Articles
Guides
- 🚀 Get started
Install faofishingreport, update the FAO data, produce the first charts for the Northeast Atlantic (FAO area 27) and write a Word report in one call.
- 🎓 Tutorial: the Northeast Pacific (FAO area 67) from zero to a report
A complete worked example: get the FAO data, analyse FAO major fishing area 67 (Alaska, Canada and the US west coast) step by step with every function of the package, read and interpret each chart, find the files the package saves, and export the assessment report as Word, LaTeX and PDF.
- 💾 FAO data: download and customise
Where the data come from, how to check for and download FAO releases, the data format, and how to analyse your own subsets.
- 🌊 Fishing area analysis
fao_areas() and fishing_area_map(): the FAO major fishing areas and their subareas; fishing_area_data(), fishing_area_species() and fishing_area_country(): total catch, main species and main countries of an FAO fishing area, with all options.
- 🐟 Species and countries
species_country(), country_species() and country_analysis(): who catches a species, what a country catches in an area, and a country’s catch in all FAO areas.
- 📈 Composition, stock status and trends
species_group_composition(), stock_status(), peak_trend(), area_overview(), regime_shift(), pelagic_demersal() and fao_pd_groups(): what is caught, how the stocks have developed, and when things changed.
- 🔍 Data quality, diversity and fleets
data_quality(), diversity_concentration(), country_group_summary() and coastal_distant(): how reliable the data are, how diverse and concentrated the catch is, and who is fishing.
- 🔬 Shocks, collapses, synchrony and fleets
catch_shocks(), collapse_analysis(), catch_synchrony(), distant_water_profile() and compare_releases(): abrupt falls and collapses of the catch, how synchronously catches fluctuate, where a country’s fleets fish, and what FAO revised between two data releases, each following published methods.
- 🌡️ Sea temperature and catch temperature
fao_sst_products(), fao_area_sst(), download_sst_data() and mean_temperature_catch(): the sea surface temperature of the FAO fishing areas, how to use your own SST files, and what you must check before using the mean temperature of the catch.
- 🐠 FishBase and SeaLifeBase traits
check_fishbase_update(), download_fishbase_data(), fishbase_table(), fishbase_match() and fishbase_sources(): species traits from FishBase and SeaLifeBase, how they are matched to the FAO species items, and how the mean temperature of the catch and the CMSY++ priors use them.
- 📉 CMSY++ catch-only stock assessment
cmsy_area(), cmsy_system(), cmsy_setup(), cmsy_install_jags(), cmsy_download_jags(), cmsy_jags_versions(), cmsy_sources(), cmsy_priors(), cmsy_input(), cmsy_defaults(), cmsy_run(), cmsy_plot(), cmsy_forecast(), cmsy_compare() and cmsy_tables(): catch-only assessments of FAO catch series with the bundled CMSY++ code, FishBase priors and JAGS.
- 📝 Assessment report: Word, LaTeX and PDF
fao_report(): an assessment report of an FAO fishing area in Chinese or English in one call, as Word, LaTeX or PDF. Its contents, arguments, sections and their settings, format, citation styles, the CMSY++ part, the tables it returns and the templates of its text.
- 🎨 Customise charts and maps
fao_settings(): language, theme, colour palettes, map projection and centre, fonts, grid lines, resolution, PowerPoint output and data folders.
