inst/markdown/archive/02.tables.md
In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.
title: "Snow crab tables"
author: "Jae S. Choi"
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Set up environment
First set up environment. Data comes from:
- At seas observations of fishery (ISSDB)
- Dockside monitoring (Marfis)
- Snow crab survey
These are mostly imported and formatted in 01_snowcrab.R
#| eval: true
#| output: false
require(aegis)
# Get data and format based upon parameters:
year.assessment = 2023
p = bio.snowcrab::load.environment( year.assessment=year.assessment )
# loadfunctions( "aegis")
# loadfunctions( "bio.snowcrab") # in case of local edits
# require(ggplot2)
# require(data.table)
require(gt) # table formatting
outtabledir = file.path( p$annual.results, "tables" )
years = as.character(1996: year.assessment)
regions = c("cfanorth", "cfasouth", "cfa4x")
nregions = length(regions)
FD = fishery_data() # mass in tonnes
fda = FD$summary_annual
dt = as.data.frame( fda[ which(fda$yr %in% c(year.assessment - c(0:10))),] )
dt = dt[,c("region", "yr", "Licenses", "TAC", "landings", "effort", "cpue")]
names(dt) = c("Region", "Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")
rownames(dt) = NULL
odb0 = setDT(observer.db("odb"))
odb0$region = NA
for ( reg in regions) {
r = polygon_inside(x = odb0, region = aegis.polygons::polygon_internal_code(reg), planar=FALSE)
odb0$region[r] = reg
}
Fishery statistics from at sea observations
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-perf
#| tbl-cap: "Fishery performance statistics in NENS. Units are: TACs and Landings (tons, t), Effort ($\\times 10^3$ trap hauls, th) and CPUE (kg/th)."
ii = which(dt$Region=="cfanorth")
oo = dt[ii, c("Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")]
gt::gt(oo) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-perf
#| tbl-cap: "Fishery performance statistics in SENS. Units are: TACs and Landings (tons, t), Effort ($\\times 10^3$ trap hauls, th) and CPUE (kg/th)."
ii = which(dt$Region=="cfasouth")
oo = dt[ii, c("Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")]
gt::gt(oo) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-perf
#| tbl-cap: "Fishery performance statistics in 4X. Units are: TACs and Landings (tons, t), Effort ($\\times 10^3$ trap hauls, th) and CPUE (kg/th). There were no landings or TACs in 2018/2019 due to indications of low abundance. The 2022 season is ongoing."
ii = which(dt$Region=="cfa4x")
oo = dt[ii, c("Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")]
gt::gt(oo) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
At sea observed data
Carapace condition from observed data < 95mm CW
#| eval: true
#| output: false
odb = odb0[ cw < 95 & prodcd_id==0 & shell %in% c(1:5) & region %in% regions & sex==0, ] # male
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-sublegal
#| tbl-cap: "Fishery performance statistics in NENS. Distribution of at sea observations of males less than 95 mm CW by year and shell condition."
resN = dcast( odb0[ region=="cfanorth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
if ( "NA" %in% names(resN) ) resN$"NA" = NULL
names(resN) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resN$Total = rowSums( resN[, 2:6 ], na.rm=TRUE)
resN[, 2:6 ] = round(resN[, 2:6 ] / resN$Total * 100, digits=2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-sublegal
#| tbl-cap: "Fishery performance statistics in SENS. Distribution of at sea observations of males less than 95 mm CW by year and shell condition."
resS = dcast( odb0[ region=="cfasouth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
if ( "NA" %in% names(resS)) resS$"NA" = NULL
names(resS) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resS$Total = rowSums( resS[, 2:6 ], na.rm=TRUE)
resS[, 2:6 ] = round(resS[, 2:6 ] / resS$Total * 100, digits=2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-sublegal
#| tbl-cap: "Fishery performance statistics in 4X. Distribution of at sea observations of males less than 95 mm CW by year and shell condition."
resX = dcast( odb0[ region=="cfa4x", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
if ("NA" %in% names(resX)) resX$"NA" = NULL
names(resX) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resX$Total = rowSums( resX[, 2:6 ], na.rm=TRUE)
resX[, 2:6 ] = round(resX[, 2:6 ] / resX$Total * 100, digits=2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Carapace condition from observed data >= 95mm CW
#| eval: true
#| output: false
odb = odb0[ cw >= 95 & cw < 170 & prodcd_id==0 & shell %in% c(1:5) & region %in% regions & sex==0, ] # male
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-comm
#| tbl-cap: "Fishery performance statistics in NENS. Distribution of at sea observations of males greater than 95 mm CW by year and shell condition."
