DOI: 10.5061/dryad.0vt4b8h9s
title: Time dependence of sediment accretion rates: Short- and long-term variability in an urban tidal marsh

description: Understanding the temporal variability of sediment accretion is crucial
 for assessing the resilience of tidal marshes to accelerated sea-level
 rise, particularly in urban settings where sediment delivery and hydrology
 are frequently altered. This study investigates sediment accretion across
 multiple timescales in Tinicum Marsh, an urban tidal wetland in
 Philadelphia. Using event-scale sediment traps, annual SET-MH
 measurements, and decadal radioisotope dating, the research reveals that
 sediment accretion rates vary significantly with timescale, aligning with
 the Sadler Effect. Event-based rates were much higher than annual and
 decadal rates, especially during storms, which delivered more mineral-rich
 sediments. Accretion was influenced by elevation and distance from tidal
 channels, and substantial shallow subsidence was observed. Although
 current accretion exceeds long-term sea-level rise, it only marginally
 keeps up with recent rates, highlighting the need for multi-scale analysis
 to assess marsh resilience.
description: # Time dependence of sediment accretion rates: Short- and long-term
 variability in an urban tidal marsh Dataset DOI:
 [10.5061/dryad.0vt4b8h9s](10.5061/dryad.0vt4b8h9s) ## Description of the
 data and file structure ### Files and variables #### File:
 Event-Based_.csv **Description:** This dataset contains event-based
 sediment deposition data collected from Tinicum Marsh, located in
 Philadelphia, PA. Sediment traps were deployed, and sediment deposition
 was measured following individual rainfall or tidal events to capture
 short-term sediment deposition across transects and plots. The dataset
 includes raw measurements (e.g., sediment dry weight) and calculated
 metrics such as the area of sediment trap filter (sq/m) and deposition
 rate (mm/yr), and was collected between 2011 and 2024 **Missing Values:**
 Field values in the data files of "NA" or "-" or blank
 fields (empty cells) should be treated as no data available. #####
 Variables * Batch/Project: Identifier for the collection batch, based on
 the date samples were retrieved from the field at Tinicum Marsh * Date
 collected: Date when the sample was collected, formatted as m/d/yy * Event
 type: (character) Classification of the hydrological event into a storm
 event and a non-storm event * Transect: : (numeric) Transect number where
 the sediment trap was deployed * Plot: Plot number within each transect *
 Sediment Dry Wt (g): (numeric) Mass of dried sediment collected (grams) *
 area of filter (sq. cm): (numeric) Area of the filter used to collect
 sediment, in square centimeters. * area of filter (sq. m): (numeric)
 Filter area converted to square meters * the number of filters/sq
 m: (numeric) Multiplier indicating how many filters would fit in one
 square meter * sediment g/sq m over event: (numeric) Sediment mass
 normalized to per square meter over the event * sed g/sq m per
 hour: Sediment flux rate per square meter per hour (sediment trap exposure
 time) * sed/ g/m2/year: (numeric) Annualized sediment deposition rate in
 g/m²/year * bulk density (g/cm3): (numeric) Estimated bulk density of
 sediment sample * bulk density (g/m3): (numeric) Bulk density converted to
 grams per cubic meter * deposition rate (m/yr): (numeric) Vertical
 accretion rate calculated from sediment mass and bulk density
 (meters/year) * deposition rate (mm/yr): (numeric) Same as above,
 converted to millimeters/year * Trap Area (sq m of Tinicum): (numeric)
 Surface area of the sediment trap in square meters * Exposure Time
 (hours): (numeric) Duration the sediment trap was deployed * Rainfall
 (inches): (numeric) Rainfall associated with the event * Water level NAVD
 88 (m): (numeric) Water elevation during the event, referenced to NAVD 88
 * Distance to main channel (m): (numeric) Distance from the plot to the
 main tidal channel * Elevation (NAVD 88 m): (numeric) Ground elevation at
 the plot location, referenced to NAVD 88 #### File:
 Annual_SET-A-C_(SETr_Raw_data).csv **Description:**  This dataset contains
 raw surface elevation table (SET) measurements from Tinicum Marsh, located
 in Philadelphia, Pennsylvania. Measurement were collected annually from
 three stations (SET-A, SET-B, SET-C). Each row corresponds to a single arm
 deployment and includes individual SET pin measurements (1- 9) in
 millimeters, along with QA/QC codes that indicate measurement reliability
 following National Estuarine Research Reserve Systems (NERRS) SETr
 protocols. The data was collected between 2011 and 2024. **Missing
 Values** Field values in the data files of "NA" or "-"
 or blank fields (empty cells) should be treated as no data available.
