data-raw/lingcod_discard_ratios.R
In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021
#' ---
#' title: "Lingcod discard ratios"
#' author: "Ian G. Taylor"
#' date: "`r format(Sys.time(), '%B %d, %Y')`"
#' output:
#' bookdown::html_document2:
#' keep_md: true
#' ---
#+ setup_knitr, echo = FALSE
utils_knit_opts(type = "data-raw")
# stuff related to exploring discard ratios
# data provided by Chantel are in
# \\nwcfile\FRAM\Assessments\CurrentAssessments\lingcod_2021\data\wcgop
# copied on Ian's computer to c:/SS/Lingcod/Lingcod_2021/data/WCGOP/
# Loading WCGOP discard rates
info_ncs <- read.csv(file.path(
"data-raw",
"CONFIDENTIAL_DATA_lingcod_OB_DisRatios_boot_ncs_All_Gears_4010__2021-03-08.csv"
))
info_cs <- read.csv(file.path(
"data-raw",
"CONFIDENTIAL_DATA_lingcod_OB_DisRatios_boot_cs_All_Gears_4010__2021-03-08.csv"
))
info_em <- read.csv(file.path(
"data-raw",
"CONFIDENTIAL_DATA_lingcod_DisRatios_noboot_cs_EM_All_Gears_4010__2021-03-08.csv"
))
### TO DO:
# bottom trawl: combine em + cs + ncs for 2011 onward,
# use ncs for 2002-2011
# BottomTrawl only
# fixed gear: combine em + cs + ncs for 2011 onward,
# use ncs for 2002-2011
# FixedGears + HKL + Pot
### look at total by gear within each group
# EM only significant in 2018 and 2019 and still small compared to catch-shares
aggregate(info_em$Observed_DISCARD.MTS + info_em$Observed_RETAINED.MTS,
FUN = function(x){ round(sum(x), 1) },
by = list(gear2 = info_em$gear2,
ryear = info_em$ryear,
Area = info_em$Area))
## gear2 ryear Area x
## 1 BottomTrawl 2015 North4010 0.1
## 2 MidwaterTrawl 2015 North4010 2.7
## 3 Pot 2015 North4010 5.0
## 4 BottomTrawl 2016 North4010 0.4
## 5 MidwaterTrawl 2016 North4010 7.3
## 6 Pot 2016 North4010 0.2
## 7 BottomTrawl 2017 North4010 3.4
## 8 MidwaterTrawl 2017 North4010 7.9
## 9 Pot 2017 North4010 0.4
## 10 BottomTrawl 2018 North4010 3.9
## 11 MidwaterTrawl 2018 North4010 14.7
## 12 Pot 2018 North4010 2.0
## 13 BottomTrawl 2019 North4010 20.6
## 14 MidwaterTrawl 2019 North4010 14.6
## 15 Pot 2019 North4010 2.5
## 16 BottomTrawl 2015 South4010 2.5
## 17 Pot 2015 South4010 0.0
## 18 BottomTrawl 2016 South4010 6.5
## 19 Pot 2016 South4010 0.0
## 20 BottomTrawl 2017 South4010 15.1
## 21 Pot 2017 South4010 0.1
## 22 BottomTrawl 2018 South4010 36.0
## 23 Pot 2018 South4010 0.0
## 24 BottomTrawl 2019 South4010 26.0
## 25 Pot 2019 South4010 0.1
# catch-shares in the south is similar in magnitude to EM
aggregate(info_cs$Observed_DISCARD.MTS + info_cs$Observed_RETAINED.MTS,
FUN = function(x){ round(sum(x), 1) },
by = list(gear2 = info_cs$gear2,
ryear = info_cs$ryear,
Area = info_cs$Area))
