inst/markdown/02_survey_summary.md
In jae0/snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.
title: "Snow crab survey summary"
keywords:
- snow crab trawl survey results
- basic tables and figures
abstract: |
Snow crab demographic structure and environmental conditions.
fontsize: 12pt
metadata-files:
- _metadata.yml
params:
year_assessment: 2024
year_start: 1999
data_loc: "~/bio.data/bio.snowcrab"
sens: 1
debugging: FALSE
model_variation: logistic_discrete_historical
#| eval: true
#| output: false
#| echo: false
#| label: setup
require(knitr)
knitr::opts_chunk$set(
root.dir = data_root,
echo = FALSE,
out.width="6.2in",
fig.retina = 2,
dpi=192
)
# things to load into memory (in next step) via _load_results.qmd
toget = c( "fishery_results", "ecosystem" )
{{< include _load_results.qmd >}}
Overview of locations and counts
Map: Survey locations
#| label: fig-map-survey-locations
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| fig.show: hold
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Survey locations."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
loc = file.path( data_loc, "output", "maps", "survey.locations" )
years = year_assessment + c(0:-3)
fn = check_file_exists( file.path( loc, paste( "survey.locations", years, "png", sep=".") ))
include_graphics( fn )
Survey counts
#| label: tbl-survey-summary
#| echo: false
#| results: asis
#| eval: true
#| output: true
#| layout-ncol: 1
#| tbl-cap: "Summary of trawl survey"
#| tbl-subcap:
#| - "(a)"
#| - "(b)"
#| - "(c)"
#| - "(d)"
for (r in 1:nregions) {
reg = regions[r]
REG = reg_labels[r]
cat( REG, "\n")
oo = set0[ region==reg, .(
Nstations = .N,
Nmale = sum(no.male.all, na.rm=TRUE) ,
Nfemale = sum(no.female.all, na.rm=TRUE),
Mmalemature = sum(no.male.mat, na.rm=TRUE),
Mfemalemature = sum(no.female.mat, na.rm=TRUE)
), by=.(yr)]
oo$Total = oo$Nmale + oo$Nfemale
names(oo) = c("Year", "No. stations", "No. male", "No. female", "No. male mature", "No. female mature", "No. total" )
oo = oo[order(Year), ]
out = 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))
print(out)
cat("\n\n")
}
Carapace condition of males >= 95 mm CW
#| label: tbl-survey-cc-mature
#| echo: false
#| results: asis
#| eval: true
#| output: true
#| layout-ncol: 1
#| tbl-cap: "Carapace condition of males >= 95 mm CW captured in the survey"
#| tbl-subcap:
#| - "(a)"
#| - "(b)"
#| - "(c)"
#| - "(d)"
det = det0[ cw >= 95 ,] # commercial sized crab only
for (r in 1:nregions) {
reg = regions[r]
REG = reg_labels[r]
cat( REG, "\n")
oo = dcast( det[ region==reg & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
keep = c("fishyr", "1", "2", "3", "4", "5" )
oo = oo[,..keep]
names(oo) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
oo$Total = rowSums( oo[, 2:6 ], na.rm=TRUE)
oo[, 2:6 ] = round(oo[, 2:6 ] / oo$Total * 100, digits=1)
oo = oo[order(Year), ]
out = 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))
print(out)
cat("\n\n")
}
Size structure by carapace condition of mature males
#| label: fig-sizefeq-male-mature-survey-cc
#| echo: false
#| results: asis
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 6
#| fig-cap: "Size-structure and carapace condition of mature males."
odir = file.path( data_loc, "assessments", year_assessment, "figures", "size.freq", "carapacecondition" )
years = year_assessment + c(0:-3)
cat("$~$ \n\n")
for (r in 1:nregions) {
reg = regions[r]
REG = reg_labels[r]
cat( REG, "\n\n" )
fns = paste( "sizefreq", reg, years, "png", sep="." )
fn = check_file_exists(file.path( odir, fns ) )
for (ff in fn) show_image(ff)
cat("\n\n")
}
$~$
Size structure and maturity of males
#| label: fig-sizefeq-male
#| eval: true
#| output: true
#| fig-cap: "Size-frequency (areal density; no/km$^2$) histograms by carapace width of male Snow Crab. The vertical line represents the legal size (95 mm). Immature animals are shown with light coloured bars, mature with dark."
