-view (axial and radial) ICP-OES).

Quality control steps included use of method blanks, instrument calibration standards, instrument performance check standards, and reference lichen samples. The measurement quality objectives (MQOs) are the same as the confidence and tolerance levels that accompany each standard reference material or check standard certification sheet. Quality control/quality assurance (QC/QA) for air-quality sampling in our study followed the EPA Quality Assurance Guidance document (USEPA 2016). Details of the laboratory QC/QA steps are provided in Appendix S1 of the Jovan et al. Ecosphere article.

2. Methods for processing the data: 
<describe how the submitted data were generated from the raw or collected data> See DATA & FILE OVERVIEW section 1

3. Instrument- or software-specific information needed to interpret the data: 
<include full name and version of software, and any necessary packages or libraries needed to run scripts>

4. Standards and calibration information, if appropriate: QC/QA for the ICP-OES metals data in moss are provided in Appendix S1 of the Jovan et al. Ecosphere article. 

5. Environmental/experimental conditions: Industrial-adjacent neighborhoods in the Duwamish Valley

6. Describe any quality-assurance procedures performed on the data: see #4 above (in this section). See also Derrien et al. 2020 article comparing results from youth and expert-collected moss samples.

7. People involved with sample collection, processing, analysis and/or submission: Data collection and processing was led by 22 youth participants of the Duwamish Valley Youth Corps. Over 55 people from 9 institutions participated in this study. Please see Study Partners and Roles section of Jovan et al (Ecoscience) and also the Acknowledgements section.


DATA-SPECIFIC INFORMATION FOR: Unaveraged_data_all_metals_June8.csv

1. Number of variables: 33

2. Number of cases/rows: 99

3. Variable List: LabNum <our internal tracking number and unique identifier for each sample> SampleName <another name for each sample. 'R' indicates sample was a replicate>	GridCellNu <the number of the grid cell sampled for moss> Expert <1 = samplee collected by expert, 0 = sample collected by youth>  Collection_date	Field_Lat	Field_Long	<see periodic table for full names of the elememts that follow. All values are mg/kg in moss besides P, K, Mg, Ca, S, which are given in %. Note that ICP-OES is not very sensitive to Se; negative values indicate concentrations beneath instrument detection limits>P	K	Mg	Ca	S	Mo	Mn	Fe	Ni	Cu	Zn	B	Na	Sr	Ba	Ti	Al	Si	V	Cr	Co	Cd	Pb	As	Se

4. Missing data codes: 
<list code/symbol and definition> NONE

5. Specialized formats or other abbreviations used: See #3 above in this section

DATA-SPECIFIC INFORMATION FOR: Final_forMAPSV3


1. Number of variables: 29

2. Number of cases/rows: 79

3. Variable List: See list for Unaveraged_data_all_metals_June8.csv. The main difference is this dataset contains averages for replicate samples, only youth-collected data are included, and concentrations below the instrument's detection limits are set as the detection limit/2 (e.g. the many negative values for Se are now all 0.1525)

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 

ATA-SPECIFIC INFORMATION FOR: Portland_fulldataset


1. Number of variables: 6

2. Number of cases/rows: 353

3. Variable List: Ni, Cr, Co, Cd, Pb, As. All values are in mg/kg. Note that concentrations below the instrument's detection limits are set as zero. The full dataset and documentation can be found here: https://usfs.maps.arcgis.com/apps/webappviewer/index.html?id=14766acdb73e4eb194ba3ada0ce8539d

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 

ATA-SPECIFIC INFORMATION FOR: seattleparks


1. Number of variables: 9

2. Number of cases/rows: 25

3. Variable List: Location <name of sample location> Lat <latitude of sampling location> long <longitude of sample location> As (moss) <arsenic measured in moss>, Cd (moss) <cadmium measured in moss>, Co (moss) <cobalt measured in moss>, Cr (moss) <chromium measured in moss>, Ni (moss) <nickel measured in moss>, Pb (moss) <lead measured in moss>. All element values are in mg/kg. Note that concentrations below the instrument's detection limits are set as zero. More information on the dataset can be found here: https://www.greenseattle.org/wp-content/uploads/2018/04/MossSoilMonitoring_GSP_Report-reduced.pdf

4. Missing data codes: 
<list code/symbol and definition>n

5. Specialized formats or other abbreviations used: 