## gear2 ryear Area x
## 1 BottomTrawl 2011 North4010 272.7
## 2 HKL 2011 North4010 0.4
## 3 MidwaterTrawl 2011 North4010 4.6
## 4 Pot 2011 North4010 3.0
## 5 BottomTrawl 2012 North4010 356.1
## 6 HKL 2012 North4010 0.2
## 7 MidwaterTrawl 2012 North4010 4.3
## 8 Pot 2012 North4010 1.9
## 9 BottomTrawl 2013 North4010 328.2
## 10 HKL 2013 North4010 0.3
## 11 MidwaterTrawl 2013 North4010 8.6
## 12 Pot 2013 North4010 2.6
## 13 BottomTrawl 2014 North4010 222.4
## 14 HKL 2014 North4010 0.3
## 15 MidwaterTrawl 2014 North4010 13.4
## 16 Pot 2014 North4010 1.4
## 17 BottomTrawl 2015 North4010 165.2
## 18 HKL 2015 North4010 1.2
## 19 Pot 2015 North4010 3.8
## 20 BottomTrawl 2016 North4010 249.1
## 21 HKL 2016 North4010 0.3
## 22 Pot 2016 North4010 1.9
## 23 BottomTrawl 2017 North4010 602.3
## 24 HKL 2017 North4010 0.2
## 25 Pot 2017 North4010 2.4
## 26 BottomTrawl 2018 North4010 411.9
## 27 HKL 2018 North4010 0.3
## 28 Pot 2018 North4010 1.0
## 29 BottomTrawl 2019 North4010 400.9
## 30 HKL 2019 North4010 0.0
## 31 Pot 2019 North4010 2.0
## 32 BottomTrawl 2011 South4010 7.3
## 33 Pot 2011 South4010 0.0
## 34 BottomTrawl 2012 South4010 15.7
## 35 Pot 2012 South4010 0.3
## 36 BottomTrawl 2013 South4010 16.3
## 37 HKL 2013 South4010 0.0
## 38 Pot 2013 South4010 0.0
## 39 BottomTrawl 2014 South4010 18.5
## 40 HKL 2014 South4010 0.0
## 41 Pot 2014 South4010 0.1
## 42 BottomTrawl 2015 South4010 29.7
## 43 Pot 2015 South4010 0.0
## 44 BottomTrawl 2016 South4010 18.0
## 45 BottomTrawl 2017 South4010 9.0
## 46 HKL 2017 South4010 0.0
## 47 Pot 2017 South4010 0.1
## 48 BottomTrawl 2018 South4010 15.5
## 49 BottomTrawl 2019 South4010 58.4
# non-catch-shares
aggregate(info_ncs$Observed_DISCARD.MTS +
info_ncs$Observed_RETAINED.MTS,
FUN = function(x){round(sum(x),1)},
by = list(gear2 = info_ncs$gear2,
ryear = info_ncs$ryear,
Area = info_ncs$Area))
## gear2 ryear Area x
## 1 BottomTrawl 2002 North4010 38.4
## 2 HKL 2002 North4010 1.3
## 3 Pot 2002 North4010 0.2
## 4 BottomTrawl 2003 North4010 24.0
## 5 FixedGears 2003 North4010 1.1
## 6 HKL 2003 North4010 1.6
## 7 Pot 2003 North4010 0.8
## 8 BottomTrawl 2004 North4010 29.3
## 9 FixedGears 2004 North4010 5.4
## 10 HKL 2004 North4010 0.9
## 11 Pot 2004 North4010 0.4
## 12 ShrimpTrawl 2004 North4010 0.0
## 13 BottomTrawl 2005 North4010 101.0
## 14 FixedGears 2005 North4010 5.0
## 15 HKL 2005 North4010 4.5
## 16 Pot 2005 North4010 1.5
## 17 ShrimpTrawl 2005 North4010 0.0
## 18 BottomTrawl 2006 North4010 75.5
## 19 FixedGears 2006 North4010 4.7
## 20 HKL 2006 North4010 7.8
## 21 Pot 2006 North4010 3.5
## 22 BottomTrawl 2007 North4010 30.3
## 23 FixedGears 2007 North4010 3.9
## 24 HKL 2007 North4010 1.3
## 25 Pot 2007 North4010 2.2
## 26 ShrimpTrawl 2007 North4010 0.1
## 27 BottomTrawl 2008 North4010 29.9
## 28 FixedGears 2008 North4010 3.9
## 29 HKL 2008 North4010 4.8
## 30 Pot 2008 North4010 2.3
## 31 ShrimpTrawl 2008 North4010 0.0
## 32 BottomTrawl 2009 North4010 44.7
## 33 FixedGears 2009 North4010 3.1
## 34 HKL 2009 North4010 1.6
## 35 Pot 2009 North4010 1.9
## 36 ShrimpTrawl 2009 North4010 0.0
## 37 BottomTrawl 2010 North4010 11.9
## 38 FixedGears 2010 North4010 2.8
## 39 HKL 2010 North4010 2.2
## 40 Pot 2010 North4010 2.3
## 41 ShrimpTrawl 2010 North4010 0.0
## 42 FixedGears 2011 North4010 5.5
## 43 HKL 2011 North4010 1.7
## 44 Pot 2011 North4010 1.2
## 45 ShrimpTrawl 