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.
Arguments
- area_data
FAO catch data:
fishing_area_data()$area_data, or any subset ofload_fao_data()(e.g. one country, or several fishing areas).- definition
The groups counted as pelagic and demersal: "de_leiva_moreno" (default) or "grainger_garcia" (see above and
fao_pd_groups()).- pelagic, demersal
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" (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
A logical value. If TRUE (default), charts are saved in
figures/png/summary/.- table
A logical value. If TRUE (default), tables are saved in
tables/.- lang
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
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 withfao_settings(pptx = TRUE).- plot_show
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
The name used in the output file names. Default is the fishing area (or the country) of the data.
Value
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.
Details
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.
Which species are pelagic and which demersal
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.
Interpretation
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.
References
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
Examples
if (FALSE) { # \dontrun{
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")
} # }