cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ubsepv
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus squarrosus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 297 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021580-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17164462
title: R scripts for Yangtze Estuary fish community analysis

description: # 长江口鱼类生态网络分析代码 (2018–2023)  # Ecological Network Analysis of Fish Communities in the Yangtze Estuary (2018–2023)

## 简介 | Introduction本项目包含用于构建和分析 **2018–2023 年长江口鱼类生态网络** 的 R 脚本。  代码基于鱼类群落调查数据,自动生成网络结构图、度分布图、网络拓扑指标以及关键节点表,帮助评估禁渔政策对群落结构和稳定性的影响。  

This repository contains R scripts for constructing and analyzing **fish ecological networks in the Yangtze Estuary from 2018–2023**.  The code produces network diagrams, degree distribution plots, network metrics, and key node tables, providing insights into the effects of the fishing ban on community structure and stability.  

---

## 文件说明 | Files- **ecological_network.R** : 主 R 脚本(构建网络、计算指标、绘图)。    *Main R script for network construction, metrics calculation, and visualization.*  - **fish_community.csv** : 示例数据(物种、丰度、营养级、食性类型)。    *Example dataset (species, abundance, trophic level, diet type).*  - **requirements.txt** : 所需 R 包列表。    *List of required R packages.*  - **LICENSE** : 许可证文件。    *License file.*  

---

## 环境依赖 | Dependencies- R >= 4.2.0  - 所需 R 包 | Required packages:    `igraph`, `readr`, `dplyr`, `ggplot2`, `ggraph`, `tidyr`, `openxlsx`, `scales`, `poweRlaw`, `showtext`

---

## 使用方法 | Usage1. 将 `fish_community.csv` 放在代码目录下。     Place `fish_community.csv` in the same directory.  2. 运行 `ecological_network.R` 脚本。     Run the `ecological_network.R` script.  3. 输出结果将自动保存到桌面,包括:     - 网络结构图 (PDF)     - 度分布图 (PDF)     - 网络指标汇总表 (Excel)     - 物种编号对照表 (Excel)     - 关键节点表 (Excel)  

   Outputs will be saved to your Desktop, including:     - Network diagrams (PDF)     - Degree distribution plots (PDF)     - Summary of network metrics (Excel)     - Species label lookup table (Excel)     - Key node summary table (Excel)  

---

## 作者信息 | Author- **姓名 / Name**: Zhang Cheng  gong- **单位 / Affiliation**: Shanghai Ocean University  - **ORCID**: [填写你的 ORCID]  

---

## 许可证 | License本代码遵循 **GPL-3.0** 协议,可自由使用、修改和分发,但请保留作者署名。  This code is licensed under the **GPL-3.0** license. You are free to use, modify, and distribute it with proper attribution.  

---

## 引用 | Citation如果您在研究中使用了本代码,请引用以下条目:  

If you use this code in your research, please cite:
DOI: 10.5281/zenodo.17164463
title: R scripts for Yangtze Estuary fish community analysis

description: # 长江口鱼类生态网络分析代码 (2018–2023)  # Ecological Network Analysis of Fish Communities in the Yangtze Estuary (2018–2023)

## 简介 | Introduction本项目包含用于构建和分析 **2018–2023 年长江口鱼类生态网络** 的 R 脚本。  代码基于鱼类群落调查数据,自动生成网络结构图、度分布图、网络拓扑指标以及关键节点表,帮助评估禁渔政策对群落结构和稳定性的影响。  

This repository contains R scripts for constructing and analyzing **fish ecological networks in the Yangtze Estuary from 2018–2023**.  The code produces network diagrams, degree distribution plots, network metrics, and key node tables, providing insights into the effects of the fishing ban on community structure and stability.  

---

## 文件说明 | Files- **ecological_network.R** : 主 R 脚本(构建网络、计算指标、绘图)。    *Main R script for network construction, metrics calculation, and visualization.*  - **fish_community.csv** : 示例数据(物种、丰度、营养级、食性类型)。    *Example dataset (species, abundance, trophic level, diet type).*  - **requirements.txt** : 所需 R 包列表。    *List of required R packages.*  - **LICENSE** : 许可证文件。    *License file.*  

---

## 环境依赖 | Dependencies- R >= 4.2.0  - 所需 R 包 | Required packages:    `igraph`, `readr`, `dplyr`, `ggplot2`, `ggraph`, `tidyr`, `openxlsx`, `scales`, `poweRlaw`, `showtext`

