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(bio.datadirectory, "bio.snowcrab", "reports", year, "JanuaryMeetings", "fishery")
wd2 = file.path(bio.datadirectory, "bio.snowcrab", "reports", year, "JanuaryMeetings", "acoustic")
Overview
Commercial Fishery
Landings
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, "CFA23_weekly_landing.pdf"))
Spring Landings
knitr::include_graphics(file.path(wd, "percent_spring_landings.pdf"))
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"))
Weekly CPUE
knitr::include_graphics(file.path(wd, "weekly_cpue_smoothed2.pdf"))
Catch Rate Locations
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "cpue", paste("cpue.", year, ".png", sep = "")))
Crab Size
knitr::include_graphics(file.path(wd, "mean_cw_observed.pdf"))
Crab Size
knitr::include_graphics(file.path(wd, "cw_vs_mass.pdf"))
Crab Size
knitr::include_graphics(file.path(wd, "mean_weight_observed.pdf"))
knitr::include_graphics(file.path(wd, "cfa23_past_two_years_fishing_positions.pdf"))
Seasonal Fishing Patterns
::: 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"))
:::
:::
At-Sea Observer
At-Sea Observer Coverage
knitr::include_graphics(file.path(wd, "observersummary2.pdf"))
Catch Composition
::: columns
::: column
knitr::include_graphics(file.path(wd, paste(year-1, "_S-ENS_size_freq.pdf", sep = "")))
:::
::: column
knitr::include_graphics(file.path(wd, paste(year, "_S-ENS_size_freq.pdf", sep = "")))
:::
:::
Catch Composition
::: columns
::: column
knitr::include_graphics(file.path(wd, "S-ENS_Spring_size_freq.pdf"))
:::
::: column
knitr::include_graphics(file.path(wd, "S-ENS_Summer_size_freq.pdf"))
:::
:::
Softshell Catches
knitr::include_graphics(file.path(wd, "softsummary2.pdf"))
Softshell Catches
knitr::include_graphics(file.path(wd, "soft_crab_by_month.pdf"))
Softshell Catches
knitr::include_graphics(file.path(wd, "cfa23_soft_crab_positions_68.pdf"))
Survey
knitr::include_graphics(file.path(wd, "All_Survey_Stations.pdf"))
Female Crab
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "figures", "size.freq", "survey", "female.pdf"))
Mature Female Distribution
::: columns
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "totmass.female.mat", paste("totmass.female.mat.", year-1, ".png", sep = "")))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "totmass.female.mat", paste("totmass.female.mat.", year, ".png", sep = "")))
:::
:::
Units: mt/km2
Male Crab
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "figures", "size.freq", "survey", "male.pdf"))
Commercial Male Distribution
::: columns
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "R0.mass", paste("R0.mass.", year-1, ".png", sep = "")))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "R0.mass", paste("R0.mass.", year, ".png", sep = "")))
:::
:::
Units: mt/km2
Predation
::: columns
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "ms.mass.10.pdf"))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.10", paste("ms.mass.10.", year-1, ".png", sep = "")))
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.10", paste("ms.mass.10.", year, ".png", sep = "")))
:::
:::
Predation
:::: columns
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "ms.mass.201.pdf"))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.201", paste("ms.mass.201.", year-1, ".png", sep = "")))
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.201", paste("ms.mass.201.", year, ".png", sep = "")))
:::
:::
Coexistent Species
::: columns
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "ms.mass.2211.pdf"))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.2211", paste("ms.mass.2211.", year-1, ".png", sep = "")))
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.2211", paste("ms.mass.2211.", year, ".png", sep = "")))
:::
:::
Temperatures
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "t.pdf"))
Temperatures
::: columns
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "t", paste("t.", year-1, ".png", sep = "")))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "t", paste("t.", year, ".png", sep = "")))
:::
:::
St Anns Bank Acoustic Receivers
Acoustic Receivers
::: columns
::: column
-
Collaborative project since 2015
-
Two lines of 23 acoustic receivers within the MPA
-
Detect animals we tag (snow crab, cod, etc) as well as other
projects from along the eastern seaboard
:::
::: column
knitr::include_graphics(file.path(wd2, "V2LSCF.receiver.line.locations.pdf"))
:::
:::
Detections
knitr::include_graphics(file.path(wd2, "V2LSCF.detected.projects.map.pdf"))
Detections
knitr::include_graphics(file.path(wd2, "V2LSCF.species.pie.chart.pdf"))
Detections
knitr::include_graphics(file.path(wd2, "V2LSCF.species.by.month.pdf"))
Temperatures
knitr::include_graphics(file.path(wd2, "V2LSCF.temperature.pdf"))
DFO Business
Current Collaborative Agreement (CA)
::: block
- 2020/20 is the final of a five year CA
-
Funds remaining at the end of the year (April 1, 2020) will be
returned to participants
-
\% of each license recalculates annually based on previous season's
quota
-
Working on a new 5 year CA.
