pelagic_demersal(): 中上层/底层渔获比 • faofishingreport

英文原页：pelagic_demersal()

说明

本函数按年份和年代计算数据中每个FAO海洋渔区的中上层鱼类渔获量与底层鱼类渔获量之比（中上层/底层比，P/D）。Caddy（1993）提出，海域的营养盐富集有利于寿命短、以浮游生物为食的中上层鱼类，而不利于底层鱼类；de Leiva Moreno等（2000）用中上层与底层渔获上岸量之比作为欧洲周边半封闭海域营养水平的替代指标。

English

This function calculates the ratio of pelagic to demersal catch (P/D) of each FAO marine fishing area in the data, by year and by decade. Caddy (1993) proposed that nutrient enrichment of a sea favours short-lived plankton-feeding pelagic fishes over demersal fishes, and de Leiva Moreno et al. (2000) used the ratio of pelagic to demersal landings as a proxy for the nutrient level of the semi-enclosed seas around Europe.

用法

pelagic_demersal(
  area_data,
  definition = c("de_leiva_moreno", "grainger_garcia"),
  pelagic = NULL,
  demersal = NULL,
  by = c("area", "division"),
  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).
definition: 计为中上层和底层的类群：“de_leiva_moreno”（默认）或”grainger_garcia”（见上文和fao_pd_groups()）。
English
The groups counted as pelagic and demersal: “de_leiva_moreno” (default) or “grainger_garcia” (see above and fao_pd_groups()).
pelagic, demersal: 计为中上层和底层的ISSCAAP类群（英文名称，与FAO数据中的一致，例如”Herrings, sardines, anchovies”），用以代替definition中的类群。默认为NULL。
English
ISSCAAP groups (English names as in the FAO data, e.g. “Herrings, sardines, anchovies”) counted as pelagic and demersal instead of those of definition. Default is NULL.
by: “area”（默认）表示按FAO主要渔区计算，“division”表示按load_fao_divisions()渔获数据中的分区计算（例如地中海和黑海的GFCM分区，即de Leiva Moreno等（2000）所用的单元）。
English
“area” (default) for the FAO major areas, or “division” for the divisions of the catch data of load_fao_divisions() (e.g. the GFCM divisions of the Mediterranean and Black Sea, the units of de Leiva Moreno et al. 2000).
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包含三个数据框的列表：

yearly：每个渔区每年一行：中上层、底层、其他和总渔获量（吨），P/D，中上层渔获量占中上层与底层渔获量之和的比例，计为中上层或底层的渔获量所占的比例，以及未鉴定的海洋鱼类所占的比例；
decades：每个渔区每个年代一行：各年P/D的平均值、最低值和最高值，以及该年代的渔获量；
groups：数据中的ISSCAAP类群、每个类群的计法及其渔获量。

by = "division"时，area和area_en为各分区，area_code为分区代码，文件名中的_pelagic_demersal改为_pelagic_demersal_divisions（例如<label>_pelagic_demersal_divisions_ratio.png）。图表保存在figures/png/summary/：<label>_pelagic_demersal_ratio.png（逐年P/D，每个渔区一个分图），以及<label>_pelagic_demersal.png和..._share.png（中上层、底层和其他渔获量）。表格保存在tables/：<label>_pelagic_demersal.csv、..._decades.csv和..._groups.csv。

English

Invisibly, a list of three data frames:

yearly: one row per area and year: pelagic, demersal, other and total catch (tonnes), P/D, the pelagic share of the pelagic and demersal catch, the share of the catch counted as pelagic or demersal, and the share of unidentified marine fishes;
decades: one row per area and decade: mean, lowest and highest yearly P/D, and the catch of the decade;
groups: the ISSCAAP groups of the data, how each is counted and its catch.

With by = "division", area and area_en hold the divisions, area_code their codes, and _pelagic_demersal in the file names becomes _pelagic_demersal_divisions (e.g. <label>_pelagic_demersal_divisions_ratio.png). Charts are saved in figures/png/summary/: <label>_pelagic_demersal_ratio.png (P/D by year, one panel per area), and <label>_pelagic_demersal.png and ..._share.png (pelagic, demersal and other catch). Tables are saved in tables/: <label>_pelagic_demersal.csv, ..._decades.csv and ..._groups.csv.

详细说明

对每个渔区和每一年，P/D = sum(P) / sum(D)，即计为中上层的类群的渔获量（吨）除以计为底层的类群的渔获量。一个年代的比值是该年代各年比值的平均值（做法同Hondorp等，2010），并给出各年比值中的最低值和最高值，因为de Leiva Moreno等（2000）报告的是平均值和范围。

English

For each area and year, P/D = sum(P) / sum(D), the catch (tonnes) of the groups counted as pelagic divided by the catch of the groups counted as demersal. The ratio of a decade is the mean of its yearly ratios (as Hondorp et al. 2010), with the lowest and highest yearly ratio, as de Leiva Moreno et al. (2000) reported mean values and ranges.

