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collapse_analysis(): 渔业崩溃

Source: vignettes/articles/zh/reference/collapse_analysis.Rmd
collapse_analysis.Rmd

英文原页：collapse_analysis()

说明

本函数用Mullon等（2005）或Worm等（2006）的定义找出已崩溃的渔获量序列，给出崩溃序列的数量、崩溃发生的时间、所在的渔区和物种类群，并按Mullon等（2005）的方法给出崩溃前下降过程的形态。

English

This function finds collapsed catch series, with the definitions of Mullon et al. (2005) or Worm et al. (2006), and gives how many series collapsed, when, in which areas and species groups and, following Mullon et al. (2005), the shape of the decline before the collapse.

用法 

collapse_analysis(
  area_data,
  method = c("mullon2005", "worm2006"),
  exclude_countries = c("Un. Sov. Soc. Rep.", "Yugoslavia SFR", "Czechoslovakia",
    "South Africa", "Namibia", "China"),
  complete_years = 20,
  min_mean_catch = 500,
  min_total_catch = 10000,
  null_model = TRUE,
  n_sim = 100,
  plot = TRUE,
  table = TRUE,
  lang = NULL,
  pptx = getOption("faofishingreport.pptx", FALSE),
  plot_show = fao_setting("plot_show"),
  label = NULL
)

参数

area_data
FAO渔获数据：fishing_area_data()$area_data，或load_fao_data()的任意子集（例如一个国家，或几个渔区）。
English FAO catch data: fishing_area_data()$area_data, or any subset of load_fao_data() (e.g. one country, or several fishing areas).
method
“mullon2005”（默认）或”worm2006”。
English “mullon2005” (default) or “worm2006”.
exclude_countries
方法为”mullon2005”时剔除的国家。默认为Mullon等（2005）剔除的国家。
English Countries left out with method “mullon2005”. Default is those left out by Mullon et al. (2005).
complete_years
方法为”mullon2005”时，序列在数据最后这么多年中的每一年都必须有记录。默认为20。
English With method “mullon2005”, series must have a record in each of the last this many years of the data. Default is 20.
min_mean_catch
方法为”mullon2005”时，序列的最低年平均渔获量（吨/年）。默认为500。
English With method “mullon2005”, the minimum mean catch of a series in tonnes a year. Default is 500.
min_total_catch
方法为”worm2006”时，一个渔业的最低总渔获量（吨）。默认为10000。
English With method “worm2006”, the minimum total catch of a fishery in tonnes. Default is 10 000.
null_model
逻辑值。为TRUE（默认）时，在没有趋势的随机序列（零模型）上重复分析（Wilberg和Miller，2007）。
English A logical value. If TRUE (default), the analysis is repeated on random series with no trend (Wilberg and Miller 2007).
n_sim
零模型随机数据集的个数。默认为100。
English The number of random data sets of the null model. Default is 100.
plot
逻辑值。为TRUE（默认）时，图表保存在figures/png/summary/。
English A logical value. If TRUE (default), charts are saved in figures/png/summary/.
table
逻辑值。为TRUE（默认）时，表格保存在tables/。
English A logical value. If TRUE (default), tables are saved in tables/.
lang
图表文字和名称的语言：“en”（英文）、“zh”（中文）或”both”（中英双语）。默认为NULL，即使用fao_settings()设置的语言（未更改时为”en”）。
English The language of the chart text and names: “en” (English), “zh” (Chinese) or “both” (Chinese and English). Default is NULL, which uses the language set with fao_settings() (“en” unless changed).
pptx
逻辑值。为TRUE时，图表还另存为可编辑的PowerPoint文件，保存在figures/pptx/summary/。默认为FALSE，可以用fao_settings(pptx = TRUE)为所有函数统一更改。
English A logical value. If TRUE, charts are also saved as editable PowerPoint files in figures/pptx/summary/. Default is FALSE, which can be changed for all functions with fao_settings(pptx = TRUE).
plot_show
逻辑值。为TRUE时，每张图在保存的同时也画在绘图窗口中（例如RStudio的Plots窗格），便于立即查看。默认为FALSE，可以用fao_settings(plot_show = TRUE)为所有函数统一更改。无论是否显示，图表都会保存为文件（plot = TRUE）。
English A logical value. If TRUE, each chart is also drawn in the plot window (e.g. the Plots pane of RStudio) as it is saved, to look at it at once. Default is FALSE, which can be changed for all functions with fao_settings(plot_show = TRUE). The charts are saved as files (plot = TRUE) either way.
label
输出文件名中使用的名称。默认为数据所属的渔区（或国家）。
English The name used in the output file names. Default is the fishing area (or the country) of the data.

返回值

以不可见方式返回一个列表，包括series（每条序列一行：最高值、崩溃年份和类型）、summary（按类型统计的崩溃序列数量和比例，并附零模型的结果）、by_year（每年的崩溃次数，或处于崩溃状态的渔业所占的比例）和by_group（按FAO渔区和物种类群统计的崩溃序列比例）。

English

Invisibly, a list with series (one row per series: maximum, collapse year and type), summary (number and share of collapsed series by type, with the null model), by_year (collapses or the share of collapsed fisheries in each year) and by_group (share of collapsed series by FAO area and species group).