中文文档
- faofishingreport 中文文档
用 FAO 全球捕捞产量数据，按渔区、国家和物种生成报告用的图表、地图和表格，支持中文、英文和中英双语。
- 🚀 快速入门
安装faofishingreport，更新FAO数据，为东北大西洋（FAO 27渔区）绘制第一批图表，并一键生成Word报告。
- 🎓 教程：东北太平洋（FAO 67区）从零到报告
一个完整的实例：获取FAO数据，用本包的几乎全部函数一步步分析FAO 67渔区（阿拉斯加、加拿大和美国西海岸），看懂并解读每张图，找到本包保存的文件，并把评估报告导出为Word、LaTeX和PDF。
- 💾 FAO数据：下载与自定义
数据从哪里来，如何检查和下载FAO的新版本，数据格式是什么样的， 以及如何分析自己的数据子集。
- 🌊 渔区分析
fao_areas()和fishing_area_map()：FAO主要渔区及其分区；fishing_area_data()、fishing_area_species()和fishing_area_country()：某个FAO渔区的总产量、主要物种和主要捕捞国家，以及全部选项。
- 🐟 物种与国家分析
species_country()、country_species()和country_analysis()：某个物种由哪些国家捕捞，某个国家在一个渔区捕什么，以及某个国家在全部FAO渔区的产量。
- 📈 类群结构、资源状态与趋势
species_group_composition()、stock_status()、peak_trend()、area_overview()、regime_shift()、pelagic_demersal()和fao_pd_groups()：捕捞了什么，各种群如何发展，以及何时发生了变化。
- 🔍 数据质量、多样性与船队
data_quality()、diversity_concentration()、country_group_summary()和coastal_distant()：数据有多可靠，产量的多样性和集中程度如何，以及是谁在捕捞。
- 🔬 渔获骤变、渔业崩溃、同步性与远洋捕捞
catch_shocks()、collapse_analysis()、catch_synchrony()、distant_water_profile()和compare_releases()：按已发表的方法识别渔获量的骤降和崩溃，衡量各渔获序列波动的同步程度，追踪一个国家的船队在哪些渔区作业，并查看FAO在两个数据版本之间修订了什么。
- 🌡️ 海表温度与渔获平均温度
fao_sst_products()、fao_area_sst()、download_sst_data()和mean_temperature_catch()：FAO渔区的海表温度，如何使用自己的SST文件，以及使用渔获平均温度之前必须核对的内容。
- 🐠 FishBase 与 SeaLifeBase 物种特征
check_fishbase_update()、download_fishbase_data()、fishbase_table()、fishbase_match()和fishbase_sources()：FishBase与SeaLifeBase的物种特征，它们如何与FAO物种条目匹配，以及渔获平均温度和CMSY++先验如何使用这些特征。
- 📉 CMSY++仅渔获量资源评估
cmsy_area()、cmsy_system()、cmsy_setup()、cmsy_install_jags()、cmsy_download_jags()、cmsy_jags_versions()、cmsy_sources()、cmsy_priors()、cmsy_input()、cmsy_defaults()、cmsy_run()、cmsy_plot()、cmsy_forecast()、cmsy_compare()和cmsy_tables()：用包内置的CMSY++代码、FishBase先验和JAGS，对FAO渔获序列做仅渔获量评估。
- 📝 一键生成评估报告（Word、LaTeX、PDF）
fao_report()：一次调用即可生成某个FAO渔区的中文或英文评估报告（Word、LaTeX或PDF）。本文介绍报告的内容、参数、各分析章节及其设置、格式、引文格式、CMSY++部分、返回的表格以及报告文字的模板。
- 🎨 自定义图表与地图
fao_settings()：语言、主题、色板、地图投影与中心、字体、网格线、分辨率、PowerPoint输出和数据文件夹。
🧩 Extensions · 扩展
Other FAO datasets, not part of the Word report · FAO其他数据集，不纳入Word报告
- 🚢 Trade and employment
load_fao_trade(), catch_trade(), fao_capture_groups(), load_fao_employment(), employment_summary() and catch_per_fisher(): how much of a country’s catch is exported, and how many people fish and farm, from two more FAO datasets.
- 🚢 贸易与就业
load_fao_trade()、catch_trade()、fao_capture_groups()、load_fao_employment()、employment_summary()和catch_per_fisher()：用FAO另外两个数据集看一国渔获有多少出口，以及有多少人从事捕捞和养殖。