uid=AND,o=lter,dc=ecoinformatics,dc=org all public read HT006 Sherri L. Johnson

US Forest Service ;Pacific NW Research Station ;3200 SW Jefferson Way Corvallis OR 97331 USA

541-758-7771 sherri.johnson2@usda.gov sherri.johnson@oregonstate.edu https://www.fs.fed.us/research/people/profile.php?alias=sherrijohnson Sherri L. Johnson

US Forest Service ;Pacific NW Research Station ;3200 SW Jefferson Way Corvallis OR 97331 USA

541-758-7771 sherri.johnson2@usda.gov sherri.johnson@oregonstate.edu https://www.fs.fed.us/research/people/profile.php?alias=sherrijohnson Principal Investigator Judith L. Li

Oregon State University;Dept. of Fisheries & Wildlife;104 Nash Hall Corvallis OR 97331 USA

(541) 737-1093 judyli@comcast.net judith.li@oregonstate.edu http://oregonstate.edu/dept/pnw-erc/personnel/li.htm Other Researcher Mark D Schulze

H.J. Andrews Experimental Forest; PO Box 300 Blue River OR 97413

541-822-6336 mark.schulze@oregonstate.edu Other Researcher Ivan Arismendi

3100 SW Jefferson Way Corvallis Oregon 97330 USA

541-750-7443 541-231-8921 ivan.arismendi@oregonstate.edu ivanarsmendi@gmail.com https://fw.oregonstate.edu/users/ivan-arismendi Other Researcher Christina Murphy christina.a.murphy@gmail.com Other Researcher Sherri L. Johnson

US Forest Service ;Pacific NW Research Station ;3200 SW Jefferson Way Corvallis OR 97331 USA

541-758-7771 sherri.johnson2@usda.gov sherri.johnson@oregonstate.edu https://www.fs.fed.us/research/people/profile.php?alias=sherrijohnson Creator 2017-07-14 The H.J Andrews phenology research included this study of stream temperatures at six headwater streams where springtime emergence of stream macroinvertebrates were collected. Streams were selected across an elevational gradient and with young riparian forests as well as old growth riparian forests. One site was a stream that originated in a cold water spring and the site was a stream that drys late in the summer. Stream temperature loggers were placed in protective housings and stream temperatures collected year-round starting May 2009-July 2014. Data were evaluated for quality control and missing periods were filled. These data document the thermal environment that stream macroinvertebrates experience and that influence their timing of emergence (database SA025). populations phenology water temperature forests streams LTER controlled vocabulary populations LTER core research areas Data Use Agreement: The re-use of scientific data has the potential to greatly increase communication, collaboration and synthesis within and among disciplines, and thus is fostered, supported and encouraged. This Data Set is released under the Creative Commons license CC BY "Attribution" (see: https://creativecommons.org/licenses/by/4.0/). Creative Commons license CC BY - Attribution is a license that allows others to distribute, remix, tweak, and build upon your work (even commercially), as long as you are credited for the original creation. This license accommodates maximum dissemination and use of licensed materials. It is considered professional conduct and an ethical obligation to acknowledge the work of other scientists. The Data User is asked to provide attribution of the original work if this data package is shared in whole or by individual parts or used in the derivation of other products. A recommended citation is provided for each Data Set in the Andrews LTER data catalog (see: http://andlter.forestry.oregonstate.edu/data/catalog/datacatalog.aspx). A generic citation is also provided for this Data Set on the website https://portal.edirepository.org in the summary metadata page. Data Users are thus strongly encouraged to consider consultation, collaboration and/or co-authorship with the Data Set Creator. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed and all data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. General acknowledgement: Data were provided by the HJ Andrews Experimental Forest research program, funded by the National Science Foundation's Long-Term Ecological Research Program (DEB 2025755), US Forest Service Pacific Northwest Research Station, and Oregon State University. http://andlter.forestry.oregonstate.edu/data/abstract.aspx?dbcode=HT006 HJ Andrews Experimental Forest streams - phenology emergence sites -122.25750000 -122.12050000 44.26640000 44.20700000 457 1000 meter 2009-01-01 2014-07-31 These stream temperature data were collected to support phenological research focused on increasing our understanding of factors that influence instream insect responses across the Andrews Experimental Forest. Species, taxa and communities within and across trophic levels are likely responding differently to thermal conditions.

