In brent0/SCReports: Generate Snow Crab Reports

knitr::opts_chunk$set(echo = FALSE)
library(dplyr)
options(dplyr.summarise.inform = FALSE)
library(ggplot2)
library(ggforce)
library(tidyr)
library(data.table)
library(scales)
library(knitr) 
library(ggrepel) 
library(tidyverse) 

library(kableExtra)

year = 2023
wd = file.path(data_root, "bio.snowcrab", "reports", year, "JanuaryMeetings", "fishery")
wd2 = file.path(data_root, "bio.snowcrab", "reports", year, "JanuaryMeetings", "acoustic")
wd3 = file.path(data_root, "bio.snowcrab", "reports", year, "JanuaryMeetings", "survey")
wd4 = file.path(data_root, "bio.snowcrab", "reports")

Overview

• Commercial Fishery

• At-Sea Observer

• Survey

Commercial Fishery

---

Area Overview

knitr::include_graphics(file.path(wd4, "areamap2.png"))

---

Vessels Active by Year

knitr::include_graphics(file.path(wd, "vessels_per_year.pdf"))

---

Annual Catch Rates

knitr::include_graphics(file.path(wd, "annual_cpue_kg.pdf"))

---

Landings

For official reports, please refer to https://inter-j01.dfo-mpo.gc.ca/mqr/quotareports

knitr::include_graphics(file.path(wd, "landing_data_Tac.pdf"))

#create table with Area, Year, TAC, Landings, Catch Rate (lbs/trap) for NENS, cfa23, cfa 24 for last 3 years

---

Weekly Landings

knitr::include_graphics(file.path(wd, "weekly_landing.pdf"))

---

Spring Landings

knitr::include_graphics(file.path(wd, "percent_spring_landings.pdf"))

---

March Landings

knitr::include_graphics(file.path(wd, "percent_winter_landings.pdf"))

---

Summer Landings

knitr::include_graphics(file.path(wd, "percent_summer_landings.pdf"))

---

Landings Locations

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "landings", paste("landings.", year, ".png", sep = "")))

---

Landings Locations

::: columns ::: column 2022

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "landings", paste("landings.", year-1, ".png", sep = "")))

::: ::: column 2023

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "landings", paste("landings.", year, ".png", sep = "")))

::: :::

---

Effort Locations

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "effort", paste("effort.", year, ".png", sep = "")))

---

Effort Locations

::: columns ::: column 2022

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "effort", paste("effort.", year-1, ".png", sep = "")))

::: ::: column 2023

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "effort", paste("effort.", year, ".png", sep = "")))

::: :::

---

Weekly CPUE

knitr::include_graphics(file.path(wd, "weekly_cpue_smoothed2.pdf"))

---

Catch Rate Locations

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "cpue", paste("cpue.", year, ".png", sep = "")))
# plot(NA, xlim=c(0,5), ylim=c(0,5), bty='n',
#      xaxt='n', yaxt='n', xlab='', ylab='')
# text(1,4, paste(year, ": Did not generate yet"), pos=4)
# text(1,3, file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "cpue", paste("cpue.", year, ".png", sep = "")), pos=4)

---

Catch Rate Locations

::: columns ::: column 2022

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "cpue", paste("cpue.", year-1, ".png", sep = "")))

::: ::: column 2023

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "cpue", paste("cpue.", year, ".png", sep = "")))

::: :::

Yearly Fishing Patterns

---

knitr::include_graphics(file.path(wd, "nens_past_two_years_fishing_positions.pdf"))

---

knitr::include_graphics(file.path(wd, "cfa23_past_two_years_fishing_positions.pdf"))

---

knitr::include_graphics(file.path(wd, "cfa24zoom_past_two_years_fishing_positions.pdf"))

---

knitr::include_graphics(file.path(wd, "cfa4x_past_two_years_fishing_positions.pdf"))

Seasonal Fishing Patterns

---

::: columns ::: column

knitr::include_graphics(file.path(wd, "nens_spring_fishing_positions.pdf"))

::: ::: column

knitr::include_graphics(file.path(wd, "nens_summer_fishing_positions.pdf"))

::: :::

---

::: columns ::: column

knitr::include_graphics(file.path(wd, "cfa23_spring_fishing_positions.pdf"))

::: ::: column

knitr::include_graphics(file.path(wd, "cfa23_summer_fishing_positions.pdf"))

::: :::

---

::: columns ::: column

knitr::include_graphics(file.path(wd, "cfa24zoom_spring_fishing_positions.pdf"))

::: ::: column

knitr::include_graphics(file.path(wd, "cfa24zoom_summer_fishing_positions.pdf"))

::: :::

At-Sea Observer

*Due to the small number of observed trips in 2020 to now, this section is presented as a point of interest only.

