R/int_st_peche_commerciale.R
In EffetsCumulatifsNavigation/ceanav: Research compendium for project on the assessment cumulative effects of marine vessel activities in the St. Lawrence
Defines functions
st_peche_commerciale
Documented in
st_peche_commerciale
#' Pêches commerciales
#'
#' Couche de données transformées pour les pêches commerciales dans le Saint-Laurent
#'
#' @keywords pêche commerciale
#' @keywords stresseurs
#'
#' @export
#'
#' @details Cette fonction importe et formatte les données pour l'analyse d'effets cumulatifs
#'
st_peche_commerciale <- function() {
# Load gear type dataset and fishing data
load_format("data0033")
load_format("data0034")
load_format("data0035")
# MAJ 2023:
load_format("data0083")
data_metadata <- c("0033","0034","0035", "0083")
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Classify gear types
# -------------------
# NOTE:
#
# Fishing activities are performed using a variety of gears types, e.g. trap,
# trawl, dredge, driftnet, hand line, longline, scuba diving, purse seine, seine,
# beach seine and jig fishing. Intensity of fishing activities was divided among
# gear types and based on their respective types of environmental impacts.
# Gear classification is done using the classification presented in Halpern
# et al. (2008) and Halpern et al. (2015a) and is broken down into 5 distinct
# classes:
#
# - demersal destructive (DD),
# - demersal, non-destructive, low-bycatch (DNL),
# - demersal, non-destructive, high-bycatch (DNH),
# - pelagic, low-bycatch (PLB),
# - pelagic, high-bycatch (PHB),
# - hunting (HN)
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data0034$gearClass <- ""
data0034$gearClass[data0034$Codes == 0] <- NA # Valeur manquante","Null data",""
data0034$gearClass[data0034$Codes == 1] <- NA # Engin fixe","Fixed gear","F"
data0034$gearClass[data0034$Codes == 2] <- NA # Engin mobile","Mobile gear","M"
data0034$gearClass[data0034$Codes == 3] <- "DNH" # Casier","Trap","F"
data0034$gearClass[data0034$Codes == 4] <- "PHB" # Filet maillant","Gill net","F"
data0034$gearClass[data0034$Codes == 5] <- "PHB" # Filet maillant et ligne à main","Gill net and hand line","F"
data0034$gearClass[data0034$Codes == 6] <- "DD" # Drague","Dredge","M"
data0034$gearClass[data0034$Codes == 9] <- "DD" # Chalut à perche pour la crevette","Shrimp beam trawl",""
data0034$gearClass[data0034$Codes == 10] <- "DD" # "Chalut de fond à panneaux (indéterminé)","Bottom otter trawl (unspecified)","M"
data0034$gearClass[data0034$Codes == 11] <- "DD" # "Chalut de fond à panneaux (de côté)","Bottom otter trawl (side)","M"
data0034$gearClass[data0034$Codes == 12] <- "DD" # "Chalut de fond à panneaux (arrière)","Bottom otter trawl (stern)","M"
data0034$gearClass[data0034$Codes == 13] <- "PHB" # "Chalut mésopélagique (indéterminé)","Midwater trawl (unspecified)","M"
data0034$gearClass[data0034$Codes == 14] <- "PHB" # "Chalut mésopélagique (de côté)","Midwater trawl (side)","M"
data0034$gearClass[data0034$Codes == 15] <- "PHB" # "Chalut mésopélagique (arrière)","Midwater trawl (stern)","M"
data0034$gearClass[data0034$Codes == 16] <- "DD" # "Chalut de fond boeuf","Bottom pair trawl","M"
data0034$gearClass[data0034$Codes == 17] <- "PHB" # "Chalut pélagique boeuf","Midwater pair trawl","M"
data0034$gearClass[data0034$Codes == 18] <- "PHB" # "Chalut semi-pélagique","Semi-midwater trawl","M"
data0034$gearClass[data0034$Codes == 19] <- "DD" # "Chalut à crevettes","Shrimp trawl","M"
data0034$gearClass[data0034$Codes == 21] <- "DNH" # "Seine danoise","Danish seine","M"
data0034$gearClass[data0034$Codes == 22] <- "DNH" # "Seine écossaise","Scottish seine","M"
data0034$gearClass[data0034$Codes == 24] <- "DNH" # "Seine de plage","Beach and bar seine","F"
data0034$gearClass[data0034$Codes == 25] <- "DNH" # "Senne de plage modifiée","Tuck seine","F"
data0034$gearClass[data0034$Codes == 27] <- "PHB" # "Filet maillant turbot","Turbot gill net","F"
data0034$gearClass[data0034$Codes == 28] <- "PHB" # "Filet maillant morue","Cod gill net","F"
data0034$gearClass[data0034$Codes == 29] <- "PHB" # "Filet maillant maquereau","Mackerel gill net","F"
data0034$gearClass[data0034$Codes == 30] <- "PHB" # "Filet maillant hareng","Herring gill net","F"
data0034$gearClass[data0034$Codes == 31] <- "PLB" # "Seine bourse","Purse seine","M"
data0034$gearClass[data0034$Codes == 32] <- "PHB" # "Lampara","Lampara","M"
data0034$gearClass[data0034$Codes == 33] <- "DNH" # "Seine coulissante (boeuf)","Pair seine","M"
data0034$gearClass[data0034$Codes == 34] <- "PHB" # "Filet maillant plie","Plaice gill net","F"
data0034$gearClass[data0034$Codes == 35] <- "PHB" # "Filet dérivant hareng","Herring drift net","F"
data0034$gearClass[data0034$Codes == 36] <- "PHB" # "Filet dérivant maquereau","Mackerel drift net","F"
data0034$gearClass[data0034$Codes == 37] <- "PHB" # "Palangre morue","Cod - longline","F"
data0034$gearClass[data0034$Codes == 38] <- "PHB" # "Palangre plie","Plaice - longline","F"
data0034$gearClass[data0034$Codes == 39] <- "PHB" # "Palangre flétan","Turbot - longline","F"
data0034$gearClass[data0034$Codes == 40] <- "PHB" # "Palangre thon","Tuna - longline","F"
data0034$gearClass[data0034$Codes == 41] <- "PHB" # "Filet maillant (fixe)","Gillnet (set or fixed)","F"
data0034$gearClass[data0034$Codes == 42] <- "PHB" # "Filet maillant (dérivant)","Gillnet (drift)","F"