#| fig-dpi: 144
#| fig-height: 10
if (params$sens==1) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey")
} else if (params$sens==2) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey", "split")
}
include_graphics( file.path( sf_outdir, "male.denl.png" ) )
Size structure maturity of females
#| label: fig-sizefeq-female
#| eval: true
#| output: true
#| fig-cap: "Size-frequency (areal density; no/km$^2$) histograms by carapace width of female Snow Crab. Immature animals are shown with light coloured bars, mature with dark."
#| fig-dpi: 144
#| fig-height: 10
if (params$sens==1) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey")
} else if (params$sens==2) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey", "split")
}
fn = file.path( sf_outdir, "female.denl.png" )
include_graphics( fn )
Timeseries and maps of survey variables of interest
Bottom temperature: trawl survey
#| label: fig-temperature-bottom-ts
#| eval: true
#| output: true
#| fig-cap: "Annual variations in bottom temperature ($^\\circ$C) observed during the Snow Crab survey. The horizontal (black) line indicates the long-term, median temperature within each subarea. Error bars represent standard errors."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("t", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-figures-temperature-bottom-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Bottom temperature ($^\\circ$C) observed during the Snow Crab survey."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab", "annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "t", paste( "t", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Sex ratios
#| label: fig-sexratio-mat-ts
#| eval: true
#| output: true
#| fig-cap: "The crude, unadjusted geometric mean of sex ratios (proportion female) of mature Snow Crab. Error bars represent 95\\% Confidence Intervals. Note the absence of data in 2020. Prior to 2004, surveys were conducted in the Spring."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("sexratio.mat", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-sexratio-mat-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Snow Crab survey sex ratios (proportion female) of mature Snow Crab."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab", "annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "sexratio.mat", paste( "sexratio.mat", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Mature female
#| label: fig-totno-female-mat-ts
#| eval: true
#| output: true
#| fig-cap: "The crude, unadjusted geometric mean of mature female density log$_{10}$(no/km$^2$) from the Snow Crab survey. Error bars represent 95\\% Confidence Intervals. Note the absence of data in 2020. Prior to 2004, surveys were conducted in the Spring."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("totno.female.mat", "png", sep=".") )
include_graphics( fn )
#| label: fig-totno-female-mat-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Mature female density log$_{10}$(no/km$^2$) from the Snow Crab survey."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "totno.female.mat", paste( "totno.female.mat", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Fishable biomass
#| label: fig-R0-ts
#| eval: true
#| output: true
#| fig-cap: "The crude, unadjusted geometric mean fishable biomass density log$_{10}$(t/km$^2$) from the Snow Crab survey. Error bars represent 95\\% Confidence Intervals. Note the absence of data in 2020. Prior to 2004, surveys were conducted in the Spring."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("R0.mass", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-R0-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Snow Crab survey fishable component biomass density log$_{10}$(t/km$^2$)."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "R0.mass", paste( "R0.mass", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Fishable mean size
#| label: fig-cw-male-mat-ts
#| eval: true
#| output: true
#| fig-cap: "Mean size of mature male Snow Crab log$_{10}$(CW; mm) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("cw.male.mat.mean", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-cw-male-mat-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Snow Crab survey fishable component mean carapace width; log$_{10}$(CW; mm)."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab", "annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "cw.male.mat.mean", paste( "cw.male.mat.mean", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Potential Predators
The main predators, based on literature and stomach content analysis, are:
cod, haddock, halibut, plaice, wolfish, thornyskate, smoothskate, winterskate.