---

At-Sea Observer Coverage

knitr::include_graphics(file.path(wd, "observersummary2.pdf"))

---

Crab Size

*Based on very small amount of observer data in 2020 to 2023

knitr::include_graphics(file.path(wd, "mean_cw_observed.pdf"))

---

Crab Size

knitr::include_graphics(file.path(wd, "cw_vs_mass.pdf"))

---

Crab Size

*Based on very small amount of observer data in 2020 to 2023

knitr::include_graphics(file.path(wd, "mean_weight_observed.pdf"))

---

Catch Composition

---

::: columns ::: column

if(file.exists(file.path(wd, paste(year-1, "_N-ENS_size_freq.pdf", sep = "")))){
  knitr::include_graphics(file.path(wd, paste(year-1, "_N-ENS_size_freq.pdf", sep = "")))
}else{
 plot(NA, xlim=c(0,5), ylim=c(0,5), bty='n', xaxt='n', yaxt='n', xlab='', ylab='')
text(1,4, paste(year-1, ": No observer data for this area"), pos=4)
}

:::

::: column

if(file.exists(file.path(wd, paste(year, "_N-ENS_size_freq.pdf", sep = "")))){
  knitr::include_graphics(file.path(wd, paste(year, "_N-ENS_size_freq.pdf", sep = "")))
}else{
  plot(NA, xlim=c(0,5), ylim=c(0,5), bty='n', xaxt='n', yaxt='n', xlab='', ylab='')
  text(1,4, paste(year, ": No observer data for this area"), pos=4)
}

::: :::

---

::: columns ::: column

if(file.exists(file.path(wd, paste(year-1, "_S-ENS_size_freq.pdf", sep = "")))){
knitr::include_graphics(file.path(wd, paste(year-1, "_S-ENS_size_freq.pdf", sep = "")))
}else{
  plot(NA, xlim=c(0,5), ylim=c(0,5), bty='n', xaxt='n', yaxt='n', xlab='', ylab='')
  text(1,4, paste(year, ": No observer data for this area"), pos=4)
}

:::

::: column

if(file.exists(file.path(wd, paste(year, "_S-ENS_size_freq.pdf", sep = "")))){
knitr::include_graphics(file.path(wd, paste(year, "_S-ENS_size_freq.pdf", sep = "")))
}else{
  plot(NA, xlim=c(0,5), ylim=c(0,5), bty='n', xaxt='n', yaxt='n', xlab='', ylab='')
  text(1,4, paste(year, ": No observer data for this area"), pos=4)
}

::: :::

Softshell Catches

knitr::include_graphics(file.path(wd, "softsummary2.pdf"))

---

Softshell Catches

knitr::include_graphics(file.path(wd, "soft_crab_by_month.pdf"))

---

N-ENS

knitr::include_graphics(file.path(wd, "nens_soft_crab_positions_68.pdf"))

---

CFA-23

knitr::include_graphics(file.path(wd, "cfa23_soft_crab_positions_68.pdf"))

---

CFA-24

knitr::include_graphics(file.path(wd, "cfa24_soft_crab_positions_68.pdf"))

Survey

• No issues

---

knitr::include_graphics(file.path(wd, "All_Survey_Stations.pdf"))

---

knitr::include_graphics(file.path(wd, "All_Survey_Stations_plus_fail.pdf"))

---

knitr::include_graphics(file.path(wd3, "SurveyStationsNone.pdf"))

---

knitr::include_graphics(file.path(wd3, "SurveyStationsBitter.pdf"))

---

Bitter Crab

knitr::include_graphics(file.path(wd3, "bitter.pdf"))

---

Survey Timing

knitr::include_graphics(file.path(wd3, "SurveyStationsTiming-10year.pdf"))

---

Temperatures

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "t.pdf"))

---

Temperatures

::: columns ::: column

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "t", paste("t.", year-1, ".png", sep = "")))

:::

::: column

knitr::include_graphics(file.path("D:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "t", paste("t.", year, ".png", sep = "")))

::: :::

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::: frame The End :::

brent0/SCReports documentation built on Feb. 28, 2025, 12:12 a.m.