2011 North4010 0.1
## 46 FixedGears 2012 North4010 7.6
## 47 HKL 2012 North4010 1.9
## 48 Pot 2012 North4010 1.6
## 49 ShrimpTrawl 2012 North4010 0.1
## 50 FixedGears 2013 North4010 9.5
## 51 HKL 2013 North4010 0.6
## 52 Pot 2013 North4010 0.2
## 53 ShrimpTrawl 2013 North4010 0.0
## 54 FixedGears 2014 North4010 6.5
## 55 HKL 2014 North4010 0.9
## 56 Pot 2014 North4010 1.5
## 57 ShrimpTrawl 2014 North4010 0.0
## 58 FixedGears 2015 North4010 10.1
## 59 HKL 2015 North4010 2.9
## 60 MidwaterTrawl 2015 North4010 6.1
## 61 Pot 2015 North4010 4.4
## 62 ShrimpTrawl 2015 North4010 0.1
## 63 BottomTrawl 2016 North4010 0.0
## 64 FixedGears 2016 North4010 8.5
## 65 HKL 2016 North4010 4.0
## 66 MidwaterTrawl 2016 North4010 0.7
## 67 Pot 2016 North4010 7.3
## 68 ShrimpTrawl 2016 North4010 0.0
## 69 BottomTrawl 2017 North4010 0.1
## 70 FixedGears 2017 North4010 9.9
## 71 HKL 2017 North4010 4.3
## 72 MidwaterTrawl 2017 North4010 2.3
## 73 Pot 2017 North4010 1.1
## 74 ShrimpTrawl 2017 North4010 0.0
## 75 BottomTrawl 2018 North4010 1.8
## 76 FixedGears 2018 North4010 8.5
## 77 HKL 2018 North4010 7.9
## 78 MidwaterTrawl 2018 North4010 2.8
## 79 Pot 2018 North4010 2.7
## 80 ShrimpTrawl 2018 North4010 0.0
## 81 BottomTrawl 2019 North4010 3.3
## 82 FixedGears 2019 North4010 8.8
## 83 HKL 2019 North4010 8.7
## 84 MidwaterTrawl 2019 North4010 1.7
## 85 Pot 2019 North4010 2.8
## 86 ShrimpTrawl 2019 North4010 0.0
## 87 BottomTrawl 2002 South4010 4.5
## 88 HKL 2002 South4010 0.2
## 89 MidwaterTrawl 2002 South4010 0.2
## 90 BottomTrawl 2003 South4010 4.5
## 91 FixedGears 2003 South4010 1.2
## 92 HKL 2003 South4010 0.3
## 93 Pot 2003 South4010 0.0
## 94 BottomTrawl 2004 South4010 9.0
## 95 FixedGears 2004 South4010 1.9
## 96 HKL 2004 South4010 0.0
## 97 Pot 2004 South4010 0.6
## 98 BottomTrawl 2005 South4010 6.9
## 99 FixedGears 2005 South4010 1.1
## 100 HKL 2005 South4010 0.1
## 101 Pot 2005 South4010 0.0
## 102 ShrimpTrawl 2005 South4010 0.0
## 103 BottomTrawl 2006 South4010 2.2
## 104 FixedGears 2006 South4010 0.6
## 105 HKL 2006 South4010 0.0
## 106 Pot 2006 South4010 1.4
## 107 BottomTrawl 2007 South4010 9.4
## 108 FixedGears 2007 South4010 0.6
## 109 HKL 2007 South4010 0.0
## 110 Pot 2007 South4010 0.7
## 111 BottomTrawl 2008 South4010 5.7
## 112 FixedGears 2008 South4010 0.4
## 113 HKL 2008 South4010 0.0
## 114 Pot 2008 South4010 0.2
## 115 BottomTrawl 2009 South4010 10.8
## 116 FixedGears 2009 South4010 0.6
## 117 Pot 2009 South4010 0.1
## 118 BottomTrawl 2010 South4010 2.3
## 119 FixedGears 2010 South4010 0.7
## 120 Pot 2010 South4010 0.2
## 121 BottomTrawl 2011 South4010 0.0
## 122 FixedGears 2011 South4010 1.0
## 123 HKL 2011 South4010 0.2
## 124 Pot 2011 South4010 0.0
## 125 FixedGears 2012 South4010 1.5
## 126 HKL 2012 South4010 0.3
## 127 Pot 2012 South4010 0.0
## 128 BottomTrawl 2013 South4010 0.0
## 129 FixedGears 2013 South4010 1.9
## 130 Pot 2013 South4010 0.1
## 131 BottomTrawl 2014 South4010 0.0
## 132 FixedGears 2014 South4010 1.6