data0034$gearClass[data0034$Codes == 43] <- "PHB" # "Filet maillant (indéterminé)","Gillnet (unspecified)","F"
data0034$gearClass[data0034$Codes == 44] <- "PHB" # "Carrelet","Square net","F"
data0034$gearClass[data0034$Codes == 45] <- "DNH" # "Parc fermé","Box net",""
data0034$gearClass[data0034$Codes == 46] <- "DNH" # "Filet à poche","Bag net",""
data0034$gearClass[data0034$Codes == 47] <- "DNH" # "Verveux","Fyke net",""
data0034$gearClass[data0034$Codes == 48] <- "PHB" # "Filet haut fond","Shoal net","F"
data0034$gearClass[data0034$Codes == 50] <- "PHB" # "Palangrotte","Setheared hooks","F"
data0034$gearClass[data0034$Codes == 51] <- "PHB" # "Palangre","Longline","F"
data0034$gearClass[data0034$Codes == 52] <- "PHB" # "Palangre à requin","Shark longline","F"
data0034$gearClass[data0034$Codes == 53] <- "PLB" # "Turlutte","Jigger","F"
data0034$gearClass[data0034$Codes == 54] <- "PLB" # "Ligne trainante","Troller lines","F"
data0034$gearClass[data0034$Codes == 55] <- "PLB" # "Turlutte mécanique calmar","Mechanized squid jigger","F"
data0034$gearClass[data0034$Codes == 56] <- "PLB" # "Turlutte automatisée (ligne à main)","Automated jigger (hand line) ","F"
data0034$gearClass[data0034$Codes == 57] <- NA # "Dispositif mécanique (maquereau)","Mechanical device (mackerel)","F"
data0034$gearClass[data0034$Codes == 58] <- "PLB" # "Canne et moulinet (amorçage)","Rod and reel (chumming)","F"
data0034$gearClass[data0034$Codes == 59] <- "PLB" # "Ligne à main (appâtée)","Hand line (baited)","F"
data0034$gearClass[data0034$Codes == 60] <- "PLB" # "Pêche à la ligne","Angling","F"
data0034$gearClass[data0034$Codes == 61] <- "DNH" # "Trappe","Trap net","F"
data0034$gearClass[data0034$Codes == 62] <- "DNH" # "Casier non spécifié","Pot ","F"
data0034$gearClass[data0034$Codes == 63] <- "DNH" # "Fascine","Weir","F"
data0034$gearClass[data0034$Codes == 64] <- "PHB" # "Carrelet fixe","Stationary lift nets","F"
data0034$gearClass[data0034$Codes == 65] <- "DNH" # "Vivier à homard","Lobster pound","F"
data0034$gearClass[data0034$Codes == 66] <- "DNH" # "Casier japonais","Japanese trap","F"
data0034$gearClass[data0034$Codes == 67] <- "DNH" # "Casier rectangulaire","Rectangular trap","F"
data0034$gearClass[data0034$Codes == 68] <- "DNH" # "Casier conique","Conical trap","F"
data0034$gearClass[data0034$Codes == 69] <- "DNH" # "Casier pyramidal","Pyramidal trap","F"
data0034$gearClass[data0034$Codes == 70] <- "DNL" # "Épuisette","Dip net",""
data0034$gearClass[data0034$Codes == 71] <- "DD" # "Drague non spécifiée","Dredge (boat)",""
data0034$gearClass[data0034$Codes == 72] <- "DD" # "Drague à main","Dredge (hand)","F"
data0034$gearClass[data0034$Codes == 72] <- "DD" # "Râteau hydraulique","Hydraulic rake","M"
data0034$gearClass[data0034$Codes == 73] <- NA # "Engin mécanisé","Automatic gear","F"
data0034$gearClass[data0034$Codes == 74] <- "DD" # "Drague hydraulique à convoyeur","Hydraulic device","M"
data0034$gearClass[data0034$Codes == 75] <- "DNL" # "Plongée avec outil manuel","Diving with hand tool","F"
data0034$gearClass[data0034$Codes == 76] <- NA # "Câble","Rope",""
data0034$gearClass[data0034$Codes == 77] <- "DD" # "Drague à concombre de mer","Sea Cucumber drag","M"
data0034$gearClass[data0034$Codes == 78] <- "DNH" # "Casier à crabe commun (3 pieds)","Rock crab trap (3 feet)","F"
data0034$gearClass[data0034$Codes == 79] <- "DNH" # "Casier à crabe commun (4 pieds)","Rock crab trap (4 feet)","F"
data0034$gearClass[data0034$Codes == 80] <- "DNH" # "Casier conique (3 pieds)","Conical trap (3 feet)","F"
data0034$gearClass[data0034$Codes == 81] <- "DNL" # "Harpon et lance","Harpoon and spear","M"
data0034$gearClass[data0034$Codes == 82] <- "HN" # "Pêche (chasse) du phoque","Seal hunting","F"
data0034$gearClass[data0034$Codes == 83] <- "DNL" # "Foène","Spear",""
data0034$gearClass[data0034$Codes == 84] <- "DNH" # "Nasse à anguille","Eel pot","F"
data0034$gearClass[data0034$Codes == 85] <- "DNL" # "Harpon électrique","Electric harpoon","M"
data0034$gearClass[data0034$Codes == 86] <- "DNH" # "Baril de Myxine du nord","Hagfish Barrel","F"
data0034$gearClass[data0034$Codes == 87] <- "DNH" # "Casier conique (4 pieds)","","F"
data0034$gearClass[data0034$Codes == 88] <- "DNH" # "Casier à buccin (0,15 mètre cube et moins)","Trap net less than 0.15 m3","F"
data0034$gearClass[data0034$Codes == 89] <- "DNH" # "Casier à buccin (0,16 à 0,30 mètre cube)","Trap net 0.16 m3 to 0.30 m3","F"
data0034$gearClass[data0034$Codes == 90] <- NA # "Divers","Miscellaneous","F"
data0034$gearClass[data0034$Codes == 91] <- "DNL" # "Râteaux et pinces","Rakes and tongs","F"
data0034$gearClass[data0034$Codes == 92] <- "DNH" # "Viviers","Retaining Ponds","F"
data0034$gearClass[data0034$Codes == 93] <- "DD" # "Râteau traînant","Drag rake","M"
data0034$gearClass[data0034$Codes == 94] <- "DNL" # "Coupeur","Cutter",""
data0034$gearClass[data0034$Codes == 95] <- NA # "Bateau à déchargement","Pumper",""
data0034$gearClass[data0034$Codes == 96] <- "DNL" # "Main et outils à main","Hand and hand held tools","F"
data0034$gearClass[data0034$Codes == 98] <- "DNH" # "Mélange de casiers","Mixed of trap - crab","F"
data0034$gearClass[data0034$Codes == 99] <- NA # "Engin fixe non spécifié","Unspecified fixed gear","F"
data0034$gearClass[data0034$Codes == 99] <- NA # "Engin mobile non spécifié","Unspecified mobile gear","M"