resN = dcast( odb[ region=="cfanorth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resN) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resN$Total = rowSums( resN[, 2:6 ], na.rm=TRUE)
resN[, 2:6 ] = round(resN[, 2:6 ] / resN$Total * 100, digits=2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-comm
#| tbl-cap: "Fishery performance statistics in SENS. Distribution of at sea observations of males greater than 95 mm CW by year and shell condition."
resS = dcast( odb[ region=="cfasouth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resS) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resS$Total = rowSums( resS[, 2:6 ], na.rm=TRUE)
resS[, 2:6 ] = round(resS[, 2:6 ] / resS$Total * 100, digits=2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-comm
#| tbl-cap: "Fishery performance statistics in 4X. Distribution of at sea observations of males greater than 95 mm CW by year and shell condition."
resX = dcast( odb[ region=="cfa4x", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resX) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resX$Total = rowSums( resX[, 2:6 ], na.rm=TRUE)
resX[, 2:6 ] = round(resX[, 2:6 ] / resX$Total * 100, digits=2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Percent soft from observed data
There are two possible definitions:
- durometer < 68 (Soft, Total)
- carapace conditions 1 and 2 (SoftSC, TotalSC)
#| eval: true
#| output: true
odb = odb0[ cw >= 95 & cw < 170 & prodcd_id==0 & shell %in% c(1:5) & region %in% regions & sex==0, ] # male
shell_condition = odb[ !is.na(odb$region), .N, by=.(region, fishyr, shell) ]
shell_condition[, total:=sum(N, na.rm=TRUE), by=.(region, fishyr)]
shell_condition$percent = round(shell_condition$N / shell_condition$total, 3) * 100
shell_condition$Year = shell_condition$fishyr
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-soft-durometer
#| tbl-cap: "Fishery performance statistics in NENS. Distribution of at sea observations of males soft-shelled based on durometer (<68) and shell condition (1 and 2, SC)."
softN = odb[ region=="cfanorth" & durometer < 68, .(Soft=.N), by=.(fishyr ) ]
totalN = odb[ region=="cfanorth" & is.finite(durometer) , .(Total=.N), by=.(fishyr) ]
resN = softN[totalN, on="fishyr"]
resN = resN[, .(Year=fishyr, Soft=round(Soft/Total*100,2), Total=Total) ]
ssN = shell_condition[ region=="cfanorth" & shell %in% c(1,2), .(SoftSC=sum(percent), TotalSC=unique(total)[1]), by=.(Year)]
resN = resN[ssN, on="Year"]
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-soft-durometer
#| tbl-cap: "Fishery performance statistics in SENS. Distribution of at sea observations of males soft-shelled based on durometer (<68) and shell condition (1 and 2, SC)."
softS = odb[ region=="cfasouth" & durometer < 68, .(Soft=.N), by=.(fishyr ) ]
totalS = odb[ region=="cfasouth" & is.finite(durometer) , .(Total=.N), by=.(fishyr) ]
resS = softS[totalS, on="fishyr"]
resS = resS[, .(Year=fishyr, Soft=round(Soft/Total*100,2), Total=Total) ]
ssS = shell_condition[ region=="cfasouth" & shell %in% c(1,2), .(SoftSC=sum(percent), TotalSC=unique(total)[1]), by=.(Year)]
resS = resS[ssS, on="Year"]
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-soft-durometer
#| tbl-cap: "Fishery performance statistics in 4X. Distribution of at sea observations of males soft-shelled based on durometer (<68) and shell condition (1 and 2, SC)."
softX = odb[ region=="cfa4x" & durometer < 68, .(Soft=.N), by=.(fishyr ) ]
totalX = odb[ region=="cfa4x" & is.finite(durometer) , .(Total=.N), by=.(fishyr) ]
resX = softX[totalX, on="fishyr"]
resX = resX[, .(Year=fishyr, Soft=round(Soft/Total*100,2), Total=Total) ]
ssX = shell_condition[ region=="cfa4x" & shell %in% c(1,2), .(SoftSC=sum(percent), TotalSC=unique(total)[1]), by=.(Year)]
resX = resX[ssX, on="Year"]
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Compare discard rates Maritimes:
NENS:discard
#| eval: true
#| output: true
#| warning: false
#| error: false
#| label: table-fishery-nens-discard
#| tbl-cap: "Fishery performance statistics in NENS. Average by-catch discard rate by weight observed (kg/trap haul; and standard deviation, SD)."