An update history is logged and maintained with each new version of every dataset.

notPlanned Study code and preliminary metadata established Version1 2011-01-25 Daily and hourly data for the stream temperature phenology emergence sites is posted from 2009 through July 31, 2014. Version2 2016-06-09 Metadata for abstract, purpose, experimental design and methods including program documentation are added. EML will include updated intellectual rights and check sums for both entities. Version3 2017-07-14 Information Manager

Andrews Forest LTER Program US Forest Service Pacific Northwest Research Station 3200 SW Jefferson Way Corvallis OR 97331

hjaweb@fsl.orst.edu http://andrewsforest.oregonstate.edu/ Andrews Forest LTER Site

Forest Ecosystems and Society Department in Forestry Oregon State University 201K Richardson Hall Corvallis OR 97331-5752

(541) 737-8480 lterweb@fsl.orst.edu http://andrewsforest.oregonstate.edu/ Field Methods - HT006 Temperature sensors (Onset Hobo U22-001 (accuracy 0.2 C)) were programmed to record instantaneous temperatures at 30 min intervals and placed in protective flow through housings and secured into the streams. Data were downloaded at a minimum of twice per year. Quality Assurance - HT006 After sensors were downloaded, high resolution data were put through a series of programs for quality control and for filling missing values before generating the hourly averages. A major concern of quality control was to detect when the sensors were not in the stream and recording air temperatures. When data anomalies or gaps in data were found, data were filled using the regression relationships with other sensors from this project and from stream temperature data from stream gages. Regressions were calculated using the best fit with other sensors during periods of time when the full data were available. After the averaging and filling, data were also visually evaluated for outliers. If outliers were found, estimates were calculated and inserted. Statistics - HT006 Evaluation of the high resolution temperatures (15 and 20 minute intervals) were conducted and questionable data flagged. Before calculation of hourly averages, flagged data were removed and missing values calculated using regression relationships with other temperature data from Andrews Forest for that period. Script name: WaTeR.py This script was designed to flag, clean, average by hour, and fill data from air temperature sensors deployed at the HJ Andrews. Datasets: The script currently creates folders: flagged, cleaned, reference, and filled. These contain: flagged original data with flags cleaned data with the flags removed reference cleaned data averaged into hourly timesteps filled cleaned data which has been filled using other files in the reference folder based on their respective regressions summary daily values with min, max and mean Requires: Python, SciPy and NumPy Note: This program was written for data loggers started during June (daylight savings time). Since ONSET uses the computer clock for time stamps, raw times are in PDT not PST. Hourly averaging changes times to PST and matches reference file format (where the hour represents the average of temperatures in the preceding hour). If original logger start dates are not in PDT, there is a line of code (currently 313) which can be turned on. Settings: This may be run for a file or folder. The file or folder should be found in the same directory as the script. Input the file or folder name (e.g. INPUTFOLDER="Folder") and comment out the unused line (e.g. #INPUTFILE). Input files should contain the site name as this name is retained through processing. Date limits should be specified under the '#Date limits' heading. These form the bookends in which the program will attempt to fill gaps using the available reference files. Reference files are stored together in a folder (e.g. REFERENCE_DIR = "RS data for PC sites") and are labeled with *reformatted* to distinguish them from reference files which have not been modified to match the required input format. All sites are added as they are run, so this should be run twice if they are not already included in the reference folder and you want them as reference files for sites run in the same batch. Site files will not be used if they have *cleaned*, *filled* or *flagged* in their file name to avoid using processed data. Reference files must be in the correct format and include *reformatted* in their filename or they will not be used. These labels are consistent with the output files from this script as well as the script to convert reference data downloaded from the Andrews website (convert_reference_data.py). Description: This script serves to flag, prune, average (by hour), and fill air temperature data as detailed below. Step 1: Flagging (Original time steps); Output file – (input file name)_flagged_00-0000.csv, where 00-0000 is the month-year of the last data point Flagging identifies for each line (date/time) entry: nodata - Date/time recorded on the logger but contains no data. Interval does not equal 15 or 20 minutes – The time between samples was not as programmed extreme – Any temperature exceeding 20 deg C or less than -20 deg C (outside of the sensor range) jump – If the change in temperature exceeds 5 deg C in one time interval air – A forward rolling window, flags when the variation in temperatures within the 24hr period is greater than the TVAR_MAX (specified at the opening of the code, currently 1.5 deg C and the temperatures are below TMIN (currently 0.2 deg C) air_past – Looks back and flags if a 'Snow' flag is present in the past 24 hours Step 2: Pruning (Original time step); Output file – (input file name)_cleaned_00-000.csv Pruning removes lines containing extreme, air_past, air, jump and nodata. Step 3: Averaging (Hourly time step); Output file – (input file name)_00-0000_reformatted.csv Averaging uses only values remaining after pruning. The number of values used to calculate the average is included as a new column. Notes: The command for saving this output file includes the path for the reference folder, if that folder is changed, it should also be changed in this section (or a new folder will be made with the files but they will not be used for filling). Averaging follows the convention used for Andrews weather stations where the hour represents the average of temperatures in the preceding hour. The output is in PST (while all previous outputs are in PDT, matching the raw input). Step 4: Filling (Hourly time step); Output file – (input file name)_filled_00-000.csv The script uses cleaned data and compares remaining entries to reference files (see Settings). This is done as a linear regression of the cleaned data with each reference file, the output includes the R2 which can be found in the text file corresponding to the input file name. Prior to filling, the script creates placeholder hours bounded by the date range specified under “Date limits” which is the range in which filling is attempted. These values are set at 1000 degrees. The script aims to fill missing (1000 degree) data by moving sequentially through the reference data in order of fit (R2). The linear regression equation is used to modify the reference value for that data point and it replaces the 1000 degree placeholder. The reference file used in the temperature value filling is listed in a neighboring column. If all reference files are examined and no data is found to replace the missing value placeholder, the placeholder is retained, thus 1000 degrees should be treated as "no data". Step 5: Max, min, mean (Daily time step); Output file – (input file name)_daily_00-0000.csv The script ignores 1000 degree data and calculates daily max, min and mean temperature values from the filled dataset. The number of records (hours) used in the calculation is listed in the column 'count.' Figures: Data points over time with flagged (and cleaned) data shown in red. Located within the "flagged" folder as .pdfs. Andrews Phenology sites Sampling frequency: 30 minutes Six streams phenology sites were selected to evaluate the variability of springtime aquatic insect emergence and phenology (SA025) across the Andrews Forest. Stream temperature sensors were installed in these six streams and temperatures measured year round so that calculations of themal accumulation and degree days could occur. At low elevation, a gaged stream through old growth forest and a stream through a young forest were selected. At high elevation, a similar pair of gaged streams were selected. Prior information on insect community composition and seasonal emergence (SA022) was used to select these sites. Two additional sites were selected; one was a cold water stream whose hydrology and thermal regime is greatly impacted by a headwater spring. The final site was located near the cold water spring and in a stream that goes dry in the later summer. HJA Phenology Emergence Site 1 (WS01 stream) -122.25750000 -122.25750000 44.20700000 44.20700000 457 457 meter HJA Phenology Emergence Site 2 (WS02 stream) -122.24930000 -122.24930000 44.21450000 44.21450000 487 487 meter HJA Phenology Emergence Site 3 (WS08 stream) -122.17070000 -122.17070000 44.26640000 44.26640000 959 959 meter HJA Phenology Emergence Site 4 (WS07 stream) -122.17560000 -122.17560000 44.26510000 44.26510000 940 940 meter HJA Phenology Emergence Site 5 (Cold Creek) -122.12400000 -122.12400000 44.22950000 44.22950000 1000 1000 meter HJA Phenology Emergence Site 6 (South Creek) -122.12050000 -122.12050000 44.22720000 44.22720000 1000 1000 meter HJA Phenology Sites -122.26083000 -122.11159208 44.28199677 44.20198189 1314 1314 meter Andrews Experimental Forest (HJA) -122.26172200 -122.10084700 44.28196400 44.19770400 1631 1631 meter