---

## 使用方法 | Usage1. 将 `fish_community.csv` 放在代码目录下。     Place `fish_community.csv` in the same directory.  2. 运行 `ecological_network.R` 脚本。     Run the `ecological_network.R` script.  3. 输出结果将自动保存到桌面,包括:     - 网络结构图 (PDF)     - 度分布图 (PDF)     - 网络指标汇总表 (Excel)     - 物种编号对照表 (Excel)     - 关键节点表 (Excel)  

   Outputs will be saved to your Desktop, including:     - Network diagrams (PDF)     - Degree distribution plots (PDF)     - Summary of network metrics (Excel)     - Species label lookup table (Excel)     - Key node summary table (Excel)  

---

## 作者信息 | Author- **姓名 / Name**: Zhang Cheng  gong- **单位 / Affiliation**: Shanghai Ocean University  - **ORCID**: [填写你的 ORCID]  

---

## 许可证 | License本代码遵循 **GPL-3.0** 协议,可自由使用、修改和分发,但请保留作者署名。  This code is licensed under the **GPL-3.0** license. You are free to use, modify, and distribute it with proper attribution.  

---

## 引用 | Citation如果您在研究中使用了本代码,请引用以下条目:  

If you use this code in your research, please cite:
DOI: 10.15468/dl.xznpug
title: Occurrence Download

description: A dataset containing 2778 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Diplazium caudatum)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2778 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021581-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2suz6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus americanus",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021582-250914085247600/datasets/export for details.
DOI: 10.6084/m9.figshare.30171262
title: Source data for "Universal Driven Critical Dynamics near the Boundary"

description: The celebrated Kibble-Zurek mechanism (KZM) describes the scaling of physical quantities when external parameters sweep through a critical point. Boundaries are ubiquitous in real systems, and critical behaviors near the boundary have attracted extensive research. Different boundary universality classes, including ordinary, special, extraordinary, and surface transitions, have been identified. However, the driven critical dynamics near boundaries remains unexplored. Here, we systematically investigate the driven critical dynamics in various boundary universality classes of the Ising model in both two and three dimensions, and discover a wealth of dynamic scaling behaviors. We find that for heating dynamics in all boundary universality classes, as well as for cooling dynamics in special, extraordinary, and surface transitions, the dynamic scaling behaviors of the order parameter can be described by a normal generalization of the KZM, called boundary finite-time scaling (BFTS). In contrast, for cooling dynamics in ordinary transition, we discover an abnormal logarithmic scaling on the driving rate. Moreover, for the special transition, in addition to temper-ature driving, we also consider the driven dynamics by driving the surface couplings. For increasing the surface coupling across the special transition point along the line of the ordinary transition, the prerequisite of the KZM, which requires that the correlation length/time in the initial state to be short-ranged, breaks down. We develop a generalized BFTS for a nonequilibrium initial state characterized by the waiting time, or the “age”, of the boundary. Possible generalizations are also discussed.
DOI: 10.6084/m9.figshare.30171262.v1
title: Source data for "Universal Driven Critical Dynamics near the Boundary"

description: The celebrated Kibble-Zurek mechanism (KZM) describes the scaling of physical quantities when external parameters sweep through a critical point. Boundaries are ubiquitous in real systems, and critical behaviors near the boundary have attracted extensive research. Different boundary universality classes, including ordinary, special, extraordinary, and surface transitions, have been identified. However, the driven critical dynamics near boundaries remains unexplored. Here, we systematically investigate the driven critical dynamics in various boundary universality classes of the Ising model in both two and three dimensions, and discover a wealth of dynamic scaling behaviors. We find that for heating dynamics in all boundary universality classes, as well as for cooling dynamics in special, extraordinary, and surface transitions, the dynamic scaling behaviors of the order parameter can be described by a normal generalization of the KZM, called boundary finite-time scaling (BFTS). In contrast, for cooling dynamics in ordinary transition, we discover an abnormal logarithmic scaling on the driving rate. Moreover, for the special transition, in addition to temper-ature driving, we also consider the driven dynamics by driving the surface couplings. For increasing the surface coupling across the special transition point along the line of the ordinary transition, the prerequisite of the KZM, which requires that the correlation length/time in the initial state to be short-ranged, breaks down. We develop a generalized BFTS for a nonequilibrium initial state characterized by the waiting time, or the “age”, of the boundary. Possible generalizations are also discussed.
DOI: 10.5281/zenodo.17160044
title: Makassar's Gold Street
title: Jalan Perdagangan Emas di Makassar