 Variables * set_id: (character) Identifier for the SET station * year:
 Year of the measurement, formatted as YYYY * month: Month of the
 measurement, formatted as M * day: Day of the measurement, formatted as D
 * arm_position: Coded identifier for SET arm orientation *
 arm_qaqc_code: (character) QA/QC code for SET arm deployment (See [SETr
 QA/QC
 Guide](https://nerrssciencecollaborative.org/media/files/Guide%20to%20the%20SETr%20Workflow_updated%207_2_20.pdf) for full code explanations) * pin_1_height_mm: (numeric) Measured pin 1 height in millimeters * pin_2_height_mm: (numeric) Measured pin 2 height in millimeters * pin_3_height_mm: (numeric) Measured pin 3 height in millimeters * pin_4_height_mm: (numeric) Measured pin 4 height in millimeters * pin_5_height_mm: (numeric) Measured pin 5 height in millimeters * pin_6_height_mm: (numeric) Measured pin 6 height in millimeters * pin_7_height_mm: (numeric) Measured pin 7 height in millimeters * pin_8_height_mm: (numeric) Measured pin 8 height in millimeters * pin_9_height_mm: (numeric) Measured pin 9 height in millimeters * pin_1_qaqc_code: QA/QC code for SET arm deployment (See [SETr QA/QC Guide](https://nerrssciencecollaborative.org/media/files/Guide%20to%20the%20SETr%20Workflow_updated%207_2_20.pdf) for full code explanations) * pin_2_qaqc_code: (character) QA/QC codes for pin 2 measurement * pin_3_qaqc_code: (character) QA/QC codes for pin 3 measurement * pin_4_qaqc_code: (character) QA/QC codes for pin 4 measurement * pin_5_qaqc_code: (character) QA/QC codes for pin 5 measurement * pin_6_qaqc_code: (character) QA/QC codes for pin 6 measurement * pin_7_qaqc_code: (character) QA/QC codes for pin 7 measurement * pin_8_qaqc_code: (character) QA/QC codes for pin 8 measurement * pin_9_qaqc_code: (character) QA/QC codes for pin 9 measurement #### File: Annual_SETr_processed_Output.csv **Description:** This dataset contains long-format SET data collected from Tinicum Marsh in Philadelphia, Pennsylvania. It represents the processed output of the Annual SET A–C (SETr Raw Data) after being reformatted using the **[SETr package](https://github.com/swmpkim/SETr_Reserve_Template/tree/master/R_scripts)**, which converts the original wide-format dataset into individual pin-level records. Each row corresponds to a single measurement from one of nine pins on a SET arm and includes the observation date, pin height in millimeters, and associated QA/QC codes. **Missing Values:** Field values in the data files of "NA" or "-" or blank fields (empty cells) should be treated as no data available. ##### Variables * set_id: (character) Identifier for the SET station * year: Year of the measurement, formatted as YYYY * month: Month of the measurement, formatted as M * day: Day of the measurement, formatted as D * arm_position: Numeric code representing the SET arm orientation * arm_qaqc_code: (character) QA/QC code for arm position as above * pin_number: (numeric) Pin number on the SET arm (1 through 9) * Height: Pin height relative to the SET arm * height_mm: (numeric) Pin height in millimeters * qaqc_code: (character) QA/QC code for pin measurements as above * Pin: Identifier for each pin #### File: Annual_Accretion_(MH)_Data.csv **Description:** This dataset contains annual marsh surface accretion measurements from Marker Horizon (MH) plots at Tinicum Marsh in Philadelphia, Pennsylvania. Measurements were taken from multiple MH subplots (e.g., TIN_01_A, TIN_01_B) across three SET stations (SET-A, SET-B, SET-C). Accretion was measured as the vertical sediment accumulation (in mm) above feldspar marker horizons. Each record corresponds to a single subplot and date of observation. The data was collected between 2011 and 2024. **Missing Values:** Field values in the data files of "NA" or "-" or blank fields (empty cells) should be treated as no data available. ##### Variables * set_id: (character) Identifier for the SET station where MH plots were located * mh_id: Unique identifier for the marker horizon subplot * date: Full date of measurement in M/D/YY format * month: Month of the observation, formatted as M * day: Day of the observation, formatted as D * year: Year of the observation, formatted as YY * Accretion mm: (numeric) Measured vertical accretion in millimeters above the marker horizon #### File: Core_Raw_Data.csv **Description:** This dataset contains radioisotope (Pb-210 and Ra-226) activity and bulk density measurements from three sediment cores (Core-A, Core B, and Core C) collected near the SET monitoring stations in Tinicum Marsh, Philadelphia, PA. The cores were collected on April 13, 2012. These measurements were used to generate age-depth models for estimating long-term sediment accumulation rates using the [rPlum](https://cloud.r-project.org/web/packages/rplum/vignettes/rplum.html) Bayesian modeling approach. **Missing Values:** Field values in the data files of "NA" or "-" or blank fields (empty cells) should be treated as no data available. ##### Variables * Core ID: (character) Identifier for the sediment core * Depth.cm: Depth in centimeters from the top of the core * Bulk.density.g.cm.3: (numeric) Dry bulk density of the sample in grams per cubic centimeter * Total Pb210.Bg.kg.: (numeric) Total unsupported Pb-210 activity in becquerels per kilogram * Sd.210Pb.: (numeric) Standard deviation of Pb-210 activity * Ra226.Bq.kg: Supported Ra-226 activity in becquerels per kilogram * Ra226_SD.Bq.kg.: (numeric) Standard deviation of Ra-226 activity * Thickness.cm: (numeric) Thickness of the sediment interval in centimeters #### File: Core-A-C_(rPlum_Output).csv **Description:** This dataset contains the output from Bayesian age-depth modeling conducted using the rPlum package (see details above) on the three sediment cores collected near SET stations in Tinicum Marsh, Philadelphia, PA. Each row represents model-derived age estimates at a given depth. ##### Variables * Core-ID: (character) Identifier for the sediment core * depth (cm): (numeric) Depth in centimeters from the core top * minimum age: (numeric) Lower bound of modeled age (in years relative to reference year) * maximum age: (numeric) Upper bound of modeled age (in years) * median age: (numeric) Median modeled age (in years) * mean age: (numeric) Mean modeled age (in years) * year: Modeled calendar year #### File: Event-based_OM.csv **Description:** This dataset contains organic matter content measured from surface sediment samples collected after individual storm and non-storm events at Tinicum Marsh, Philadelphia, PA. Samples were taken at specific transects and plots corresponding to sediment trap deployments. ##### Variables * Date collected: Date when the sample was retrieved, in m/d/yy format * Event type: (character) Classification of the event that preceded sampling * Transect: (numeric) Transect number where sediment traps were deployed and the sample was collected * Plot: (numeric) Plot number within each transect * % Organic Matter: Percent of organic matter by weight, estimated via loss-on-ignition #### File: MH-OM.csv **Description:** This dataset includes organic matter content from samples collected at Marker Horizon (MH) plots associated with SET stations in Tinicum Marsh, Philadelphia, PA. ##### Variables * Date collected: Sampling date in m/d/yy format * SET: (character) Identifier for the Surface Elevation Table station * Plot: Subplot identifier where the MH sample was collected * % Organic Matter: Percent of organic matter #### File: Core_OM.csv **Description:** This dataset provides organic carbon composition and porosity estimates from three sediment cores (A–C) collected in Tinicum Marsh near SET monitoring stations. These measurements characterize the vertical structure of sediment in terms of mineral, organic, and pore volume percentages. ##### Variables * Core: (character) Identifier for the sediment core * Bulk density (g/cm2): Average bulk density with standard error * Mineral accumulation rate (g/m2/yr): Annual rate of mineral sediment accumulation * Mineral Volume (%): Percentage of the core volume composed of mineral matter * Organic accumulation rate (g/m2/yr): Annual rate of organic matter accumulation * Organic Volume (%): Percentage of core volume composed of organic matter * Porespace Volume (%): Volume percentage of pore space in the sediment * Organic Carbon (%): Organic carbon concentration by weight * Total Nitrogen (%): Total nitrogen concentration by weight ## Code/software The data were processed and analyzed using R (version 4.2.2), a free and open-source software environment for statistical computing and graphics. The following R packages were used: * **SETr**: Used for processing Surface Elevation Table (SET) and Marker Horizon (MH) data, including importing raw pin measurements, applying QA/QC codes, and calculating elevation change and accretion over time. * **rplum**: Applied for age-depth modeling of radioisotope data (Pb-210), estimating sedimentation rates using a Bayesian approach. * **ggplot2**: Utilized for data visualization, including hydrographs, boxplots, and scatterplots with regression fits. * **dplyr** and **tidyr**: For data wrangling, including filtering, reshaping, and summarizing datasets. * **lubridate**: Used to handle and format date-time variables for temporal alignment of sediment data and rainfall records. * **readr**: For efficient reading of CSV files. **Workflow Summary** 1. **SET and MH data** were imported and cleaned using SETr, with QA/QC codes applied to filter measurements. Cumulative elevation change and accretion were calculated per pin, arm, and year. 2. **Event-based sediment and organic matter data** were summarized by storm vs. non-storm type, analyzed for temporal and spatial trends using dplyr, and plotted using ggplot2. 3. **Sediment core data** (bulk density, Pb-210) were used as input for the rplum package, which generated age-depth models and estimates of long-term sedimentation rates.