<para>After sensors were downloaded, high resolution data were put through a series of programs for quality control and for filling missing values before generating the hourly averages. A major concern of quality control was to detect when the sensors were not in the stream and recording air temperatures. When data anomalies or gaps in data were found, data were filled using the regression relationships with other sensors from this project and from stream temperature data from stream gages. Regressions were calculated using the best fit with other sensors during periods of time when the full data were available.</para> <para>After the averaging and filling, data were also visually evaluated for outliers. If outliers were found, estimates were calculated and inserted.</para>

Sherri L. Johnson

US Forest Service ;Pacific NW Research Station ;3200 SW Jefferson Way Corvallis OR 97331 USA

541-758-7771 sherri.johnson2@usda.gov sherri.johnson@oregonstate.edu https://www.fs.fed.us/research/people/profile.php?alias=sherrijohnson Principal Investigator Julia A. Jones

Oregon State University;Department of Geosciences; Wilkinson Hall 104 Corvallis OR 97331-5506 USA

(541) 737-1224 Julia.Jones@oregonstate.edu geojulia@comcast.net http://ceoas.oregonstate.edu/profile/jones/ http://orcid.org/0000-0001-9429-8925 Principal Investigator Matthew G Betts

Department of Forest Ecosystems and Society; 201E Richardson Hall; College of Forestry; Oregon State University Corvallis OR 97331

(541) 737-3841 matt.betts@oregonstate.edu http://www.fsl.orst.edu/flel/index.htm Principal Investigator Michael P. Nelson

Department of Forest Ecosystems and Society; 201K Richarson Hall; College of Forestry; Oregon State University Corvallis OR 97331