-
Will still be a \"Use of Fish\" approach with science quota
-
Please DO NOT send payment until invoice is received, not just CA
for signature
:::
Collaborative Agreement (CA)
knitr::include_graphics(file.path(bio.datadirectory, "bio.snowcrab", "reports", year, "JanuaryMeetings", "business", "Spending.Breakdown.pdf"))
Meeting and Document Schedule
::: block
- Current:
- Industry Meetings (Jan), RAP (late Feb), AC Meetings (early
March)
- Framework preceding RAP this year.
- Preliminary report, Res Doc ( 150 pages), SAR (30 pages)
-
Future:
-
In-house review of assessment (mid Feb), Industry Meetings (late
Feb), AC Meetings (March)
-
Preliminary report, Stock update (30 pages)
-
Full RAP, Res Doc every 3 years
:::
::: frame
The End
:::
brent0/SCReports documentation built on Feb. 28, 2025, 12:12 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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(bio.datadirectory, "bio.snowcrab", "reports", year, "JanuaryMeetings", "fishery") wd2 = file.path(bio.datadirectory, "bio.snowcrab", "reports", year, "JanuaryMeetings", "acoustic")
Overview
Commercial Fishery
Landings
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, "CFA23_weekly_landing.pdf"))
Spring Landings
knitr::include_graphics(file.path(wd, "percent_spring_landings.pdf"))
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"))
Weekly CPUE
knitr::include_graphics(file.path(wd, "weekly_cpue_smoothed2.pdf"))
Catch Rate Locations
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "logbook", "snowcrab", "annual", "cpue", paste("cpue.", year, ".png", sep = "")))
Crab Size
knitr::include_graphics(file.path(wd, "mean_cw_observed.pdf"))
Crab Size
knitr::include_graphics(file.path(wd, "cw_vs_mass.pdf"))
Crab Size
knitr::include_graphics(file.path(wd, "mean_weight_observed.pdf"))
knitr::include_graphics(file.path(wd, "cfa23_past_two_years_fishing_positions.pdf"))
Seasonal Fishing Patterns
::: 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"))
::: :::
At-Sea Observer
At-Sea Observer Coverage
knitr::include_graphics(file.path(wd, "observersummary2.pdf"))
Catch Composition
::: columns ::: column
knitr::include_graphics(file.path(wd, paste(year-1, "_S-ENS_size_freq.pdf", sep = "")))
:::
::: column
knitr::include_graphics(file.path(wd, paste(year, "_S-ENS_size_freq.pdf", sep = "")))
::: :::
Catch Composition
::: columns ::: column
knitr::include_graphics(file.path(wd, "S-ENS_Spring_size_freq.pdf"))
:::
::: column
knitr::include_graphics(file.path(wd, "S-ENS_Summer_size_freq.pdf"))
::: :::
Softshell Catches
knitr::include_graphics(file.path(wd, "softsummary2.pdf"))
Softshell Catches
knitr::include_graphics(file.path(wd, "soft_crab_by_month.pdf"))
Softshell Catches
knitr::include_graphics(file.path(wd, "cfa23_soft_crab_positions_68.pdf"))
Survey
knitr::include_graphics(file.path(wd, "All_Survey_Stations.pdf"))
Female Crab
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "figures", "size.freq", "survey", "female.pdf"))
Mature Female Distribution
::: columns ::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "totmass.female.mat", paste("totmass.female.mat.", year-1, ".png", sep = "")))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "totmass.female.mat", paste("totmass.female.mat.", year, ".png", sep = "")))
::: :::
Units: mt/km2
Male Crab
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "figures", "size.freq", "survey", "male.pdf"))
Commercial Male Distribution