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Classify gear mobility
# ----------------------
# NOTE:
#
# Gear types can also be further classified into fixed or mobile engines based
# on their mobility. We used these two mobility classes to generate a buffer of
# impact around each fishing activity coordinates to consider potential spatial
# uncertainty associated with locations and the fact that mobile engines can be
# tracted over several kilometers during fishing activities and that we do not
# have the beginning and end points of mobile fishing events. Buffer sizes for
# fixed (F) and mobile (M) engine is of 200 and 2000 meters, respectively.
#
# The index holds the mobility information for almost all gear types, but some
# are missing. We manually add them here. Categories 81 and 85 were also changed
# from mobile to fixed for the purposes of our analysis, even though it does not
# affect the actual data we are working with because there are no observations of
# those gear types in the study area for this project.
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data0034$Categorie[data0034$Codes == 0] <- NA # Valeur manquante","Null data",""
data0034$Categorie[data0034$Codes == 9] <- "M" # Chalut à perche pour la crevette","Shrimp beam trawl",""
data0034$Categorie[data0034$Codes == 45] <- "F" # "Parc fermé","Box net",""
data0034$Categorie[data0034$Codes == 46] <- "F" # "Filet à poche","Bag net",""
data0034$Categorie[data0034$Codes == 47] <- "F" # "Verveux","Fyke net",""
data0034$Categorie[data0034$Codes == 70] <- "F" # "Épuisette","Dip net",""
data0034$Categorie[data0034$Codes == 71] <- "M" # "Drague non spécifiée","Dredge (boat)",""
data0034$Categorie[data0034$Codes == 76] <- "F" # "Câble","Rope",""
data0034$Categorie[data0034$Codes == 83] <- "F" # "Foène","Spear",""
data0034$Categorie[data0034$Codes == 94] <- "F" # "Coupeur","Cutter",""
data0034$Categorie[data0034$Codes == 95] <- "M" # "Bateau à déchargement","Pumper",""
# ---
data0034$Categorie[data0034$Codes == 81] <- "F" # "Harpon et lance","Harpoon and spear","M"
data0034$Categorie[data0034$Codes == 85] <- "F" # "Harpon électrique","Electric harpoon","M"
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Classify and filter fisheries data
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data0034 <- data0034 %>%
select(Codes, gearClass, mobility = Categorie)
# -----
peche <- left_join(data0033, data0034, by = c("engin" = "Codes")) %>%
filter(!is.na(gearClass)) %>%
filter(!is.na(mobility))
# -----
peche <- peche %>%
filter(as.Date(date_cap) >= as.Date("2010-01-01"))
# -----
# LBS to KG
uid <- peche$un_mes == "P"
peche$pd_deb[uid] <- peche$pd_deb[uid] * 0.453592
# -----
peche <- unique(peche)
# ------------------------------------------------------------
# NOTE: For metadata
species_cible <- sort(unique(peche$prespvis))
species <- table(peche$cod_esp) %>%
as.data.frame() %>%
rename(ESP_STAT = Var1) %>%
mutate(ESP_STAT = as.numeric(as.character(ESP_STAT))) %>%
left_join(data0035, by = "ESP_STAT") %>%
select(ID = ESP_STAT, Scientific = DL_ESP, Espece = DF_ESP,
Species = DA_ESP, Freq)
gear_freq <- table(peche$gearClass) %>%
as.data.frame()
# ------------------------------------------------------------
# -----
peche <- peche %>%
group_by(date_cap, latit_ori, longit_ori, gearClass, mobility) %>%
summarise(catch = sum(pd_deb))
# -----
fix <- peche[peche$mobility == "F", ] %>%
st_buffer(200)
mob <- peche[peche$mobility == "M", ] %>%
st_buffer(2000)
peche <- bind_rows(fix, mob)
# -----
peche <- peche %>%
arrange(as.Date(date_cap))
# -----
peche$ID <- 1:nrow(peche)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Measure intensity
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data(grid1p)
grid1p$ID <- 1:nrow(grid1p)
# # -----
# peche$year <- format(as.Date(peche$date_cap), "%Y")
# years <- unique(peche$year)
# type <- unique(peche$gearClass)
# comb <- expand.grid(type, years, stringsAsFactors = F)
# colnames(comb) <- c('type','years')
#
# # Empty list to store fishing intensity by gear type and by year
# intensity <- vector('list', nrow(comb))
# names(intensity) <- apply(comb, 1, paste, collapse = "-")
#
# # Fishing intensity evaluation
# for(i in 1:length(intensity)) {
# uid <- peche$year == comb[i, 'years'] & peche$gearClass == comb[i, 'type']
# intensity[[i]] <- fishingMetrics(peche[uid, ], grid1p)
# }
#
# -----
peche_commerciale <- grid1p %>%
mutate(
DNL = fishingMetrics(peche[peche$gearClass == 'DNL', ], .)[, 2],
DNH = fishingMetrics(peche[peche$gearClass == 'DNH', ], .)[, 2],
DD = fishingMetrics(peche[peche$gearClass == 'DD', ], .)[, 2],
PLB = fishingMetrics(peche[peche$gearClass == 'PLB', ], .)[, 2],
PHB = fishingMetrics(peche[peche$gearClass == 'PHB', ], .)[, 2]
) %>%
select(-ID) %>%
# ugly
mutate(
DNL = ifelse(DNL == 0, NA, DNL),
DNH = ifelse(DNH == 0, NA, DNH),
DD = ifelse(DD == 0, NA, DD),
PLB = ifelse(PLB == 0, NA, PLB),
PHB = ifelse(PHB == 0, NA, PHB)
)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Pêches secteur fluvial
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data(aoi)
data(grid1p)
grid1p$ID <- 1:nrow(grid1p)
dat <- dplyr::select(data0083, PECHE) |>
sf::st_intersection(aoi) |>
dplyr::select(-FID)
uid <- sf::st_join(grid1p, dat) |>