详细说明

  • “mullon2005”（默认）：一条序列是一个国家在一个FAO渔区对一个物种或一个属的渔获量。按Mullon等（2005，第112页）的做法，剔除以下数据：未鉴定到属或种的条目；exclude_countries中的国家（默认为Mullon等剔除的国家：前苏联、南斯拉夫和捷克斯洛伐克，它们的序列随国家的消失而结束；南非和纳米比亚，它们的序列被拆分；以及中国，他们认为其序列失真）；最后complete_years（20）年中有缺失年份的序列；以及年平均渔获量低于min_mean_catch（500）吨的序列。如果在序列出现最高渔获量Xmax之后的某一年起，渔获量连续4年低于Xmax/10，则该序列已崩溃；这4年中的第一年为崩溃年Dc（第113页）。崩溃前的下降过程：若从Dc-8到Dc-3的每一年渔获量都高于Xmax/4，为平台型；若从Dc-10到Dc渔获量与时间的相关系数低于-0.7，为平滑型；其余为波动型（第114页）。Mullon等没有说明这些规则按什么顺序判定；本函数按上述顺序判定。距序列第一年不足10年的崩溃不作分类。Mullon等在1950—2000年的1519条序列中发现366次崩溃（24%）：21%为平台型，33%为平滑型，45%为波动型。
  • “worm2006”：一个渔业是所有国家合计的一个物种条目在一个FAO渔区的渔获量（Worm等（2006）使用的是Sea Around Us数据中各大海洋生态系统内的物种）。总渔获量低于min_total_catch（10000吨）的渔业不纳入分析。渔业从其渔获量首次达到最高值10%的那一年开始；某年渔获量低于其最高值的10%时，该渔业在该年处于崩溃状态（回升到该值以上即为恢复）。本函数逐年给出当前处于崩溃状态的渔业所占的比例，以及至少崩溃过一次的渔业所占的比例（Worm等，2006，正文及补充材料第4—5页）。

仅凭渔获量数据，无法区分种群的崩溃与管理、市场或报告方式造成的渔获量下降。Wilberg和Miller（2007）表明，按Worm等（2006）的定义，没有趋势的随机渔获量序列同样会得出“崩溃”渔业比例不断上升的结果，因为序列的最高值随序列长度的增加而增大；null_model = TRUE时，本函数在这类随机序列（平稳的一阶自回归对数正态序列，变异系数为80%，自相关为0.75，与Wilberg和Miller（2007）相同）上重复同样的分析，随机序列的起始年份和长度与真实序列相同，以作对照。

English
  • “mullon2005” (default): A series is the catch of one species or genus by one country in one FAO area. Left out, as by Mullon et al. (2005, p. 112): items not identified to genus or species; the countries in exclude_countries (by default those Mullon et al. left out: the former USSR, Yugoslavia and Czechoslovakia, whose series end with the country; South Africa and Namibia, whose series were split; and China, whose series they considered distorted); series with a missing year among the last complete_years (20) years; and series whose mean catch is below min_mean_catch (500) tonnes a year. A series has collapsed when, in a year after its maximum catch Xmax, catch stays below Xmax/10 for 4 consecutive years; the first of these years is the collapse year Dc (p. 113). The decline before the collapse is plateau if catch was above Xmax/4 in every year from Dc-8 to Dc-3, smooth if the correlation between catch and time from Dc-10 to Dc is below -0.7, and erratic otherwise (p. 114). Mullon et al. do not say in which order the rules apply; they are applied here in that order. Collapses less than 10 years after the first year of the series are not classified. Mullon et al. found 366 collapses among 1,519 series from 1950 to 2000 (24%): 21% plateau, 33% smooth and 45% erratic.
  • “worm2006”: A fishery is the catch of one species item in one FAO area, all countries together (Worm et al. 2006 used species in large marine ecosystems from Sea Around Us data). Fisheries with a total catch below min_total_catch (10 000 tonnes) are left out. A fishery starts when its catch first reaches 10% of its maximum, and is collapsed in a year when its catch is below 10% of its maximum (recovered when it is back above). The function gives, for each year, the share of fisheries currently collapsed and the share that have collapsed at least once (Worm et al. 2006, main text and supplementary pp. 4-5).

Catch data alone cannot tell a collapse of the stock from a fall in catch caused by management, markets or reporting. Wilberg and Miller (2007) showed that random catch series with no trend also give a growing share of “collapsed” fisheries with the definition of Worm et al. (2006), because the maximum of a series grows with its length; with null_model = TRUE the function repeats the analysis on such random series (stationary first-order autoregressive lognormal series with a coefficient of variation of 80% and an autocorrelation of 0.75, as in Wilberg and Miller 2007), with the same start years and lengths as the real series, for comparison.

参考文献

Mullon, C., Freon, P. and Cury, P. (2005). The dynamics of collapse in world fisheries. Fish and Fisheries 6: 111-120. doi:10.1111/j.1467-2979.2005.00181.x

Wilberg, M.J. and Miller, T.J. (2007). Comment on “Impacts of biodiversity loss on ocean ecosystem services”. Science 316: 1285. doi:10.1126/science.1137946

Worm, B., Barbier, E.B., Beaumont, N. et al. (2006). Impacts of biodiversity loss on ocean ecosystem services. Science 314: 787-790. doi:10.1126/science.1132294

示例 

collapse_analysis(load_fao_data(), lang = "zh")                   # Mullon et al. (2005), world
FAO27 <- fishing_area_data("Atlantic, Northeast", plot = FALSE)
collapse_analysis(FAO27$area_data, method = "worm2006")