::: columns ::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "R0.mass", paste("R0.mass.", year-1, ".png", sep = "")))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "R0.mass", paste("R0.mass.", year, ".png", sep = "")))
::: :::
Units: mt/km2
Predation
::: columns ::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "ms.mass.10.pdf"))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.10", paste("ms.mass.10.", year-1, ".png", sep = "")))
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.10", paste("ms.mass.10.", year, ".png", sep = "")))
::: :::
Predation
:::: columns ::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "ms.mass.201.pdf"))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.201", paste("ms.mass.201.", year-1, ".png", sep = "")))
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.201", paste("ms.mass.201.", year, ".png", sep = "")))
::: :::
Coexistent Species
::: columns ::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "ms.mass.2211.pdf"))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.2211", paste("ms.mass.2211.", year-1, ".png", sep = "")))
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "bycatch", "ms.mass.2211", paste("ms.mass.2211.", year, ".png", sep = "")))
::: :::
Temperatures
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "assessments", year, "timeseries", "survey", "t.pdf"))
Temperatures
::: columns ::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "t", paste("t.", year-1, ".png", sep = "")))
:::
::: column
knitr::include_graphics(file.path("C:", "bio.data", "bio.snowcrab", "output", "maps", "survey", "snowcrab", "annual", "t", paste("t.", year, ".png", sep = "")))
::: :::
St Anns Bank Acoustic Receivers
Acoustic Receivers
::: columns ::: column
-
Collaborative project since 2015
-
Two lines of 23 acoustic receivers within the MPA
-
Detect animals we tag (snow crab, cod, etc) as well as other projects from along the eastern seaboard :::
::: column
knitr::include_graphics(file.path(wd2, "V2LSCF.receiver.line.locations.pdf"))
::: :::
Detections
knitr::include_graphics(file.path(wd2, "V2LSCF.detected.projects.map.pdf"))
Detections
knitr::include_graphics(file.path(wd2, "V2LSCF.species.pie.chart.pdf"))
Detections
knitr::include_graphics(file.path(wd2, "V2LSCF.species.by.month.pdf"))
Temperatures
knitr::include_graphics(file.path(wd2, "V2LSCF.temperature.pdf"))
DFO Business
Current Collaborative Agreement (CA)
::: block - 2020/20 is the final of a five year CA
-
Funds remaining at the end of the year (April 1, 2020) will be returned to participants
-
\% of each license recalculates annually based on previous season's quota
-
Working on a new 5 year CA.
-
Will still be a \"Use of Fish\" approach with science quota
-
Please DO NOT send payment until invoice is received, not just CA for signature :::
Collaborative Agreement (CA)
knitr::include_graphics(file.path(bio.datadirectory, "bio.snowcrab", "reports", year, "JanuaryMeetings", "business", "Spending.Breakdown.pdf"))
Meeting and Document Schedule
::: block - Current:
- Industry Meetings (Jan), RAP (late Feb), AC Meetings (early
March)
- Framework preceding RAP this year.
- Preliminary report, Res Doc ( 150 pages), SAR (30 pages)
-
Future:
-
In-house review of assessment (mid Feb), Industry Meetings (late Feb), AC Meetings (March)
-
Preliminary report, Stock update (30 pages)
-
Full RAP, Res Doc every 3 years :::
-
::: frame The End :::
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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