sf::st_drop_geometry() |>
dplyr::group_by(ID) |>
dplyr::summarize(
PECHE = ifelse(
is.na(PECHE),
NA,
max(PECHE, na.rm = TRUE)
)
) |>
dplyr::distinct() |>
dplyr::rename(peche_fleuve = PECHE)
peche_commerciale$ID <- 1:nrow(peche_commerciale)
peche_commerciale <- dplyr::left_join(peche_commerciale, uid, by = "ID") |>
dplyr::select(-ID)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Update metadata
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
meta <- load_metadata("int_st_peche_commerciale")
# -----
meta$rawData <- data_metadata
# -----
meta$dataDescription$spatial$extent <- st_bbox(data0033)
# -----
peche$years <- format(as.Date(peche$date_cap), "%Y")
meta$dataDescription$temporal$start <- min(peche$years)
meta$dataDescription$temporal$end <- max(peche$years)
# -----
meta$dataDescription$categories$accronyme <- c("DD", "DNL", "DNH", "PLB", "PHB","peche_fleuve")
meta$dataDescription$categories$english <- c(
"Demersal, destructive, high-bycatch",
"Demersal, non-destructive, low-bycatch",
"Demersal, non-destructive, high-bycatch",
"Pelagic, low-bycatch",
"Pelagic, high-bycatch",
"Commercial fisheries in fluvial sector"
)
meta$dataDescription$categories$francais <- c(
"Démersale destructive, prises accessoires élevées",
"Démersale non-destructive, prises accessoires faibles",
"Démersale non-destructive, prises accessoires élevées",
"Pélagique prises accessoires faibles",
"Pélagique prises accessoires élevées",
"Pêches commerciales au sein du secteur fluvial"
)
meta$dataDescription$categories$source <- rep(paste0(meta$rawData, collapse = ","),
length(meta$dataDescription$categories$accronyme))
meta$dataDescription$categories$description <- c(
"Activités de pêches commerciales à l'aide d'engins de pêche démersaux pouvant causer des dommages aux habitats ou au substrat, e.g. chalut et drague.",
"Activités de pêches commerciales à l'aide d'engins de pêche démersaux avec peu ou en l'absence de prises accessoires et ne causant aucune modification des habitats, e.g. la pêche en plongée sous-marine.",
"Activités de pêches commerciales à l'aide d'engins de pêche démersaux avec d'importantes prises accessoires et ne causant aucune modification des habitats, e.g. casier et senne.",
"Activités de pêches commerciales à l'aide d'engins de pêche pélagiques avec peu ou en l'absence de prises accessoires et ne causant aucune modification des habitats, e.g. pêche à la ligne, senne bourse.",
"Activités de pêches commerciales à l'aide d'engins de pêche pélagiques avec d'importantes prises accessoires et ne causant aucune modification des habitats, e.g. filet maillant et palangre.",
"Activités de pêches commerciales à l'aide de verveux au printemps, à l'été et à l'automne, caclculé en nombre moyen de verveux déployés par jour au sein de segments divisant la section fluviale de l'aire d'étude."
)
meta$dataDescription$categories$description_en <- c(
"Commercial fishing activities using demersal fishing gear that may damage habitats or substrate, e.g. trawling and dragging.",
"Commercial fishing activities using demersal fishing gear with little or no bycatch and not causing habitat modification, e.g., deep-sea fishing.",
"Commercial fishing activities using demersal fishing gear with high bycatch and not causing habitat modification, e.g., trap and seine.",
"Commercial fishing activities using pelagic fishing gear with little or no bycatch and not causing habitat modification, e.g., line fishing, purse seine.",
"Commercial fishing activities using pelagic fishing gear with high bycatch and not causing habitat modification, e.g., gillnet and longline.",
"Commercial fisheries activities using fyke nets during the spring, the summer and the fall, measured as the mean number of fyke nets deployed par day in segments dividing the fluvial sector of the study area."
)
meta$dataDescription$categories$zonesNA <- c(
rep("fluvial_peche", 5),
"berge_fluvial"
)
# ----- frequence
dat <- data.frame(acr = meta$dataDescription$categories$accronyme) %>%
left_join(gear_freq, by = c("acr" = "Var1"))
meta$dataDescription$categories$frequence <- dat$Freq
# -----
obs <- peche %>% group_by(years) %>% summarize(total = n())
meta$dataDescription$observations$total <- sum(obs$total)
meta$dataDescription$observations$moyenne <- round(mean(obs$total), 0)
meta$dataDescription$observations$sd <- round(sd(obs$total), 0)
# -----
meta$dataDescription$especes$cible <- species_cible
meta$dataDescription$especes$capture <- species
# --- For proper referencing in markdown syntax
meta$dataDescription$categories$mdref <- modif_md(meta$dataDescription$categories$accronyme)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Export
# ------
#
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# -----
write_yaml(meta, "./data/data-metadata/int_st_peche_commerciale.yml")
# -----
st_write(obj = peche_commerciale,
dsn = "./data/data-integrated/st_peche_commerciale.geojson",
delete_dsn = TRUE,
quiet = TRUE)
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Clean global environment
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
clean()
# ------------------------------------------------------------------------- #}
}
EffetsCumulatifsNavigation/ceanav documentation built on April 17, 2023, 1:02 p.m.