541-737-9221 mpnelson@oregonstate.edu http://www.michaelpnelson.com http://orcid.org/0000-0001-6917-4752 Principal Investigator David Bell david.bell@usda.gov david.bell@oregonstate.edu https://lemma.forestry.oregonstate.edu/about/david-bell Principal Investigator The H.J. Andrews Experimental Forest is a living laboratory that provides unparalleled opportunities for the study of forest and stream ecosystems in the central Cascade Range of Oregon. Since 1980, as a part of the National Science Foundation Long Term Ecological Research (NSF-LTER) program, the Andrews Experimental Forest has become a leader in the analysis of forest and stream ecosystem dynamics. Long-term field experiments and measurement programs have focused on climate dynamics, streamflow, water quality, and vegetation succession. Currently researchers are working to develop concepts and tools needed to predict effects of natural disturbance, land use, and climate change on ecosystem structure, function, and species composition. The Andrews Experimental Forest is administered cooperatively by the USDA Forest Service Pacific Northwest Research Station, Oregon State University and the Willamette National Forest. Funding for the research program comes from the National Science Foundation (NSF), US Forest Service Pacific Northwest Research Station, Oregon State University, and other sources. Data were provided by the HJ Andrews Experimental Forest research program, funded by the National Science Foundation's Long-Term Ecological Research Program (DEB 2025755), US Forest Service Pacific Northwest Research Station, and Oregon State University. National Science Foundation: DEB1440409 The Andrews Forest is situated in the western Cascade Range of Oregon, and covers the entire 15,800-acre (6400-ha) drainage basin of Lookout Creek. Elevation ranges from 1350 to 5340 feet (410 to 1630 m). Broadly representative of the rugged mountainous landscape of the Pacific Northwest, the Andrews Forest contains excellent examples of the region's conifer forests and associated wildlife and stream ecosystems. These forests are among the tallest and most productive in the world, with tree heights of often greater than 250 ft (75 m). Streams are steep, cold and clean, providing habitat for numerous aquatic organisms. 1 HT00601 Daily stream temperature at phenology core emergence sites: HT00601.csv 717619 6601535a8367730dacd13af5a2a50873 1 \r\n column , " http://andlter.forestry.oregonstate.edu/ltermeta/ltersearch/dataaccess.aspx?docid=HT00601_v2.csv 2009-01-01 2014-07-31 DBCODE FSDB Database Code char(5) HT006 FSDB Database Code HT006 ENTITY Entity Number numeric(2,0) number 1 natural 1.0000 1.0000 SITECODE Site code char(5) PE001 HJA Phenology Emergence Site 1 (WS01 stream) PE002 HJA Phenology Emergence Site 2 (WS02 stream) PE003 HJA Phenology Emergence Site 3 (WS08 stream) PE004 HJA Phenology Emergence Site 4 (WS07 stream) PE005 HJA Phenology Emergence Site 5 (Cold Creek) PE006 HJA Phenology Emergence Site 6 (South Creek) SITETYPE Type of measurement site: core phenology emergence site char(2) PE Core phenology emergence stream site QC_LEVEL Quality control flag indicates level of quality checking performed char(2) 1A Data is published and unlikely to change - automated range checking and manual review has been conducted 1D Data is published and unlikely to change - data is derived or aggregated from published data of level 1A 2A Data is published and unlikely to change - Level 1A data has been modified such that data gaps may be filled or problem data may be removed 2D Data is published and unlikely to change - data is derived or aggregated from published data of level 2A DATE Date datetime YYYY-MM-DD 1/1/2009 12:00:00 AM 7/31/2014 12:00:00 AM WATERTEMP_MEAN_DAY Mean temperature