Atlantic cod
#| label: fig-atlcod-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Atlantic cod log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 10
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-atlcod-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Atlantic cod, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 10
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Haddock
#| label: fig-haddock-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Haddock log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 11
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-haddock-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Haddock, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 11
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Halibut
#| label: fig-halibut-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Halibut log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 30
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-halibut-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Halibut, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 30
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
American plaice
#| label: fig-amerplaice-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of American plaice log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 40
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-amerplaice-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: American plaice, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 40
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Striped Atlantic wolffish
#| label: fig-stripatlwolffish-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Striped Atlantic wolffish log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 50
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-stripatlwolffish-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Striped Atlantic wolffish, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 50
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Thorny skate
#| label: fig-thornyskate-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Thorny skate log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 201
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-thornyskate-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Thorny skate, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 201
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Smooth skate
#| label: fig-smoothskate-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Smooth skate log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 202
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-smoothskate-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Smooth skate, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 202
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Winter skate
#| label: fig-winterskate-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Winter skate log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 204
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-winterskate-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Winter skate, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 204
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Potential Competitors
The main potential predators, based on literature and overlpping distributions are:
northernshrimp, jonahcrab, lessertoadcrab.
Northern shrimp
#| label: fig-northernshrimp-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Northern shrimp log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2211
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-northernshrimp-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Northern shrimp, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2211
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Jonah crab
Not exactly a competitor. Similar habitat except warmer areas so more an indicator of bottom temperatures.
#| label: fig-jonahcrab-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Jonah crab log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2511
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-jonahcrab-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Jonah crab, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2511
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Arctic Lyre crab (Lesser toad crab)
Slightly more shallow environments than snow crab.
#| label: fig-lyrecrab-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Arctic Lyre crab log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2521
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-lyrecrab-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Arctic Lyre crab, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2521
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Northern stone crab
#| label: fig-nstonecrab-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Northern stone crab log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2523
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-nstonecrab-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Northern stone crab, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2523
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
<!--