哪些物种属于中上层，哪些属于底层

FAO数据为每个物种条目指定了一个ISSCAAP物种类群，因此本函数按类群计算（见fao_pd_groups()）。可以选用两种已发表的定义：

“de_leiva_moreno”（默认）：小型中上层鱼类对比底层鱼类和甲壳类，与de Leiva Moreno等（2000）相同：中上层为鲱、沙丁鱼、鳀类；底层为鲆鲽类、鳕和无须鳕类、其他沿岸鱼类和其他底层鱼类，以及各海洋甲壳类类群（蟹类、螯龙虾类、帝王蟹类、虾类、其他海洋甲壳类）。与该研究一样，金枪鱼及其他大型中上层鱼类、其他中上层鱼类（主要是竹荚鱼和鲭等中型中上层鱼类）、未鉴定的鱼类、头足类及其他软体动物，以及洄游性鱼类均不计入；鲨鳐类（该研究未提及）和磷虾也不计入。
“grainger_garcia”：全部中上层鱼类对比全部底层鱼类，与Grainger和Garcia（1996）对各大洋的做法相同：中上层为鲱、沙丁鱼、鳀类，金枪鱼和旗鱼类，以及其他中上层鱼类；底层为鲆鲽类、鳕和无须鳕类、其他沿岸鱼类和其他底层鱼类、鲨鳐类，以及未鉴定的海洋鱼类。无脊椎动物不计入。

也可以用pelagic和demersal指定其他类群。

已发表的研究是逐个物种（按栖息地或食性）划分的，而不是按ISSCAAP类群划分，而且FAO在2001年修订了ISSCAAP鱼类类群33、34和37，因此这些研究的数值与本函数的结果只能粗略比较。有些类群混有中上层和底层物种：例如，其他沿岸鱼类（类群33）包括玉筋鱼和鲻，有些研究把它们计为中上层鱼类。

English

The FAO data give each species item an ISSCAAP species group, so the function counts groups (see fao_pd_groups()). Two published definitions are available:

“de_leiva_moreno” (default): Small pelagic fishes against demersal fishes and crustaceans, as de Leiva Moreno et al. (2000): pelagic = herrings, sardines, anchovies; demersal = flounders, cods and hakes, miscellaneous coastal and demersal fishes, and the marine crustacean groups (crabs, lobsters, king crabs, shrimps, miscellaneous marine crustaceans). As in that study, tunas and other large pelagics, the miscellaneous pelagic fishes (mainly medium pelagics such as horse mackerels and mackerels), unidentified fishes, cephalopods and other molluscs, and diadromous fishes are left out; sharks and rays (about which the study says nothing) and krill are left out too.
“grainger_garcia”: All pelagic against all demersal fishes, as Grainger and Garcia (1996) for the oceans: pelagic = herrings, sardines, anchovies, tunas and billfishes, and miscellaneous pelagic fishes; demersal = flounders, cods and hakes, miscellaneous coastal and demersal fishes, sharks and rays, and unidentified marine fishes. Invertebrates are left out.

Other groups can be given as pelagic and demersal.

The published studies classed each species (by habitat or diet), not ISSCAAP groups, and FAO revised the ISSCAAP fish groups 33, 34 and 37 in 2001, so their values are only roughly comparable with those of this function. Some groups mix pelagic and demersal species: for example, the miscellaneous coastal fishes (group 33) include sandeels and mullets, which some studies count as pelagic.

结果解读

de Leiva Moreno等（2000）发现，贫营养海域（例如黎凡特海和伊奥尼亚海）的P/D低于1，中营养海域（例如北海、亚得里亚海）约为1至3.5，富营养海域（例如黑海、亚速海、波罗的海）约为6至20或更高，并发现ln(P/D)与叶绿素之间呈正相关；他们指出这些分级是主观的，而且相互重叠。除营养盐外，这一比值还会因其他原因而变化：

捕捞和市场：底层鱼类通常需求更高，因此仅底层鱼类的过度捕捞就会使P/D升高（de Leiva Moreno等，2000；Caddy等，1998）；围网等渔具的管理规定也会改变P/D（Hondorp等，2010）。
溶解氧：缺氧时底层和底栖种群减少，而中上层鱼类受影响较小，因此P/D可能随缺氧而升高，而不只是随营养盐升高（de Leiva Moreno等，2000；Hondorp等，2010）。
自然变动：小型中上层鱼类种群随气候大幅波动，少数几个物种就可能左右这一比值（Grainger和Garcia，1996；Hondorp等，2010）。
报告方式：未鉴定到种的渔获量（“Marine fishes not identified”，在结果中为unidentified_pct）可能大多是底层鱼类（Grainger和Garcia，1996），而且其比例随时间变化。FAO捕捞产量数据既不包括水产养殖，也不包括丢弃的渔获。

by = "division"时，对load_fao_divisions()渔获数据中的每个分区分别计算P/D。不是具体海域的代码，例如”37.0.0 Tunas”或”37.9.0 Not known”，作为单独的单元保留。

