DOI: 10.5061/dryad.37pvmcvrq
title: Monitoring data for oyster reefs and nearby controls, including high frequency environmental parameters, carbonate chemistry, oyster growth, and other data

description: Data for Oyster reefs’ control of carbonate chemistry - implications for
 oyster reef restoration in estuaries subject to coastal ocean
 acidification. 
description: # Dataset for Oyster reefs’ control of carbonate chemistry – implications
 for oyster reef restoration in estuaries subject to coastal ocean
 acidification This set of files contains the primary data supporting the
 results/figures for this study. The data are grouped into relevant
 subfolders: Discrete sampling 2021 data High frequency environmental
 monitoring data Juvenile oyster experimental data Oyster reef growth and
 calcification data ## Description of the Data files All data are stored in
 csv file formats. Missing data are coded as nan. ### Discrete sampling
 2021 #### carbchem.csv - all discrete measures of DIC and TA along with
 relevant environmental variables The following columns are included in the
 dataset: 'datetime_utc' (date and time in Coordinated Universal
 Time), 'site' (site, sc: 'Sedge Control', sr1:
 'Sedge Reef 1', sr2: 'Sedge Reef 2')
 'ta_µmolkg-1' (total alkalinity in micromoles per kilogram)
 'dic_µmolkg-1' (dissolved inorganic carbon in micromoles per
 kilogram) 'sal' (salinity) 'temp_degc' (temperature in
 degrees celsius) 'do_sat' (dissolved oxygen in percent
 saturation) 'do_mgl' (dissolved oxygen in milligrams per liter)
 'aou'(apparent oxygen utilization in micromoles per kilogram)
 #### chlorophyll.csv - raw chlorophyll measurements by date and site The
 following columns are included in the dataset: 'date' (date),
 'chl' (chlorophyll in micrograms per liter), 'site'
 (site; sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2:
 'Sedge Reef 2') #### macroalgae.csv - replicate quadrat
 measurements of macroalgae percent cover by date and site The following
 columns are included in the dataset: 'date' (date),
 'quadrat' (quadrat number, n=8 per date), 'site'
 (site; sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2:
 'Sedge Reef 2') 'coverage_pct' (estimated percent
 cover of macroalgae within quadrat) ### High frequency environmental
 monitoring #### environmental_hf.csv - high frequency biogeochemical
 monitoring data at reef and control sites The following columns are
 included in the dataset: 'datetime_utc' (date and time in
 Coordinated Universal Time) 'temp' (temperature in degrees
 celsius) 'sal' (salinity) 'vert' (depth in meters)
 'tide' (tidal depth in meters) 'dosat' (dissolved
 oxygen in percent saturation) 'domgl' (dissolved oxygen in
 milligrams per liter) 'phn' (pH on NBS scale) 'site'
 (site; qc: 'Quogue Control', qr: 'Quogue Reef', sc:
 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge
 Reef 2') 'note' (codes for missing data;
 'cle\_cal': cleaning or recalibration occurred, 'qc'
 flagged during qc process, 'bat': battery issue prevented
 collection, 'uer' : user error inhibited logging at sites) ####
 sc_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved
 oxygen at the 'Sedge Control' site #### sr1_daily.csv - daily
 means, minima, maxima, and ranges of pH and dissolved oxygen at the
 'Sedge Reef 1' site #### sr2_daily.csv - daily means, minima,
 maxima, and ranges of pH and dissolved oxygen at the 'Sedge Reef
 2' site #### qc_daily.csv - daily means, minima, maxima, and ranges
 of pH and dissolved oxygen at the 'Quogue Control' site ####
 qr_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved
 oxygen at the 'Quogue Reef' site The following columns are
 included in the above datafiles: 'date' (date in Coordinated
 Universal Time), 'phn_mean' (mean daily pH on the NBS scale),
 'phn_min' (minimum daily pH on the NBS scale),
 'phn_max' (maximum daily pH on the NBS scale),
 'phn_range' (daily pH range on the NBS scale),
 'dosat_mean' (mean daily dissolved oxygen in percent
 saturation), 'dosat_min' (minimum daily dissolved oxygen in
 percent saturation), 'dosat_max' (maximum daily dissolved oxygen
 in percent saturation), 'dosat_range' (daily dissolved oxygen
 range in percent saturation) Data coded as nan indicates that at least one
 dissolved oxygen and/or pH measurement (collected at a 15-min frequency)
 was missing on a particular date. ### Juvenile oyster experimental data
 #### juvexpt_2020.csv - Juvenile oyster heights measured during the 2020
 field experiment in the Sedge region #### juvexpt_2021.csv - Juvenile
 oyster heights measured during the 2021 field experiment in the Sedge
 region The following columns are included in the above datafiles:
 'date' (date), 'height' (oyster height in
 millimeters), 'site' (site; sc: 'Sedge Control', sr1:
 'Sedge Reef 1', sr2: 'Sedge Reef 2') 'tray'
 (replicate experimental tray; naming indicates site and tray number, e.g.,
 sc-1: sedge control tray 1) ### Oyster reef growth and calcification data
 #### reefheight.csv - Average oyster heights measured in replicate
 'monitoring spat on shell bags' seasonally on 'Quogue
 Reef', 'Sedge Reef 1', and 'Sedge Reef 2' The
 following columns are included in the dataset: 'date' (date)
 'mbag' (replicate 'monitoring spat on shell bag'
 number) 'avg_sh' (average shell height) 'site' (site;
 qc: 'Quogue Control', qr: 'Quogue Reef', sc:
 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge
 Reef 2') #### reefdensity.csv - Average density of oysters on
 'Quogue Reef', 'Sedge Reef 1', and 'Sedge Reef
 2' by year The following columns are included in the dataset:
 'year' (year) 'mbag' (replicate 'monitoring spat
 on shell bag' number) 'r_density' (oyster density per meter
 squared, based on counts of live oysters in monitoring spat on shell bags)
 'o_growth' (average oyster growth in millimeters, based on the
 annual difference in average oyster height of oysters on replicate
 'monitoring spat on shell bags') #### sr_massheight.csv - shell
 masses and heights of oysters located on reefs within the Sedge region The
 following columns are included in the dataset: 'age' (age class
 of individual oyster in years) 'height_mm' (height in
 millimeters) 'mass_g' (mass in grams) #### calcification.csv -
 Approximations of reef-wide calcification of Sedge reefs in 2021 utilizing
 allometric relationship established in Fig. S2 The following columns are
 included in the dataset: 'site' (reef site; sr1: 'Sedge
 Reef 1' and sr2: 'Sedge Reef 2') 'mbag'
 (replicate 'monitoring spat on shell bag' number)
 '2020_hgt' (average shell height of individual oysters in 2020)
 '2021_hgt' (average shell height of individual oysters in 2021)
 '2020_mass' (average shell mass of individual oysters in 2020;
 derived from allometric relationship established in Fig. S2)
 '2021_mass' (average shell mass of individual oysters in 2021;
 derived from allometric relationship established in Fig. S2)
 '2021_gain' (average shell mass gained per individual oyster
 from 2020 to 2021; derived by subtracting '2020_mass' from
 '2021_mass') '2021_caco3' (average mass of calcium
 carbonate added from 2020 to 2021 per individual oyster; derived by
 multiplying 2021 gain by 0.95) 'density' (2021 oyster density
 per meter squared, based on counts of live oysters in monitoring spat on
 shell bags) 'reef_calc' (estimates of reef-wide calcification in
 g of calcium carbonate per meter squared; derived by multiplying
 '2021_caco3' by 'density')