for the day numeric(5,1) degrees Celsius 0.100000 real 0.2000 15.8000 WATERTEMP_MEAN_FLAG Mean water temperature flag char(1) A Accepted value E Estimated value M Missing value Q Questionable value WATERTEMP_MAX_DAY Maximum water temperature for the day numeric(5,1) degrees Celsius 0.100000 real 0.5000 16.5000 WATERTEMP_MAX_FLAG Maximum water temperature flag char(1) A Accepted value E Estimated value M Missing value Q Questionable value WATERTEMP_MIN_DAY Minimum water temperature for the day numeric(5,1) degrees Celsius 0.100000 real 0.0000 15.4000 WATERTEMP_MIN_FLAG Minimum water temperature flag char(1) A Accepted value E Esimated value M Missing value Q Questionable value REGRESSION_SITE Reference site used to estimate values using linear regression char(6) GSWS01 Andrews Watershed 1 Gaging Station GSWS02 Andrews Watershed 2 Gaging Station GSWS07 Andrews Watershed 7 Gaging Station GSWS08 Andrews Watershed 8 Gaging Station PE003 HJA Phenology Emergence Site 3 (WS08 stream) None No estimation (actual data is used) Manual Manual editing (no specific reference site) PRIMARY HT00601.SITECODE HT00601.DATE NOTNULL HT00601.DBCODE HT00601.ENTITY HT00601.SITECODE HT00601.QC_LEVEL HT00601.DATE HT00601.WATERTEMP_MEAN_FLAG HT00601.WATERTEMP_MAX_FLAG HT00601.WATERTEMP_MIN_FLAG HT00601.SITETYPE HT00601.REGRESSION_SITE 12228 2 HT00602 Hourly stream temperature at phenology core emergence sites: HT00602.csv 16146408 03c1f3bac211c93804c0cd7138d24748 1 \r\n column , " http://andlter.forestry.oregonstate.edu/ltermeta/ltersearch/dataaccess.aspx?docid=HT00602_v2.csv 2009-01-01 2014-07-31 DBCODE FSDB Database Code char(5) HT006 FSDB Database Code HT006 ENTITY Entity Number numeric(2,0) number 1 natural 2.0000 2.0000 SITECODE Site code char(5) PE001 HJA Phenology Emergence Site 1 (WS01 stream) PE002 HJA Phenology Emergence Site 2 (WS02 stream) PE003 HJA Phenology Emergence Site 3 (WS08 stream) PE004 HJA Phenology Emergence Site 4 (WS07 stream) PE005 HJA Phenology Emergence Site 5 (Cold Creek) PE006 HJA Phenology Emergence Site 6 (South Creek) SITETYPE Type of measurement site: core phenology emergence site char(2) PE Core phenology emergence stream site QC_LEVEL Quality control flag indicates level of quality checking performed char(2) 1A Data is published and unlikely to change - automated range checking and manual review has been conducted 1D Data is published and unlikely to change - data is derived or aggregated from published data of level 1A 2A Data is published and unlikely to change - Level 1A data has been modified such that data gaps may be filled or problem data may be removed 2D Data is published and unlikely to change - data is derived or aggregated from published data of level 2A DATE_TIME Date and time of probe reading datetime YYYY-MM-DD hh:mm:ss 1/1/2009 1:00:00 AM 7/31/2014 11:00:00 PM WATERTEMP_MEAN Mean water temperature over the last hour numeric(5,1) degrees Celsius 0.100000 real 0.0000 16.5000 WATERTEMP_MEAN_FLAG Mean water temperature flag char(1) A Accepted value E Estimated value M Missing value Q Questionable value REGRESSION_SITE Reference site used to estimate values using linear regression char(6) GSWS01 Andrews Watershed 1 Gaging Station GSWS02 Andrews Watershed 2 Gaging Station GSWS07 Andrews Watershed 7 Gaging Station GSWS08 Andrews Watershed 8 Gaging Station PE003 HJA Phenology Emergence Site 3 (WS08 stream) None No estimation (actual data is used) Manual Manual editing (no specific reference site) PRIMARY HT00602.SITECODE HT00602.DATE_TIME NOTNULL HT00602.DBCODE HT00602.ENTITY HT00602.SITECODE HT00602.QC_LEVEL HT00602.WATERTEMP_MEAN_FLAG HT00602.DATE_TIME HT00602.SITETYPE HT00602.REGRESSION_SITE 293466 dimensionless number, i.e., ratio, count Degrees Celsius; a common unit of temperature; constantToSI=273.18