region="cfanorth"
o = observer.db( DS="bycatch_summary", p=p, yrs=p$yrs, region=region )
resN = o$eff_summ[ order(fishyr), ]
names(resN) = c("Year", "Discards", "SD")
resN$Discards = round( resN$Discards*100, 2)
resN$SD = round( resN$SD*100, 2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| warning: false
#| error: false
#| label: table-fishery-sens-discard
#| tbl-cap: "Fishery performance statistics in SENS. Average by-catch discard rate by weight observed (kg/trap haul; and standard deviation, SD)."
region="cfasouth"
o = observer.db( DS="bycatch_summary", p=p, yrs=p$yrs, region=region )
resS = o$eff_summ[ order(fishyr), ]
names(resS) = c("Year", "Discards", "SD")
resS$Discards = round( resS$Discards*100, 2)
resS$SD = round( resS$SD*100, 2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| warning: false
#| error: false
#| label: table-fishery-4x-discard
#| tbl-cap: "Fishery performance statistics in 4X. Average by-catch discard rate by weight observed (kg/trap haul; and standard deviation, SD)."
region="cfa4x"
o = observer.db( DS="bycatch_summary", p=p, yrs=p$yrs, region=region )
resX = o$eff_summ[ order(fishyr), ]
names(resX) = c("Year", "Discards", "SD")
resX$Discards = round( resX$Discards*100, 2)
resX$SD = round( resX$SD*100, 2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Survey-based tables
Carapace condition from trawl data >= 95mm CW
#| eval: true
#| output: false
det = snowcrab.db( p=p, DS="det.georeferenced" )
setDT(det)
det$fishyr = det$yr ## the counting routine expectes this variable
det = det[ cw >= 95 ,] # commerical sized crab only
years = sort( unique( det$yr ) )
det$region = NA
for ( reg in regions) {
r = polygon_inside(x = det, region = aegis.polygons::polygon_internal_code(reg), planar=FALSE)
det$region[r] = reg
}
NENS:
#| eval: true
#| output: true
#| label: table-survey-nens-comm
#| tbl-cap: "Distribution of NENS survey: males less than 95 mm CW by year and shell condition."
resN = dcast( det[ region=="cfanorth" & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resN) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resN$Total = rowSums( resN[, 2:6 ], na.rm=TRUE)
resN[, 2:6 ] = round(resN[, 2:6 ] / resN$Total * 100, digits=2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-survey-sens-comm
#| tbl-cap: "Distribution of SENS survey: males less than 95 mm CW by year and shell condition."
resS = dcast( det[ region=="cfasouth" & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resS) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resS$Total = rowSums( resS[, 2:6 ], na.rm=TRUE)
resS[, 2:6 ] = round(resS[, 2:6 ] / resS$Total * 100, digits=2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-survey-4X-comm
#| tbl-cap: "Distribution of 4X survey: males less than 95 mm CW by year and shell condition."
resX = dcast( det[ region=="cfa4x" & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resX) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resX$Total = rowSums( resX[, 2:6 ], na.rm=TRUE)
resX[, 2:6 ] = round(resX[, 2:6 ] / resX$Total * 100, digits=2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Counts of stations in each area
#| eval: true
#| output: true
#| label: table-survey-station-count
#| tbl-cap: "Survey station counts"
set = snowcrab.db(p=p, DS="set.clean")
setDT(set)
# check towquality .. this should always == 1
if (length( unique( set$towquality) ) != 1 ) print("error -- not good tows")
set$region = NA
for (reg in c( "cfanorth", "cfasouth", "cfa4x" ) ) {
d = polygon_inside(set[,c("lon","lat")], reg)
set$region[d] = reg
}
out = dcast( set[, .(N=.N), by=.(region, yr)], yr~region, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
out[,Total:=sum(cfanorth,cfasouth,cfa4x, na.rm=TRUE)]
out = out[, .(yr, cfanorth, cfasouth, cfa4x)]
names(out) = c("Year", "NENS", "SENS", "4X")
gt::gt(out) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
jae0/bio.snowcrab documentation built on Nov. 6, 2024, 10:10 p.m.