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Defines functions st_peche_commerciale
Documented in st_peche_commerciale
#' Pêches commerciales
#'
#' Couche de données transformées pour les pêches commerciales dans le Saint-Laurent
#'
#' @keywords pêche commerciale
#' @keywords stresseurs
#'
#' @export
#'
#' @details Cette fonction importe et formatte les données pour l'analyse d'effets cumulatifs
#'
st_peche_commerciale <- function() {
# Load gear type dataset and fishing data
load_format("data0033")
load_format("data0034")
load_format("data0035")
# MAJ 2023:
load_format("data0083")
data_metadata <- c("0033","0034","0035", "0083")
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Classify gear types
# -------------------
# NOTE:
#
# Fishing activities are performed using a variety of gears types, e.g. trap,
# trawl, dredge, driftnet, hand line, longline, scuba diving, purse seine, seine,
# beach seine and jig fishing. Intensity of fishing activities was divided among
# gear types and based on their respective types of environmental impacts.
# Gear classification is done using the classification presented in Halpern
# et al. (2008) and Halpern et al. (2015a) and is broken down into 5 distinct
# classes:
#
# - demersal destructive (DD),
# - demersal, non-destructive, low-bycatch (DNL),
# - demersal, non-destructive, high-bycatch (DNH),
# - pelagic, low-bycatch (PLB),
# - pelagic, high-bycatch (PHB),
# - hunting (HN)
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data0034$gearClass <- ""
data0034$gearClass[data0034$Codes == 0] <- NA # Valeur manquante","Null data",""
data0034$gearClass[data0034$Codes == 1] <- NA # Engin fixe","Fixed gear","F"
data0034$gearClass[data0034$Codes == 2] <- NA # Engin mobile","Mobile gear","M"
data0034$gearClass[data0034$Codes == 3] <- "DNH" # Casier","Trap","F"
data0034$gearClass[data0034$Codes == 4] <- "PHB" # Filet maillant","Gill net","F"
data0034$gearClass[data0034$Codes == 5] <- "PHB" # Filet maillant et ligne à main","Gill net and hand line","F"
data0034$gearClass[data0034$Codes == 6] <- "DD" # Drague","Dredge","M"
data0034$gearClass[data0034$Codes == 9] <- "DD" # Chalut à perche pour la crevette","Shrimp beam trawl",""
data0034$gearClass[data0034$Codes == 10] <- "DD" # "Chalut de fond à panneaux (indéterminé)","Bottom otter trawl (unspecified)","M"
data0034$gearClass[data0034$Codes == 11] <- "DD" # "Chalut de fond à panneaux (de côté)","Bottom otter trawl (side)","M"
data0034$gearClass[data0034$Codes == 12] <- "DD" # "Chalut de fond à panneaux (arrière)","Bottom otter trawl (stern)","M"
data0034$gearClass[data0034$Codes == 13] <- "PHB" # "Chalut mésopélagique (indéterminé)","Midwater trawl (unspecified)","M"
data0034$gearClass[data0034$Codes == 14] <- "PHB" # "Chalut mésopélagique (de côté)","Midwater trawl (side)","M"
data0034$gearClass[data0034$Codes == 15] <- "PHB" # "Chalut mésopélagique (arrière)","Midwater trawl (stern)","M"
data0034$gearClass[data0034$Codes == 16] <- "DD" # "Chalut de fond boeuf","Bottom pair trawl","M"
data0034$gearClass[data0034$Codes == 17] <- "PHB" # "Chalut pélagique boeuf","Midwater pair trawl","M"
data0034$gearClass[data0034$Codes == 18] <- "PHB" # "Chalut semi-pélagique","Semi-midwater trawl","M"
data0034$gearClass[data0034$Codes == 19] <- "DD" # "Chalut à crevettes","Shrimp trawl","M"
data0034$gearClass[data0034$Codes == 21] <- "DNH" # "Seine danoise","Danish seine","M"
data0034$gearClass[data0034$Codes == 22] <- "DNH" # "Seine écossaise","Scottish seine","M"
data0034$gearClass[data0034$Codes == 24] <- "DNH" # "Seine de plage","Beach and bar seine","F"
data0034$gearClass[data0034$Codes == 25] <- "DNH" # "Senne de plage modifiée","Tuck seine","F"
data0034$gearClass[data0034$Codes == 27] <- "PHB" # "Filet maillant turbot","Turbot gill net","F"
data0034$gearClass[data0034$Codes == 28] <- "PHB" # "Filet maillant morue","Cod gill net","F"
data0034$gearClass[data0034$Codes == 29] <- "PHB" # "Filet maillant maquereau","Mackerel gill net","F"
data0034$gearClass[data0034$Codes == 30] <- "PHB" # "Filet maillant hareng","Herring gill net","F"
data0034$gearClass[data0034$Codes == 31] <- "PLB" # "Seine bourse","Purse seine","M"
data0034$gearClass[data0034$Codes == 32] <- "PHB" # "Lampara","Lampara","M"
data0034$gearClass[data0034$Codes == 33] <- "DNH" # "Seine coulissante (boeuf)","Pair seine","M"
data0034$gearClass[data0034$Codes == 34] <- "PHB" # "Filet maillant plie","Plaice gill net","F"
data0034$gearClass[data0034$Codes == 35] <- "PHB" # "Filet dérivant hareng","Herring drift net","F"
data0034$gearClass[data0034$Codes == 36] <- "PHB" # "Filet dérivant maquereau","Mackerel drift net","F"
data0034$gearClass[data0034$Codes == 37] <- "PHB" # "Palangre morue","Cod - longline","F"
data0034$gearClass[data0034$Codes == 38] <- "PHB" # "Palangre plie","Plaice - longline","F"
data0034$gearClass[data0034$Codes == 39] <- "PHB" # "Palangre flétan","Turbot - longline","F"
data0034$gearClass[data0034$Codes == 40] <- "PHB" # "Palangre thon","Tuna - longline","F"
data0034$gearClass[data0034$Codes == 41] <- "PHB" # "Filet maillant (fixe)","Gillnet (set or fixed)","F"
data0034$gearClass[data0034$Codes == 42] <- "PHB" # "Filet maillant (dérivant)","Gillnet (drift)","F"
data0034$gearClass[data0034$Codes == 43] <- "PHB" # "Filet maillant (indéterminé)","Gillnet (unspecified)","F"