# ------------------------------------------
# Timeseries: Larval brachyura from the SSIP data
##figure.timeseries.larvae( outdir=file.path(p$project.outputdir, "timeseries", "larvae") )
# ------------------------------------------
# Growth as a a function of instar for Scotian Shelf snow crab
figure.growth.instar( outdir=file.path(p$project.outputdir, "growth") )
# ------------------------------------------
# Map: Larval distributions from the Scotian Shelf Ichtyoplankton Program data
map.larvae( p=p, outdir=file.path(p$project.outputdir, "maps", "larvae"), conversions=conversions )
# ------------------------------------------
# Map: Spatial representation of maturity patterns of snow crab
#MG Not sure we use these maps either, check with Adam and Jae
# map.maturity( p, outdir=file.path(p$project.outputdir, "maps", "maturity"), newyear=T )
res = maturity_region_year(p) # timeseries of maturity
}
-->
jae0/snowcrab documentation built on Feb. 20, 2025, 2:27 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
title: "Snow crab survey summary" keywords: - snow crab trawl survey results - basic tables and figures abstract: | Snow crab demographic structure and environmental conditions. fontsize: 12pt metadata-files: - _metadata.yml params: year_assessment: 2024 year_start: 1999 data_loc: "~/bio.data/bio.snowcrab" sens: 1 debugging: FALSE model_variation: logistic_discrete_historical
#| eval: true
#| output: false
#| echo: false
#| label: setup
require(knitr)
knitr::opts_chunk$set(
root.dir = data_root,
echo = FALSE,
out.width="6.2in",
fig.retina = 2,
dpi=192
)
# things to load into memory (in next step) via _load_results.qmd
toget = c( "fishery_results", "ecosystem" )
{{< include _load_results.qmd >}}
Overview of locations and counts
Map: Survey locations
#| label: fig-map-survey-locations
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| fig.show: hold
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Survey locations."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
loc = file.path( data_loc, "output", "maps", "survey.locations" )
years = year_assessment + c(0:-3)
fn = check_file_exists( file.path( loc, paste( "survey.locations", years, "png", sep=".") ))
include_graphics( fn )
Survey counts
#| label: tbl-survey-summary
#| echo: false
#| results: asis
#| eval: true
#| output: true
#| layout-ncol: 1
#| tbl-cap: "Summary of trawl survey"
#| tbl-subcap:
#| - "(a)"
#| - "(b)"
#| - "(c)"
#| - "(d)"
for (r in 1:nregions) {
reg = regions[r]
REG = reg_labels[r]
cat( REG, "\n")
oo = set0[ region==reg, .(
Nstations = .N,
Nmale = sum(no.male.all, na.rm=TRUE) ,
Nfemale = sum(no.female.all, na.rm=TRUE),
Mmalemature = sum(no.male.mat, na.rm=TRUE),
Mfemalemature = sum(no.female.mat, na.rm=TRUE)
), by=.(yr)]
oo$Total = oo$Nmale + oo$Nfemale
names(oo) = c("Year", "No. stations", "No. male", "No. female", "No. male mature", "No. female mature", "No. total" )
oo = oo[order(Year), ]
out = 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))
print(out)
cat("\n\n")
}
Carapace condition of males >= 95 mm CW
#| label: tbl-survey-cc-mature
#| echo: false
#| results: asis
#| eval: true
#| output: true
#| layout-ncol: 1
#| tbl-cap: "Carapace condition of males >= 95 mm CW captured in the survey"
#| tbl-subcap:
#| - "(a)"
#| - "(b)"
#| - "(c)"
#| - "(d)"
det = det0[ cw >= 95 ,] # commercial sized crab only
for (r in 1:nregions) {
reg = regions[r]
REG = reg_labels[r]
cat( REG, "\n")
oo = dcast( det[ region==reg & !is.na(shell), .(N=.N), by=.(fishyr, shell) ], fishyr ~ shell, value.var="N", fill=0, drop=FALSE, na.rm=TRUE )
keep = c("fishyr", "1", "2", "3", "4", "5" )
oo = oo[,..keep]
names(oo) = c("Year", "CC1", "CC2", "CC3", "CC4", "CC5" )
oo$Total = rowSums( oo[, 2:6 ], na.rm=TRUE)
oo[, 2:6 ] = round(oo[, 2:6 ] / oo$Total * 100, digits=1)
oo = oo[order(Year), ]
out = 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))
print(out)
cat("\n\n")
}
Size structure by carapace condition of mature males
#| label: fig-sizefeq-male-mature-survey-cc
#| echo: false
#| results: asis
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 6
#| fig-cap: "Size-structure and carapace condition of mature males."
odir = file.path( data_loc, "assessments", year_assessment, "figures", "size.freq", "carapacecondition" )
years = year_assessment + c(0:-3)
cat("$~$ \n\n")
for (r in 1:nregions) {
reg = regions[r]
REG = reg_labels[r]
cat( REG, "\n\n" )
fns = paste( "sizefreq", reg, years, "png", sep="." )
fn = check_file_exists(file.path( odir, fns ) )
for (ff in fn) show_image(ff)
cat("\n\n")
}
$~$
Size structure and maturity of males
#| label: fig-sizefeq-male
#| eval: true
#| output: true
#| fig-cap: "Size-frequency (areal density; no/km$^2$) histograms by carapace width of male Snow Crab. The vertical line represents the legal size (95 mm). Immature animals are shown with light coloured bars, mature with dark."
#| fig-dpi: 144
#| fig-height: 10
if (params$sens==1) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey")
} else if (params$sens==2) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey", "split")
}
include_graphics( file.path( sf_outdir, "male.denl.png" ) )
Size structure maturity of females
#| label: fig-sizefeq-female
#| eval: true
#| output: true
#| fig-cap: "Size-frequency (areal density; no/km$^2$) histograms by carapace width of female Snow Crab. Immature animals are shown with light coloured bars, mature with dark."