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title: "Snow crab tables" author: "Jae S. Choi" toc: true number-sections: true highlight-style: pygments editor: render-on-save: false format: html: code-fold: true html-math-method: katex embed-resources: true pdf: pdf-engine: lualatex docx: default
Set up environment
First set up environment. Data comes from:
- At seas observations of fishery (ISSDB)
- Dockside monitoring (Marfis)
- Snow crab survey
These are mostly imported and formatted in 01_snowcrab.R
#| eval: true
#| output: false
require(aegis)
# Get data and format based upon parameters:
year.assessment = 2023
p = bio.snowcrab::load.environment( year.assessment=year.assessment )
# loadfunctions( "aegis")
# loadfunctions( "bio.snowcrab") # in case of local edits
# require(ggplot2)
# require(data.table)
require(gt) # table formatting
outtabledir = file.path( p$annual.results, "tables" )
years = as.character(1996: year.assessment)
regions = c("cfanorth", "cfasouth", "cfa4x")
nregions = length(regions)
FD = fishery_data() # mass in tonnes
fda = FD$summary_annual
dt = as.data.frame( fda[ which(fda$yr %in% c(year.assessment - c(0:10))),] )
dt = dt[,c("region", "yr", "Licenses", "TAC", "landings", "effort", "cpue")]
names(dt) = c("Region", "Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")
rownames(dt) = NULL
odb0 = setDT(observer.db("odb"))
odb0$region = NA
for ( reg in regions) {
r = polygon_inside(x = odb0, region = aegis.polygons::polygon_internal_code(reg), planar=FALSE)
odb0$region[r] = reg
}
Fishery statistics from at sea observations
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-perf
#| tbl-cap: "Fishery performance statistics in NENS. Units are: TACs and Landings (tons, t), Effort ($\\times 10^3$ trap hauls, th) and CPUE (kg/th)."
ii = which(dt$Region=="cfanorth")
oo = dt[ii, c("Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")]
gt::gt(oo) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-perf
#| tbl-cap: "Fishery performance statistics in SENS. Units are: TACs and Landings (tons, t), Effort ($\\times 10^3$ trap hauls, th) and CPUE (kg/th)."
ii = which(dt$Region=="cfasouth")
oo = dt[ii, c("Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")]
gt::gt(oo) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-perf
#| tbl-cap: "Fishery performance statistics in 4X. Units are: TACs and Landings (tons, t), Effort ($\\times 10^3$ trap hauls, th) and CPUE (kg/th). There were no landings or TACs in 2018/2019 due to indications of low abundance. The 2022 season is ongoing."
ii = which(dt$Region=="cfa4x")
oo = dt[ii, c("Year", "Licenses", "TAC", "Landings", "Effort", "CPUE")]
gt::gt(oo) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
At sea observed data
Carapace condition from observed data < 95mm CW
#| eval: true
#| output: false
odb = odb0[ cw < 95 & prodcd_id==0 & shell %in% c(1:5) & region %in% regions & sex==0, ] # male
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-sublegal
#| tbl-cap: "Fishery performance statistics in NENS. Distribution of at sea observations of males less than 95 mm CW by year and shell condition."
resN = dcast( odb0[ region=="cfanorth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
if ( "NA" %in% names(resN) ) resN$"NA" = NULL
names(resN) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resN$Total = rowSums( resN[, 2:6 ], na.rm=TRUE)
resN[, 2:6 ] = round(resN[, 2:6 ] / resN$Total * 100, digits=2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-sublegal
#| tbl-cap: "Fishery performance statistics in SENS. Distribution of at sea observations of males less than 95 mm CW by year and shell condition."
resS = dcast( odb0[ region=="cfasouth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
if ( "NA" %in% names(resS)) resS$"NA" = NULL
names(resS) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resS$Total = rowSums( resS[, 2:6 ], na.rm=TRUE)
resS[, 2:6 ] = round(resS[, 2:6 ] / resS$Total * 100, digits=2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-sublegal
#| tbl-cap: "Fishery performance statistics in 4X. Distribution of at sea observations of males less than 95 mm CW by year and shell condition."
resX = dcast( odb0[ region=="cfa4x", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
if ("NA" %in% names(resX)) resX$"NA" = NULL
names(resX) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resX$Total = rowSums( resX[, 2:6 ], na.rm=TRUE)
resX[, 2:6 ] = round(resX[, 2:6 ] / resX$Total * 100, digits=2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Carapace condition from observed data >= 95mm CW
#| eval: true
#| output: false
odb = odb0[ cw >= 95 & cw < 170 & prodcd_id==0 & shell %in% c(1:5) & region %in% regions & sex==0, ] # male
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-comm
#| tbl-cap: "Fishery performance statistics in NENS. Distribution of at sea observations of males greater than 95 mm CW by year and shell condition."