## 133 HKL 2014 South4010 0.1
## 134 Pot 2014 South4010 0.0
## 135 BottomTrawl 2015 South4010 1.4
## 136 FixedGears 2015 South4010 2.5
## 137 HKL 2015 South4010 1.1
## 138 Pot 2015 South4010 0.0
## 139 BottomTrawl 2016 South4010 2.9
## 140 FixedGears 2016 South4010 0.8
## 141 HKL 2016 South4010 0.2
## 142 Pot 2016 South4010 0.1
## 143 ShrimpTrawl 2016 South4010 0.0
## 144 BottomTrawl 2017 South4010 3.1
## 145 FixedGears 2017 South4010 1.3
## 146 HKL 2017 South4010 0.3
## 147 Pot 2017 South4010 0.1
## 148 ShrimpTrawl 2017 South4010 0.1
## 149 BottomTrawl 2018 South4010 16.2
## 150 FixedGears 2018 South4010 1.0
## 151 HKL 2018 South4010 0.1
## 152 Pot 2018 South4010 0.1
## 153 ShrimpTrawl 2018 South4010 0.1
## 154 BottomTrawl 2019 South4010 7.9
## 155 FixedGears 2019 South4010 1.5
## 156 HKL 2019 South4010 0.3
## 157 Pot 2019 South4010 0.2
## 158 ShrimpTrawl 2019 South4010 0.0
# non-catch-shares after 2011
aggregate(info_ncs$Observed_DISCARD.MTS[info_ncs$ryear >= 2011] +
info_ncs$Observed_RETAINED.MTS[info_ncs$ryear >= 2011],
FUN = sum, by = list(info_ncs$gear2[info_ncs$ryear >= 2011]))
## Group.1 x
## 1 BottomTrawl 36.78862
## 2 FixedGears 88.25765
## 3 HKL 35.33838
## 4 MidwaterTrawl 13.65291
## 5 Pot 23.61832
# conclusion: ignore shrimp trawl
info_ncs <- info_ncs[info_ncs$gear2 != "ShrimpTrawl",]
# after 2011, bottom trawl in non-catch-shares is very small compared to catch-shares
# run function to combine discard rates
disc_rate_N_TW <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "North4010",
gears = c("BottomTrawl", "MidwaterTrawl"),
fleet = 1,
min_cv = 0.05)
disc_rate_S_TW <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "South4010",
gears = c("BottomTrawl", "MidwaterTrawl"),
fleet = 1,
min_cv = 0.05)
disc_rate_N_FG <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "North4010",
gears = c("FixedGears", "HKL", "Pot"),
fleet = 2,
min_cv = 0.05)
disc_rate_S_FG <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "South4010",
gears = c("FixedGears", "HKL", "Pot"),
fleet = 2,
min_cv = 0.05)
# remove 2002 from disc_rate_S_FG because it represents on the HKL fleet with few trips
# and no observed discards
disc_rate_S_FG <- disc_rate_S_FG[disc_rate_S_FG$Yr > 2002,]
# combine the tables into a single table
data_discard_rates_WCGOP <-
rbind(data.frame(disc_rate_N_TW, Area = "North", Gear = "TW"),
data.frame(disc_rate_S_TW, Area = "South", Gear = "TW"),
data.frame(disc_rate_N_FG, Area = "North", Gear = "FG"),
data.frame(disc_rate_S_FG, Area = "South", Gear = "FG"))
rownames(data_discard_rates_WCGOP) <- 1:nrow(data_discard_rates_WCGOP)
#+ setup_usethis, echo = FALSE
# add .rda file
usethis::use_data(data_discard_rates_WCGOP, overwrite = TRUE)
#+ cleanup
rm(file_index_orbs)
rm(info_ncs)
rm(info_cs)
rm(info_em)
rm(disc_rate_N_TW)
rm(disc_rate_S_TW)
rm(disc_rate_N_FG)
rm(disc_rate_S_FG)
rm(data_discard_rates_WCGOP)
iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.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.