data0034$gearClass[data0034$Codes == 44] <- "PHB" # "Carrelet","Square net","F"
data0034$gearClass[data0034$Codes == 45] <- "DNH" # "Parc fermé","Box net",""
data0034$gearClass[data0034$Codes == 46] <- "DNH" # "Filet à poche","Bag net",""
data0034$gearClass[data0034$Codes == 47] <- "DNH" # "Verveux","Fyke net",""
data0034$gearClass[data0034$Codes == 48] <- "PHB" # "Filet haut fond","Shoal net","F"
data0034$gearClass[data0034$Codes == 50] <- "PHB" # "Palangrotte","Setheared hooks","F"
data0034$gearClass[data0034$Codes == 51] <- "PHB" # "Palangre","Longline","F"
data0034$gearClass[data0034$Codes == 52] <- "PHB" # "Palangre à requin","Shark longline","F"
data0034$gearClass[data0034$Codes == 53] <- "PLB" # "Turlutte","Jigger","F"
data0034$gearClass[data0034$Codes == 54] <- "PLB" # "Ligne trainante","Troller lines","F"
data0034$gearClass[data0034$Codes == 55] <- "PLB" # "Turlutte mécanique calmar","Mechanized squid jigger","F"
data0034$gearClass[data0034$Codes == 56] <- "PLB" # "Turlutte automatisée (ligne à main)","Automated jigger (hand line) ","F"
data0034$gearClass[data0034$Codes == 57] <- NA # "Dispositif mécanique (maquereau)","Mechanical device (mackerel)","F"
data0034$gearClass[data0034$Codes == 58] <- "PLB" # "Canne et moulinet (amorçage)","Rod and reel (chumming)","F"
data0034$gearClass[data0034$Codes == 59] <- "PLB" # "Ligne à main (appâtée)","Hand line (baited)","F"
data0034$gearClass[data0034$Codes == 60] <- "PLB" # "Pêche à la ligne","Angling","F"
data0034$gearClass[data0034$Codes == 61] <- "DNH" # "Trappe","Trap net","F"
data0034$gearClass[data0034$Codes == 62] <- "DNH" # "Casier non spécifié","Pot ","F"
data0034$gearClass[data0034$Codes == 63] <- "DNH" # "Fascine","Weir","F"
data0034$gearClass[data0034$Codes == 64] <- "PHB" # "Carrelet fixe","Stationary lift nets","F"
data0034$gearClass[data0034$Codes == 65] <- "DNH" # "Vivier à homard","Lobster pound","F"
data0034$gearClass[data0034$Codes == 66] <- "DNH" # "Casier japonais","Japanese trap","F"
data0034$gearClass[data0034$Codes == 67] <- "DNH" # "Casier rectangulaire","Rectangular trap","F"
data0034$gearClass[data0034$Codes == 68] <- "DNH" # "Casier conique","Conical trap","F"
data0034$gearClass[data0034$Codes == 69] <- "DNH" # "Casier pyramidal","Pyramidal trap","F"
data0034$gearClass[data0034$Codes == 70] <- "DNL" # "Épuisette","Dip net",""
data0034$gearClass[data0034$Codes == 71] <- "DD" # "Drague non spécifiée","Dredge (boat)",""
data0034$gearClass[data0034$Codes == 72] <- "DD" # "Drague à main","Dredge (hand)","F"
data0034$gearClass[data0034$Codes == 72] <- "DD" # "Râteau hydraulique","Hydraulic rake","M"
data0034$gearClass[data0034$Codes == 73] <- NA # "Engin mécanisé","Automatic gear","F"
data0034$gearClass[data0034$Codes == 74] <- "DD" # "Drague hydraulique à convoyeur","Hydraulic device","M"
data0034$gearClass[data0034$Codes == 75] <- "DNL" # "Plongée avec outil manuel","Diving with hand tool","F"
data0034$gearClass[data0034$Codes == 76] <- NA # "Câble","Rope",""
data0034$gearClass[data0034$Codes == 77] <- "DD" # "Drague à concombre de mer","Sea Cucumber drag","M"
data0034$gearClass[data0034$Codes == 78] <- "DNH" # "Casier à crabe commun (3 pieds)","Rock crab trap (3 feet)","F"
data0034$gearClass[data0034$Codes == 79] <- "DNH" # "Casier à crabe commun (4 pieds)","Rock crab trap (4 feet)","F"
data0034$gearClass[data0034$Codes == 80] <- "DNH" # "Casier conique (3 pieds)","Conical trap (3 feet)","F"
data0034$gearClass[data0034$Codes == 81] <- "DNL" # "Harpon et lance","Harpoon and spear","M"
data0034$gearClass[data0034$Codes == 82] <- "HN" # "Pêche (chasse) du phoque","Seal hunting","F"
data0034$gearClass[data0034$Codes == 83] <- "DNL" # "Foène","Spear",""
data0034$gearClass[data0034$Codes == 84] <- "DNH" # "Nasse à anguille","Eel pot","F"
data0034$gearClass[data0034$Codes == 85] <- "DNL" # "Harpon électrique","Electric harpoon","M"
data0034$gearClass[data0034$Codes == 86] <- "DNH" # "Baril de Myxine du nord","Hagfish Barrel","F"
data0034$gearClass[data0034$Codes == 87] <- "DNH" # "Casier conique (4 pieds)","","F"
data0034$gearClass[data0034$Codes == 88] <- "DNH" # "Casier à buccin (0,15 mètre cube et moins)","Trap net less than 0.15 m3","F"
data0034$gearClass[data0034$Codes == 89] <- "DNH" # "Casier à buccin (0,16 à 0,30 mètre cube)","Trap net 0.16 m3 to 0.30 m3","F"
data0034$gearClass[data0034$Codes == 90] <- NA # "Divers","Miscellaneous","F"
data0034$gearClass[data0034$Codes == 91] <- "DNL" # "Râteaux et pinces","Rakes and tongs","F"
data0034$gearClass[data0034$Codes == 92] <- "DNH" # "Viviers","Retaining Ponds","F"
data0034$gearClass[data0034$Codes == 93] <- "DD" # "Râteau traînant","Drag rake","M"
data0034$gearClass[data0034$Codes == 94] <- "DNL" # "Coupeur","Cutter",""
data0034$gearClass[data0034$Codes == 95] <- NA # "Bateau à déchargement","Pumper",""
data0034$gearClass[data0034$Codes == 96] <- "DNL" # "Main et outils à main","Hand and hand held tools","F"
data0034$gearClass[data0034$Codes == 98] <- "DNH" # "Mélange de casiers","Mixed of trap - crab","F"
data0034$gearClass[data0034$Codes == 99] <- NA # "Engin fixe non spécifié","Unspecified fixed gear","F"
data0034$gearClass[data0034$Codes == 99] <- NA # "Engin mobile non spécifié","Unspecified mobile gear","M"
