Data from: Sedimentary organic carbon restoration in abandoned bivalve farms via seagrass recolonisation: a case study from the Ria Formosa lagoon

These datasets support the scientific article "Carbon restoration in abandoned bivalve farms via seagrass recolonisation: a case study from the Ria Formosa lagoon" (submitted). It contains detailed data to estimate carbon stocks in bivalve farms and seagrass-colonised abandoned farms in the Ria Formosa lagoon (southern Portugal). The datasets are accompanied by analysis code, available at GitHub repository, allowing for reproducibility and further exploration of the data. The data is composed by 2 datasets with the following variables: data_cores.csv. Contains properties related to the sampling of the sediment cores. core_id_reg [character] - unique core identification code used in the field. category [factor] - present land-use category where the core were sampled (seagrass, oyster_farm, clam_farm). replicate [character] - replicate number of the core in each pond. core_date [date] - date of core collection (YYYY-MM-DD). core_latitude [numeric] - positional latitude of the core in decimal degree WGS84. core_longitude [numeric] - positional longitude of the core in decimal degree WGS84. core_depth [numeric] - depth sampled with the core (in centimeters). sample_length [numeric] - length of the sampled core (in centimeters). compaction_correction_factor [numeric] - fraction of the sample depth interval reduced due to compaction. It is calculated by dividing the core length by the core depth. compaction [numeric] - core compaction in percentage (%). It is calculated as 100*(1 - compaction_correction_factor). data_samples.csv. Contains properties of the sediment samples. core_id_reg [character] - unique core identification code used in the field. category [factor] - present land-use category where the core were sampled (seagrass, oyster_farm, clam_farm). replicate [character] - replicate number of the core in each pond. sample_id [character] - unique sample identification code. depth_middle_uncorrected [numeric] - middle depth of a sampling increment, calculating as the average of depth_min and depth_max (in centimeters), uncorrected for compaction. depth_middle [numeric] - middle depth of a sampling increment, calculating as the average of depth_min and depth_max (in centimeters). Corrected for compaction. depth_min [numeric] - minimum depth of a sampling increment, corrected for compaction (in centimeters). Corrected for compaction. depth_max [numeric] - maximum depth of a sampling increment, corrected for compaction (in centimeters). Corrected for compaction. thickness [numeric] - sample thickness (in centimeters), calculated as depth_max - depth_min. sample_volume [numeric] - volume of the sediment sample, corrected for compaction (in cubic centimeters). flag_volume [boolean] - whether there is any potential error in the sample volume (0 no, 1 yes). sample_dw [numeric] - dry mass of the sample (in grams of dry weight). flag_dw [boolean] - whether there is any potential error in the sample dw (0 no, 1 yes). percentage_organic_matter [numeric] - mass of organic matter relative to sample dry mass, obtained by loss-on-ignition (in percentage of dry weight). sample_loi_pre [numeric] - weight of the sample fraction used for loss-on-ignition (in grams of dry weight). dry_bulk_density [numeric] - dry mass per unit volume of the sample. This is calculated as the sample_dw divided by the sample_dw (in grams of dry weight per cubic centimeter). flag_dbd [boolean] - whether there is any potential error in the dry bulk density (0 no, 1 yes). percentage_organic_matter [numeric] - mass of organic matter relative to sample dry mass (as a percentage of dry weight). flag_om [boolean] - whether there is any potential error in the organic matter content (0 no, 1 yes).本数据集支撑已投稿的学术论文《通过海草重新定植实现废弃双壳贝类养殖场的碳修复：以葡萄牙南部里亚福尔摩沙潟湖为例》。数据集包含用于估算葡萄牙南部里亚福尔摩沙潟湖内双壳贝类养殖场及已被海草定植的废弃养殖场碳储量的详细数据。本数据集附带可复现研究及开展数据进一步探索的分析代码，代码托管于GitHub代码仓库中。 本数据集包含两个子数据集，各变量详情如下： data_cores.csv：包含与沉积物岩芯采样相关的各项属性数据。 - core_id_reg [字符型]：野外采样使用的唯一岩芯识别编码 - category [因子型]：岩芯采样点所在的当前土地利用类型（包括海草床、牡蛎养殖场、蛤仔养殖场） - replicate [字符型]：每个养殖池内岩芯的重复编号 - core_date [日期型]：岩芯采集日期（格式为YYYY-MM-DD） - core_latitude [数值型]：岩芯的纬度坐标，采用WGS84十进制度单位 - core_longitude [数值型]：岩芯的经度坐标，采用WGS84十进制度单位 - core_depth [数值型]：岩芯采样深度（单位：厘米） - sample_length [数值型]：采集到的岩芯总长度（单位：厘米） - compaction_correction_factor [数值型]：因压实作用导致采样深度区间缩减的比例，计算公式为岩芯总长度除以采样深度 - compaction [数值型]：岩芯压实率（单位：%），计算公式为100*(1 - 压实校正系数) data_samples.csv：包含沉积物样品的各项属性数据。 - core_id_reg [字符型]：野外采样使用的唯一岩芯识别编码 - category [因子型]：岩芯采样点所在的当前土地利用类型（包括海草床、牡蛎养殖场、蛤仔养殖场） - replicate [字符型]：每个养殖池内岩芯的重复编号 - sample_id [字符型]：唯一的样品识别编码 - depth_middle_uncorrected [数值型]：未校正压实作用的采样增量中点深度，通过depth_min与depth_max的平均值计算得到（单位：厘米） - depth_middle [数值型]：经压实校正后的采样增量中点深度，通过depth_min与depth_max的平均值计算得到（单位：厘米） - depth_min [数值型]：经压实校正后的采样增量最小深度（单位：厘米） - depth_max [数值型]：经压实校正后的采样增量最大深度（单位：厘米） - thickness [数值型]：样品厚度（单位：厘米），计算公式为depth_max - depth_min - sample_volume [数值型]：经压实校正后的沉积物样品体积（单位：立方厘米） - flag_volume [布尔型]：样品体积是否存在潜在误差（0为无误差，1为存在误差） - sample_dw [数值型]：样品干重（单位：克干重） - flag_dw [布尔型]：样品干重是否存在潜在误差（0为无误差，1为存在误差） - percentage_organic_matter [数值型]：通过烧失量法测得的有机质占样品干重的百分比（单位：%干重） - sample_loi_pre [数值型]：用于烧失量分析的样品组分干重（单位：克干重） - dry_bulk_density [数值型]：样品的干容重，即单位体积样品的干质量。原文公式存在笔误（原描述为“sample_dw divided by the sample_dw”），结合单位修正为样品干重除以样品体积（单位：克干重/立方厘米） - flag_dbd [布尔型]：干容重是否存在潜在误差（0为无误差，1为存在误差） - percentage_organic_matter [数值型]：有机质占样品干重的百分比（以干重百分比计，与前文变量定义重复） - flag_om [布尔型]：有机质含量是否存在潜在误差（0为无误差，1为存在误差）