#' ---
#' title: "Lingcod discard ratios"
#' author: "Ian G. Taylor"
#' date: "`r format(Sys.time(), '%B %d, %Y')`"
#' output:
#' bookdown::html_document2:
#' keep_md: true
#' ---
#+ setup_knitr, echo = FALSE
utils_knit_opts(type = "data-raw")
# stuff related to exploring discard ratios
# data provided by Chantel are in
# \\nwcfile\FRAM\Assessments\CurrentAssessments\lingcod_2021\data\wcgop
# copied on Ian's computer to c:/SS/Lingcod/Lingcod_2021/data/WCGOP/
# Loading WCGOP discard rates
info_ncs <- read.csv(file.path(
"data-raw",
"CONFIDENTIAL_DATA_lingcod_OB_DisRatios_boot_ncs_All_Gears_4010__2021-03-08.csv"
))
info_cs <- read.csv(file.path(
"data-raw",
"CONFIDENTIAL_DATA_lingcod_OB_DisRatios_boot_cs_All_Gears_4010__2021-03-08.csv"
))
info_em <- read.csv(file.path(
"data-raw",
"CONFIDENTIAL_DATA_lingcod_DisRatios_noboot_cs_EM_All_Gears_4010__2021-03-08.csv"
))
### TO DO:
# bottom trawl: combine em + cs + ncs for 2011 onward,
# use ncs for 2002-2011
# BottomTrawl only
# fixed gear: combine em + cs + ncs for 2011 onward,
# use ncs for 2002-2011
# FixedGears + HKL + Pot
### look at total by gear within each group
# EM only significant in 2018 and 2019 and still small compared to catch-shares
aggregate(info_em$Observed_DISCARD.MTS + info_em$Observed_RETAINED.MTS,
FUN = function(x){ round(sum(x), 1) },
by = list(gear2 = info_em$gear2,
ryear = info_em$ryear,
Area = info_em$Area))
## gear2 ryear Area x
## 1 BottomTrawl 2015 North4010 0.1
## 2 MidwaterTrawl 2015 North4010 2.7
## 3 Pot 2015 North4010 5.0
## 4 BottomTrawl 2016 North4010 0.4
## 5 MidwaterTrawl 2016 North4010 7.3
## 6 Pot 2016 North4010 0.2
## 7 BottomTrawl 2017 North4010 3.4
## 8 MidwaterTrawl 2017 North4010 7.9
## 9 Pot 2017 North4010 0.4
## 10 BottomTrawl 2018 North4010 3.9
## 11 MidwaterTrawl 2018 North4010 14.7
## 12 Pot 2018 North4010 2.0
## 13 BottomTrawl 2019 North4010 20.6
## 14 MidwaterTrawl 2019 North4010 14.6
## 15 Pot 2019 North4010 2.5
## 16 BottomTrawl 2015 South4010 2.5
## 17 Pot 2015 South4010 0.0
## 18 BottomTrawl 2016 South4010 6.5
## 19 Pot 2016 South4010 0.0
## 20 BottomTrawl 2017 South4010 15.1
## 21 Pot 2017 South4010 0.1
## 22 BottomTrawl 2018 South4010 36.0
## 23 Pot 2018 South4010 0.0
## 24 BottomTrawl 2019 South4010 26.0
## 25 Pot 2019 South4010 0.1
# catch-shares in the south is similar in magnitude to EM
aggregate(info_cs$Observed_DISCARD.MTS + info_cs$Observed_RETAINED.MTS,
FUN = function(x){ round(sum(x), 1) },
by = list(gear2 = info_cs$gear2,
ryear = info_cs$ryear,
Area = info_cs$Area))