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Classify gear mobility
# ----------------------
# NOTE:
#
# Gear types can also be further classified into fixed or mobile engines based
# on their mobility. We used these two mobility classes to generate a buffer of
# impact around each fishing activity coordinates to consider potential spatial
# uncertainty associated with locations and the fact that mobile engines can be
# tracted over several kilometers during fishing activities and that we do not
# have the beginning and end points of mobile fishing events. Buffer sizes for
# fixed (F) and mobile (M) engine is of 200 and 2000 meters, respectively.
#
# The index holds the mobility information for almost all gear types, but some
# are missing. We manually add them here. Categories 81 and 85 were also changed
# from mobile to fixed for the purposes of our analysis, even though it does not
# affect the actual data we are working with because there are no observations of
# those gear types in the study area for this project.
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data0034$Categorie[data0034$Codes == 0] <- NA # Valeur manquante","Null data",""
data0034$Categorie[data0034$Codes == 9] <- "M" # Chalut à perche pour la crevette","Shrimp beam trawl",""
data0034$Categorie[data0034$Codes == 45] <- "F" # "Parc fermé","Box net",""
data0034$Categorie[data0034$Codes == 46] <- "F" # "Filet à poche","Bag net",""
data0034$Categorie[data0034$Codes == 47] <- "F" # "Verveux","Fyke net",""
data0034$Categorie[data0034$Codes == 70] <- "F" # "Épuisette","Dip net",""
data0034$Categorie[data0034$Codes == 71] <- "M" # "Drague non spécifiée","Dredge (boat)",""
data0034$Categorie[data0034$Codes == 76] <- "F" # "Câble","Rope",""
data0034$Categorie[data0034$Codes == 83] <- "F" # "Foène","Spear",""
data0034$Categorie[data0034$Codes == 94] <- "F" # "Coupeur","Cutter",""
data0034$Categorie[data0034$Codes == 95] <- "M" # "Bateau à déchargement","Pumper",""
# ---
data0034$Categorie[data0034$Codes == 81] <- "F" # "Harpon et lance","Harpoon and spear","M"
data0034$Categorie[data0034$Codes == 85] <- "F" # "Harpon électrique","Electric harpoon","M"
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Classify and filter fisheries data
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data0034 <- data0034 %>%
select(Codes, gearClass, mobility = Categorie)
# -----
peche <- left_join(data0033, data0034, by = c("engin" = "Codes")) %>%
filter(!is.na(gearClass)) %>%
filter(!is.na(mobility))
# -----
peche <- peche %>%
filter(as.Date(date_cap) >= as.Date("2010-01-01"))
# -----
# LBS to KG
uid <- peche$un_mes == "P"
peche$pd_deb[uid] <- peche$pd_deb[uid] * 0.453592
# -----
peche <- unique(peche)
# ------------------------------------------------------------
# NOTE: For metadata
species_cible <- sort(unique(peche$prespvis))
species <- table(peche$cod_esp) %>%
as.data.frame() %>%
rename(ESP_STAT = Var1) %>%
mutate(ESP_STAT = as.numeric(as.character(ESP_STAT))) %>%
left_join(data0035, by = "ESP_STAT") %>%
select(ID = ESP_STAT, Scientific = DL_ESP, Espece = DF_ESP,
Species = DA_ESP, Freq)
gear_freq <- table(peche$gearClass) %>%
as.data.frame()
# ------------------------------------------------------------
# -----
peche <- peche %>%
group_by(date_cap, latit_ori, longit_ori, gearClass, mobility) %>%
summarise(catch = sum(pd_deb))
# -----
fix <- peche[peche$mobility == "F", ] %>%
st_buffer(200)
mob <- peche[peche$mobility == "M", ] %>%
st_buffer(2000)
peche <- bind_rows(fix, mob)
# -----
peche <- peche %>%
arrange(as.Date(date_cap))
# -----
peche$ID <- 1:nrow(peche)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Measure intensity
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data(grid1p)
grid1p$ID <- 1:nrow(grid1p)
# # -----
# peche$year <- format(as.Date(peche$date_cap), "%Y")
# years <- unique(peche$year)
# type <- unique(peche$gearClass)
# comb <- expand.grid(type, years, stringsAsFactors = F)
# colnames(comb) <- c('type','years')
#
# # Empty list to store fishing intensity by gear type and by year
# intensity <- vector('list', nrow(comb))
# names(intensity) <- apply(comb, 1, paste, collapse = "-")
#
# # Fishing intensity evaluation
# for(i in 1:length(intensity)) {
# uid <- peche$year == comb[i, 'years'] & peche$gearClass == comb[i, 'type']
# intensity[[i]] <- fishingMetrics(peche[uid, ], grid1p)
# }
#
# -----
peche_commerciale <- grid1p %>%
mutate(
DNL = fishingMetrics(peche[peche$gearClass == 'DNL', ], .)[, 2],
DNH = fishingMetrics(peche[peche$gearClass == 'DNH', ], .)[, 2],
DD = fishingMetrics(peche[peche$gearClass == 'DD', ], .)[, 2],
PLB = fishingMetrics(peche[peche$gearClass == 'PLB', ], .)[, 2],
PHB = fishingMetrics(peche[peche$gearClass == 'PHB', ], .)[, 2]
) %>%
select(-ID) %>%
# ugly
mutate(
DNL = ifelse(DNL == 0, NA, DNL),
DNH = ifelse(DNH == 0, NA, DNH),
DD = ifelse(DD == 0, NA, DD),
PLB = ifelse(PLB == 0, NA, PLB),
PHB = ifelse(PHB == 0, NA, PHB)
)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Pêches secteur fluvial
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
data(aoi)
data(grid1p)
grid1p$ID <- 1:nrow(grid1p)
dat <- dplyr::select(data0083, PECHE) |>
sf::st_intersection(aoi) |>
dplyr::select(-FID)
uid <- sf::st_join(grid1p, dat) |>
sf::st_drop_geometry() |>
dplyr::group_by(ID) |>