#| fig-dpi: 144
#| fig-height: 10
if (params$sens==1) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey")
} else if (params$sens==2) {
sf_outdir = file.path( p$annual.results, "figures", "size.freq", "survey", "split")
}
fn = file.path( sf_outdir, "female.denl.png" )
include_graphics( fn )
Timeseries and maps of survey variables of interest
Bottom temperature: trawl survey
#| label: fig-temperature-bottom-ts
#| eval: true
#| output: true
#| fig-cap: "Annual variations in bottom temperature ($^\\circ$C) observed during the Snow Crab survey. The horizontal (black) line indicates the long-term, median temperature within each subarea. Error bars represent standard errors."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("t", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-figures-temperature-bottom-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Bottom temperature ($^\\circ$C) observed during the Snow Crab survey."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab", "annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "t", paste( "t", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Sex ratios
#| label: fig-sexratio-mat-ts
#| eval: true
#| output: true
#| fig-cap: "The crude, unadjusted geometric mean of sex ratios (proportion female) of mature Snow Crab. Error bars represent 95\\% Confidence Intervals. Note the absence of data in 2020. Prior to 2004, surveys were conducted in the Spring."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("sexratio.mat", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-sexratio-mat-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Snow Crab survey sex ratios (proportion female) of mature Snow Crab."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab", "annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "sexratio.mat", paste( "sexratio.mat", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Mature female
#| label: fig-totno-female-mat-ts
#| eval: true
#| output: true
#| fig-cap: "The crude, unadjusted geometric mean of mature female density log$_{10}$(no/km$^2$) from the Snow Crab survey. Error bars represent 95\\% Confidence Intervals. Note the absence of data in 2020. Prior to 2004, surveys were conducted in the Spring."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("totno.female.mat", "png", sep=".") )
include_graphics( fn )
#| label: fig-totno-female-mat-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Mature female density log$_{10}$(no/km$^2$) from the Snow Crab survey."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "totno.female.mat", paste( "totno.female.mat", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Fishable biomass
#| label: fig-R0-ts
#| eval: true
#| output: true
#| fig-cap: "The crude, unadjusted geometric mean fishable biomass density log$_{10}$(t/km$^2$) from the Snow Crab survey. Error bars represent 95\\% Confidence Intervals. Note the absence of data in 2020. Prior to 2004, surveys were conducted in the Spring."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("R0.mass", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-R0-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Snow Crab survey fishable component biomass density log$_{10}$(t/km$^2$)."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "R0.mass", paste( "R0.mass", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Fishable mean size
#| label: fig-cw-male-mat-ts
#| eval: true
#| output: true
#| fig-cap: "Mean size of mature male Snow Crab log$_{10}$(CW; mm) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
fn = file.path( ts_outdir, paste("cw.male.mat.mean", "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-cw-male-mat-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: "Snow Crab survey fishable component mean carapace width; log$_{10}$(CW; mm)."
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_outdir = file.path( p$project.outputdir, "maps", "survey", "snowcrab", "annual" )
map_years = year_assessment + c(0:-3)
fn = check_file_exists( file.path(
map_outdir, "cw.male.mat.mean", paste( "cw.male.mat.mean", map_years, "png", sep="." )
) )
include_graphics( fn )
$~$
Potential Predators
The main predators, based on literature and stomach content analysis, are:
cod, haddock, halibut, plaice, wolfish, thornyskate, smoothskate, winterskate.