resN = dcast( odb[ region=="cfanorth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resN) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resN$Total = rowSums( resN[, 2:6 ], na.rm=TRUE)
resN[, 2:6 ] = round(resN[, 2:6 ] / resN$Total * 100, digits=2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-comm
#| tbl-cap: "Fishery performance statistics in SENS. Distribution of at sea observations of males greater than 95 mm CW by year and shell condition."
resS = dcast( odb[ region=="cfasouth", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resS) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resS$Total = rowSums( resS[, 2:6 ], na.rm=TRUE)
resS[, 2:6 ] = round(resS[, 2:6 ] / resS$Total * 100, digits=2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-comm
#| tbl-cap: "Fishery performance statistics in 4X. Distribution of at sea observations of males greater than 95 mm CW by year and shell condition."
resX = dcast( odb[ region=="cfa4x", .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resX) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resX$Total = rowSums( resX[, 2:6 ], na.rm=TRUE)
resX[, 2:6 ] = round(resX[, 2:6 ] / resX$Total * 100, digits=2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Percent soft from observed data
There are two possible definitions:
- durometer < 68 (Soft, Total)
- carapace conditions 1 and 2 (SoftSC, TotalSC)
#| eval: true
#| output: true
odb = odb0[ cw >= 95 & cw < 170 & prodcd_id==0 & shell %in% c(1:5) & region %in% regions & sex==0, ] # male
shell_condition = odb[ !is.na(odb$region), .N, by=.(region, fishyr, shell) ]
shell_condition[, total:=sum(N, na.rm=TRUE), by=.(region, fishyr)]
shell_condition$percent = round(shell_condition$N / shell_condition$total, 3) * 100
shell_condition$Year = shell_condition$fishyr
NENS:
#| eval: true
#| output: true
#| label: table-fishery-nens-soft-durometer
#| tbl-cap: "Fishery performance statistics in NENS. Distribution of at sea observations of males soft-shelled based on durometer (<68) and shell condition (1 and 2, SC)."
softN = odb[ region=="cfanorth" & durometer < 68, .(Soft=.N), by=.(fishyr ) ]
totalN = odb[ region=="cfanorth" & is.finite(durometer) , .(Total=.N), by=.(fishyr) ]
resN = softN[totalN, on="fishyr"]
resN = resN[, .(Year=fishyr, Soft=round(Soft/Total*100,2), Total=Total) ]
ssN = shell_condition[ region=="cfanorth" & shell %in% c(1,2), .(SoftSC=sum(percent), TotalSC=unique(total)[1]), by=.(Year)]
resN = resN[ssN, on="Year"]
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-fishery-sens-soft-durometer
#| tbl-cap: "Fishery performance statistics in SENS. Distribution of at sea observations of males soft-shelled based on durometer (<68) and shell condition (1 and 2, SC)."
softS = odb[ region=="cfasouth" & durometer < 68, .(Soft=.N), by=.(fishyr ) ]
totalS = odb[ region=="cfasouth" & is.finite(durometer) , .(Total=.N), by=.(fishyr) ]
resS = softS[totalS, on="fishyr"]
resS = resS[, .(Year=fishyr, Soft=round(Soft/Total*100,2), Total=Total) ]
ssS = shell_condition[ region=="cfasouth" & shell %in% c(1,2), .(SoftSC=sum(percent), TotalSC=unique(total)[1]), by=.(Year)]
resS = resS[ssS, on="Year"]
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-fishery-4x-soft-durometer
#| tbl-cap: "Fishery performance statistics in 4X. Distribution of at sea observations of males soft-shelled based on durometer (<68) and shell condition (1 and 2, SC)."
softX = odb[ region=="cfa4x" & durometer < 68, .(Soft=.N), by=.(fishyr ) ]
totalX = odb[ region=="cfa4x" & is.finite(durometer) , .(Total=.N), by=.(fishyr) ]
resX = softX[totalX, on="fishyr"]
resX = resX[, .(Year=fishyr, Soft=round(Soft/Total*100,2), Total=Total) ]
ssX = shell_condition[ region=="cfa4x" & shell %in% c(1,2), .(SoftSC=sum(percent), TotalSC=unique(total)[1]), by=.(Year)]
resX = resX[ssX, on="Year"]
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Compare discard rates Maritimes:
NENS:discard
#| eval: true
#| output: true
#| warning: false
#| error: false
#| label: table-fishery-nens-discard
#| tbl-cap: "Fishery performance statistics in NENS. Average by-catch discard rate by weight observed (kg/trap haul; and standard deviation, SD)."