dplyr::summarize(
PECHE = ifelse(
is.na(PECHE),
NA,
max(PECHE, na.rm = TRUE)
)
) |>
dplyr::distinct() |>
dplyr::rename(peche_fleuve = PECHE)
peche_commerciale$ID <- 1:nrow(peche_commerciale)
peche_commerciale <- dplyr::left_join(peche_commerciale, uid, by = "ID") |>
dplyr::select(-ID)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Update metadata
# ----------------------------------
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
meta <- load_metadata("int_st_peche_commerciale")
# -----
meta$rawData <- data_metadata
# -----
meta$dataDescription$spatial$extent <- st_bbox(data0033)
# -----
peche$years <- format(as.Date(peche$date_cap), "%Y")
meta$dataDescription$temporal$start <- min(peche$years)
meta$dataDescription$temporal$end <- max(peche$years)
# -----
meta$dataDescription$categories$accronyme <- c("DD", "DNL", "DNH", "PLB", "PHB","peche_fleuve")
meta$dataDescription$categories$english <- c(
"Demersal, destructive, high-bycatch",
"Demersal, non-destructive, low-bycatch",
"Demersal, non-destructive, high-bycatch",
"Pelagic, low-bycatch",
"Pelagic, high-bycatch",
"Commercial fisheries in fluvial sector"
)
meta$dataDescription$categories$francais <- c(
"Démersale destructive, prises accessoires élevées",
"Démersale non-destructive, prises accessoires faibles",
"Démersale non-destructive, prises accessoires élevées",
"Pélagique prises accessoires faibles",
"Pélagique prises accessoires élevées",
"Pêches commerciales au sein du secteur fluvial"
)
meta$dataDescription$categories$source <- rep(paste0(meta$rawData, collapse = ","),
length(meta$dataDescription$categories$accronyme))
meta$dataDescription$categories$description <- c(
"Activités de pêches commerciales à l'aide d'engins de pêche démersaux pouvant causer des dommages aux habitats ou au substrat, e.g. chalut et drague.",
"Activités de pêches commerciales à l'aide d'engins de pêche démersaux avec peu ou en l'absence de prises accessoires et ne causant aucune modification des habitats, e.g. la pêche en plongée sous-marine.",
"Activités de pêches commerciales à l'aide d'engins de pêche démersaux avec d'importantes prises accessoires et ne causant aucune modification des habitats, e.g. casier et senne.",
"Activités de pêches commerciales à l'aide d'engins de pêche pélagiques avec peu ou en l'absence de prises accessoires et ne causant aucune modification des habitats, e.g. pêche à la ligne, senne bourse.",
"Activités de pêches commerciales à l'aide d'engins de pêche pélagiques avec d'importantes prises accessoires et ne causant aucune modification des habitats, e.g. filet maillant et palangre.",
"Activités de pêches commerciales à l'aide de verveux au printemps, à l'été et à l'automne, caclculé en nombre moyen de verveux déployés par jour au sein de segments divisant la section fluviale de l'aire d'étude."
)
meta$dataDescription$categories$description_en <- c(
"Commercial fishing activities using demersal fishing gear that may damage habitats or substrate, e.g. trawling and dragging.",
"Commercial fishing activities using demersal fishing gear with little or no bycatch and not causing habitat modification, e.g., deep-sea fishing.",
"Commercial fishing activities using demersal fishing gear with high bycatch and not causing habitat modification, e.g., trap and seine.",
"Commercial fishing activities using pelagic fishing gear with little or no bycatch and not causing habitat modification, e.g., line fishing, purse seine.",
"Commercial fishing activities using pelagic fishing gear with high bycatch and not causing habitat modification, e.g., gillnet and longline.",
"Commercial fisheries activities using fyke nets during the spring, the summer and the fall, measured as the mean number of fyke nets deployed par day in segments dividing the fluvial sector of the study area."
)
meta$dataDescription$categories$zonesNA <- c(
rep("fluvial_peche", 5),
"berge_fluvial"
)
# ----- frequence
dat <- data.frame(acr = meta$dataDescription$categories$accronyme) %>%
left_join(gear_freq, by = c("acr" = "Var1"))
meta$dataDescription$categories$frequence <- dat$Freq
# -----
obs <- peche %>% group_by(years) %>% summarize(total = n())
meta$dataDescription$observations$total <- sum(obs$total)
meta$dataDescription$observations$moyenne <- round(mean(obs$total), 0)
meta$dataDescription$observations$sd <- round(sd(obs$total), 0)
# -----
meta$dataDescription$especes$cible <- species_cible
meta$dataDescription$especes$capture <- species
# --- For proper referencing in markdown syntax
meta$dataDescription$categories$mdref <- modif_md(meta$dataDescription$categories$accronyme)
# --------------------------------------------------------------------------------
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Export
# ------
#
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# -----
write_yaml(meta, "./data/data-metadata/int_st_peche_commerciale.yml")
# -----
st_write(obj = peche_commerciale,
dsn = "./data/data-integrated/st_peche_commerciale.geojson",
delete_dsn = TRUE,
quiet = TRUE)
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
# Clean global environment
#
# =~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~=~-~= #
clean()
# ------------------------------------------------------------------------- #}
}
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