description: This dataset originates from ethnographic fieldwork conducted in Makassar, Indonesia. It includes a curated selection of fieldnotes and photographs, each photograph accompanied by metadata (time, place, and contextual details). A README file is provided to explain the dataset’s structure, contents, and conventions.
DOI: 10.5281/zenodo.16987484
title: Makassar's Gold Street
title: Jalan Perdagangan Emas di Makassar

description: This dataset originates from ethnographic fieldwork conducted in Makassar, Indonesia. It includes a curated selection of fieldnotes and photographs, each photograph accompanied by metadata (time, place, and contextual details). A README file is provided to explain the dataset’s structure, contents, and conventions.
DOI: 10.15468/dl.3a7r9y
title: Occurrence Download

description: A dataset containing 1850 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pteris incompleta)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 1850 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021585-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97h2b2
title: Occurrence Download

description: A dataset containing 103133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gentiana lutea)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 103133 records from 430 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021574-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v5e8gk
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Draba thompsonii (C.L.Hitchc.) G.A.Mulligan & Al-Shehbaz"
 ]
}

 The dataset includes 40 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155440-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.44fgcx
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coryanthes elegantium Linden & Rchb.f."
 ]
}

 The dataset includes 28 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155439-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e3he2s
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Odorrana tiannanensis (Yang & Li, 1980)"
 ]
}

 The dataset includes 82 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021004-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.feg2g5
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Candida magnoliae (Lodder & Kreger-van Rij) S.A.Mey. & Yarrow"
 ]
}

 The dataset includes 48 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001339-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5hcvfh
title: Occurrence Download

description: A dataset containing 227902 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Castanea sativa Mill."
 ]
}

 The dataset includes 227902 records from 608 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0249794-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3t6s88
title: Occurrence Download

description: A dataset containing 2227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Country is Germany",
 "DecimalLongitude is greater than or equal to 10.4250642447482",
 "DecimalLongitude is less than 10.4281237979326",
 "DecimalLatitude is greater than or equal to 47.27011",
 "DecimalLatitude is less than or equal to 55.05864"
 ]
}

 The dataset includes 2227 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010295-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.azrfmk
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Argentina",
 "Country is Bolivia (Plurinational State of)"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Jacaranda mimosifolia D.Don",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 86 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001346-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.73wvh7
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Senna pallida var. nemorosa (Kunth) H.S.Irwin & Barneby"
 ]
}

 The dataset includes 46 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0249796-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bdfkrf
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dioscorea sandwithii B.G.Schub."
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155441-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xjjcax
title: Occurrence Download

description: A dataset containing 339 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zygosaccharomyces rouxii (Boutroux) Yarrow"
 ]
}

 The dataset includes 339 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001344-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h79chw
title: Occurrence Download

description: A dataset containing 6760 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Podocnemis expansa (Schweigger, 1812)"
 ]
}

 The dataset includes 6760 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072219-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yk8nx2
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Philippines",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gallicolumba luzonica (Scopoli, 1786)"
 ]
}

 The dataset's 2 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013145-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sosced
title: Occurrence Download

description: A dataset containing 2113 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Beauveria bassiana (Bals.-Criv.) Vuill."
 ]
}

 The dataset includes 2113 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001345-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekk3wd
title: Occurrence Download

description: A dataset containing 1573 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Enhalus acoroides (L.f.) Royle"
 ]
}

 The dataset includes 1573 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015636-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gz9kp5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arenaria fragillima Rech.fil.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072195-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gw4wrc
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cumulopuntia rossiana (Heinrich & Backeb.) F.Ritter"
 ]
}

 The dataset includes 38 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0155442-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gx46q7
title: Occurrence Download

description: A dataset containing 1122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cubozoa"
 ]
}

 The dataset includes 1122 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0246648-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uxjkbh
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Agave tequilana A. Weber",
 "TaxonKey is Agave tequilana F.A.C.Weber"
 ]
 },
 "Geometry POLYGON((-129.375 60.930432,-129.375 -56.559482,-25.3125 -56.559482,-25.3125 60.930432,-129.375 60.930432))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009380-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6muawc
title: Occurrence Download

description: A dataset containing 7018 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gerres oyena (Forsskål, 1775)"
 ]
}

 The dataset includes 7018 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010300-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mcn7qp
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Fossil",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Human Observation"
 ]
 },
 {
 "or" : [
 "Country is United States of America",
 "Country is Djibouti",
 "Country is South Africa",
 "Country is Ethiopia",
 "Country is Kenya"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Beatragus Heller, 1912"
 ]
}

 The dataset includes 58 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0244403-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdymxg
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Microascus brevicaulis S.P.Abbott"
 ]
}

 The dataset includes 173 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001358-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.