Atlantic cod
#| label: fig-atlcod-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Atlantic cod log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 10
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-atlcod-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Atlantic cod, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 10
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Haddock
#| label: fig-haddock-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Haddock log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 11
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-haddock-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Haddock, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 11
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Halibut
#| label: fig-halibut-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Halibut log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 30
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-halibut-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Halibut, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 30
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
American plaice
#| label: fig-amerplaice-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of American plaice log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 40
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-amerplaice-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: American plaice, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 40
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Striped Atlantic wolffish
#| label: fig-stripatlwolffish-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Striped Atlantic wolffish log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 50
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-stripatlwolffish-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Striped Atlantic wolffish, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 50
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Thorny skate
#| label: fig-thornyskate-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Thorny skate log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 201
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-thornyskate-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Thorny skate, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 201
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Smooth skate
#| label: fig-smoothskate-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Smooth skate log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 202
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-smoothskate-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Smooth skate, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 202
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Winter skate
#| label: fig-winterskate-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Winter skate log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 204
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-winterskate-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Winter skate, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 204
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Potential Competitors
The main potential predators, based on literature and overlpping distributions are:
northernshrimp, jonahcrab, lessertoadcrab.
Northern shrimp
#| label: fig-northernshrimp-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Northern shrimp log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2211
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-northernshrimp-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Northern shrimp, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2211
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Jonah crab
Not exactly a competitor. Similar habitat except warmer areas so more an indicator of bottom temperatures.
#| label: fig-jonahcrab-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Jonah crab log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2511
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-jonahcrab-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Jonah crab, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2511
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Arctic Lyre crab (Lesser toad crab)
Slightly more shallow environments than snow crab.
#| label: fig-lyrecrab-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Arctic Lyre crab log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2521
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-lyrecrab-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Arctic Lyre crab, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2521
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
Northern stone crab
#| label: fig-nstonecrab-ts
#| eval: true
#| output: true
#| fig-cap: "Mean density of Northern stone crab log$_{10}$(no/km$^2$) from surveys with 95\\% Confidence Intervals."
#| fig-dpi: 144
#| fig-height: 4
if (params$sens==1) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey")
} else if (params$sens==2) {
ts_outdir = file.path( p$annual.results, "timeseries", "survey", "split")
}
species_predator = 2523
bc_vars = paste("ms.no", species_predator, sep='.')
fn = file.path( ts_outdir, paste(bc_vars, "png", sep=".") )
include_graphics( fn )
$~$
#| label: fig-nstonecrab-map
#| eval: true
#| output: true
#| fig-dpi: 144
#| fig-height: 4
#| echo: false
#| layout-ncol: 2
#| fig-cap: Northern stone crab, density; log$_{10}$(no/km$^2$).
#| fig-subcap:
#| - ""
#| - ""
#| - ""
#| - ""
map_years = year_assessment + c(0:-3)
species_predator = 2523
bc_vars = paste("ms.no", species_predator, sep='.')
outdir_bc = file.path( p$project.outputdir, "maps", "survey", "snowcrab","annual", "bycatch" )
fn = check_file_exists( file.path( outdir_bc, bc_vars, paste(bc_vars, map_years, "png", sep=".") ) )
include_graphics( fn )
$~$
<!--
# ------------------------------------------ # Timeseries: Larval brachyura from the SSIP data ##figure.timeseries.larvae( outdir=file.path(p$project.outputdir, "timeseries", "larvae") )
# ------------------------------------------ # Growth as a a function of instar for Scotian Shelf snow crab figure.growth.instar( outdir=file.path(p$project.outputdir, "growth") )
# ------------------------------------------ # Map: Larval distributions from the Scotian Shelf Ichtyoplankton Program data map.larvae( p=p, outdir=file.path(p$project.outputdir, "maps", "larvae"), conversions=conversions )
# ------------------------------------------ # Map: Spatial representation of maturity patterns of snow crab #MG Not sure we use these maps either, check with Adam and Jae # map.maturity( p, outdir=file.path(p$project.outputdir, "maps", "maturity"), newyear=T )
res = maturity_region_year(p) # timeseries of maturity
} -->
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