在把P/D的变化归因于营养盐之前，应结合各类群的渔获量（类群表和渔获组成图）一起解读。没有捕捞任何中上层类群的渔区（例如南极各渔区，那里的磷虾不计入），P/D为0；图表采用对数刻度，不显示这些年份。

English

de Leiva Moreno et al. (2000) found P/D below 1 in oligotrophic seas (e.g. Levantine and Ionian seas), around 1 to 3.5 in mesotrophic seas (e.g. North Sea, Adriatic) and around 6 to 20 or more in eutrophic seas (e.g. Black Sea, Sea of Azov, Baltic), and a positive relation between ln(P/D) and chlorophyll; they described these classes as subjective and overlapping. The ratio also changes for reasons other than nutrients:

Fishing and markets: demersal fishes are usually in higher demand, so their overfishing alone raises P/D (de Leiva Moreno et al. 2000; Caddy et al. 1998); rules on gears such as purse seines change it too (Hondorp et al. 2010).
Oxygen: under hypoxia demersal and benthic stocks decline while pelagic fishes are less affected, so P/D can rise with hypoxia rather than with nutrients alone (de Leiva Moreno et al. 2000; Hondorp et al. 2010).
Natural variability: small pelagic stocks fluctuate strongly with climate, and a few species can drive the ratio (Grainger and Garcia 1996; Hondorp et al. 2010).
Reporting: catch not identified to species (“Marine fishes not identified”, shown as unidentified_pct) is probably mostly demersal (Grainger and Garcia 1996), and its share changes over time. The FAO capture data contain neither aquaculture nor discards.

With by = "division", the ratio is calculated for each division of the catch data of load_fao_divisions(). Codes that are not places, such as “37.0.0 Tunas” or “37.9.0 Not known”, are kept as their own units.

Read the ratio together with the catch of each group (the group table and the composition chart) before attributing a change to nutrients. Where no pelagic group is caught (e.g. the Antarctic areas, where krill is not counted), P/D is 0; the chart, on a log scale, leaves such years out.

参考文献

Caddy, J.F. (1993). Toward a comparative evaluation of human impacts on fishery ecosystems of enclosed and semi-enclosed seas. Reviews in Fisheries Science 1: 57-95. doi:10.1080/10641269309388535

Caddy, J.F., Carocci, F. and Coppola, S. (1998). Have peak fishery production levels been passed in continental shelf area? Some perspectives arising from historical trends in production per shelf area. Journal of Northwest Atlantic Fishery Science 23: 191-219. doi:10.2960/J.v23.a13

de Leiva Moreno, J.I., Agostini, V.N., Caddy, J.F. and Carocci, F. (2000). Is the pelagic-demersal ratio from fishery landings a useful proxy for nutrient availability? A preliminary data exploration for the semi-enclosed seas around Europe. ICES Journal of Marine Science 57: 1091-1102. doi:10.1006/jmsc.2000.0705

Grainger, R.J.R. and Garcia, S.M. (1996). Chronicles of marine fishery landings (1950-1994): trend analysis and fisheries potential. FAO Fisheries Technical Paper 359. Rome: FAO. https://www.fao.org/4/w3244e/w3244e00.htm

Hondorp, D.W., Breitburg, D.L. and Davias, L.A. (2010). Eutrophication and fisheries: separating the effects of nitrogen loads and hypoxia on the pelagic-to-demersal ratio and other measures of landings composition. Marine and Coastal Fisheries 2: 339-361. doi:10.1577/C09-020.1

示例

FAO37 <- fishing_area_data("Mediterranean and Black Sea", plot = FALSE)
pd <- pelagic_demersal(FAO37$area_data, lang = "zh")
pd$decades
pd$groups                                   # how each ISSCAAP group is counted

# All pelagic and demersal fishes (Grainger and Garcia 1996)
pelagic_demersal(FAO37$area_data, definition = "grainger_garcia", label = "FAO37_all_fishes")

# Your own groups, e.g. small and medium pelagics
pelagic_demersal(FAO37$area_data,
                 pelagic = c("Herrings, sardines, anchovies", "Miscellaneous pelagic fishes"),
                 demersal = fao_pd_groups()$isscaap_en[fao_pd_groups()$de_leiva_moreno == "demersal"],
                 label = "FAO37_small_medium_pelagic")

# The GFCM divisions of the Mediterranean and Black Sea
pelagic_demersal(load_fao_divisions("GFCM"), by = "division")

# All FAO major marine fishing areas, one panel per area
marine <- subset(load_fao_data(), FAO.major.fishing.area..Name. %in% fao_area_sst()$area_en)
pelagic_demersal(marine, label = "marine_areas")