region="cfanorth"
o = observer.db( DS="bycatch_summary", p=p, yrs=p$yrs, region=region )
resN = o$eff_summ[ order(fishyr), ]
names(resN) = c("Year", "Discards", "SD")
resN$Discards = round( resN$Discards*100, 2)
resN$SD = round( resN$SD*100, 2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| warning: false
#| error: false
#| label: table-fishery-sens-discard
#| tbl-cap: "Fishery performance statistics in SENS. Average by-catch discard rate by weight observed (kg/trap haul; and standard deviation, SD)."
region="cfasouth"
o = observer.db( DS="bycatch_summary", p=p, yrs=p$yrs, region=region )
resS = o$eff_summ[ order(fishyr), ]
names(resS) = c("Year", "Discards", "SD")
resS$Discards = round( resS$Discards*100, 2)
resS$SD = round( resS$SD*100, 2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| warning: false
#| error: false
#| label: table-fishery-4x-discard
#| tbl-cap: "Fishery performance statistics in 4X. Average by-catch discard rate by weight observed (kg/trap haul; and standard deviation, SD)."
region="cfa4x"
o = observer.db( DS="bycatch_summary", p=p, yrs=p$yrs, region=region )
resX = o$eff_summ[ order(fishyr), ]
names(resX) = c("Year", "Discards", "SD")
resX$Discards = round( resX$Discards*100, 2)
resX$SD = round( resX$SD*100, 2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Survey-based tables
Carapace condition from trawl data >= 95mm CW
#| eval: true
#| output: false
det = snowcrab.db( p=p, DS="det.georeferenced" )
setDT(det)
det$fishyr = det$yr ## the counting routine expectes this variable
det = det[ cw >= 95 ,] # commerical sized crab only
years = sort( unique( det$yr ) )
det$region = NA
for ( reg in regions) {
r = polygon_inside(x = det, region = aegis.polygons::polygon_internal_code(reg), planar=FALSE)
det$region[r] = reg
}
NENS:
#| eval: true
#| output: true
#| label: table-survey-nens-comm
#| tbl-cap: "Distribution of NENS survey: males less than 95 mm CW by year and shell condition."
resN = dcast( det[ region=="cfanorth" & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resN) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resN$Total = rowSums( resN[, 2:6 ], na.rm=TRUE)
resN[, 2:6 ] = round(resN[, 2:6 ] / resN$Total * 100, digits=2)
gt::gt(resN) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
SENS:
#| eval: true
#| output: true
#| label: table-survey-sens-comm
#| tbl-cap: "Distribution of SENS survey: males less than 95 mm CW by year and shell condition."
resS = dcast( det[ region=="cfasouth" & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resS) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resS$Total = rowSums( resS[, 2:6 ], na.rm=TRUE)
resS[, 2:6 ] = round(resS[, 2:6 ] / resS$Total * 100, digits=2)
gt::gt(resS) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
4X:
#| eval: true
#| output: true
#| label: table-survey-4X-comm
#| tbl-cap: "Distribution of 4X survey: males less than 95 mm CW by year and shell condition."
resX = dcast( det[ region=="cfa4x" & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
names(resX) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
resX$Total = rowSums( resX[, 2:6 ], na.rm=TRUE)
resX[, 2:6 ] = round(resX[, 2:6 ] / resX$Total * 100, digits=2)
gt::gt(resX) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
Counts of stations in each area
#| eval: true
#| output: true
#| label: table-survey-station-count
#| tbl-cap: "Survey station counts"
set = snowcrab.db(p=p, DS="set.clean")
setDT(set)
# check towquality .. this should always == 1
if (length( unique( set$towquality) ) != 1 ) print("error -- not good tows")
set$region = NA
for (reg in c( "cfanorth", "cfasouth", "cfa4x" ) ) {
d = polygon_inside(set[,c("lon","lat")], reg)
set$region[d] = reg
}
out = dcast( set[, .(N=.N), by=.(region, yr)], yr~region, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
out[,Total:=sum(cfanorth,cfasouth,cfa4x, na.rm=TRUE)]
out = out[, .(yr, cfanorth, cfasouth, cfa4x)]
names(out) = c("Year", "NENS", "SENS", "4X")
gt::gt(out) |> gt::tab_options(table.font.size = 12, data_row.padding = gt::px(1),
summary_row.padding = gt::px(1), grand_summary_row.padding = gt::px(1),
footnotes.padding = gt::px(1), source_notes.padding = gt::px(1),
row_group.padding = gt::px(1))
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