## gear2 ryear Area x
## 1 BottomTrawl 2011 North4010 272.7
## 2 HKL 2011 North4010 0.4
## 3 MidwaterTrawl 2011 North4010 4.6
## 4 Pot 2011 North4010 3.0
## 5 BottomTrawl 2012 North4010 356.1
## 6 HKL 2012 North4010 0.2
## 7 MidwaterTrawl 2012 North4010 4.3
## 8 Pot 2012 North4010 1.9
## 9 BottomTrawl 2013 North4010 328.2
## 10 HKL 2013 North4010 0.3
## 11 MidwaterTrawl 2013 North4010 8.6
## 12 Pot 2013 North4010 2.6
## 13 BottomTrawl 2014 North4010 222.4
## 14 HKL 2014 North4010 0.3
## 15 MidwaterTrawl 2014 North4010 13.4
## 16 Pot 2014 North4010 1.4
## 17 BottomTrawl 2015 North4010 165.2
## 18 HKL 2015 North4010 1.2
## 19 Pot 2015 North4010 3.8
## 20 BottomTrawl 2016 North4010 249.1
## 21 HKL 2016 North4010 0.3
## 22 Pot 2016 North4010 1.9
## 23 BottomTrawl 2017 North4010 602.3
## 24 HKL 2017 North4010 0.2
## 25 Pot 2017 North4010 2.4
## 26 BottomTrawl 2018 North4010 411.9
## 27 HKL 2018 North4010 0.3
## 28 Pot 2018 North4010 1.0
## 29 BottomTrawl 2019 North4010 400.9
## 30 HKL 2019 North4010 0.0
## 31 Pot 2019 North4010 2.0
## 32 BottomTrawl 2011 South4010 7.3
## 33 Pot 2011 South4010 0.0
## 34 BottomTrawl 2012 South4010 15.7
## 35 Pot 2012 South4010 0.3
## 36 BottomTrawl 2013 South4010 16.3
## 37 HKL 2013 South4010 0.0
## 38 Pot 2013 South4010 0.0
## 39 BottomTrawl 2014 South4010 18.5
## 40 HKL 2014 South4010 0.0
## 41 Pot 2014 South4010 0.1
## 42 BottomTrawl 2015 South4010 29.7
## 43 Pot 2015 South4010 0.0
## 44 BottomTrawl 2016 South4010 18.0
## 45 BottomTrawl 2017 South4010 9.0
## 46 HKL 2017 South4010 0.0
## 47 Pot 2017 South4010 0.1
## 48 BottomTrawl 2018 South4010 15.5
## 49 BottomTrawl 2019 South4010 58.4
# non-catch-shares
aggregate(info_ncs$Observed_DISCARD.MTS +
info_ncs$Observed_RETAINED.MTS,
FUN = function(x){round(sum(x),1)},
by = list(gear2 = info_ncs$gear2,
ryear = info_ncs$ryear,
Area = info_ncs$Area))
## gear2 ryear Area x
## 1 BottomTrawl 2002 North4010 38.4
## 2 HKL 2002 North4010 1.3
## 3 Pot 2002 North4010 0.2
## 4 BottomTrawl 2003 North4010 24.0
## 5 FixedGears 2003 North4010 1.1
## 6 HKL 2003 North4010 1.6
## 7 Pot 2003 North4010 0.8
## 8 BottomTrawl 2004 North4010 29.3
## 9 FixedGears 2004 North4010 5.4
## 10 HKL 2004 North4010 0.9
## 11 Pot 2004 North4010 0.4
## 12 ShrimpTrawl 2004 North4010 0.0
## 13 BottomTrawl 2005 North4010 101.0
## 14 FixedGears 2005 North4010 5.0
## 15 HKL 2005 North4010 4.5
## 16 Pot 2005 North4010 1.5
## 17 ShrimpTrawl 2005 North4010 0.0
## 18 BottomTrawl 2006 North4010 75.5
## 19 FixedGears 2006 North4010 4.7
## 20 HKL 2006 North4010 7.8
## 21 Pot 2006 North4010 3.5
## 22 BottomTrawl 2007 North4010 30.3
## 23 FixedGears 2007 North4010 3.9
## 24 HKL 2007 North4010 1.3
## 25 Pot 2007 North4010 2.2
## 26 ShrimpTrawl 2007 North4010 0.1
## 27 BottomTrawl 2008 North4010 29.9
## 28 FixedGears 2008 North4010 3.9
## 29 HKL 2008 North4010 4.8
## 30 Pot 2008 North4010 2.3
## 31 ShrimpTrawl 2008 North4010 0.0
## 32 BottomTrawl 2009 North4010 44.7
## 33 FixedGears 2009 North4010 3.1
## 34 HKL 2009 North4010 1.6
## 35 Pot 2009 North4010 1.9
## 36 ShrimpTrawl 2009 North4010 0.0
## 37 BottomTrawl 2010 North4010 11.9
## 38 FixedGears 2010 North4010 2.8
## 39 HKL 2010 North4010 2.2
## 40 Pot 2010 North4010 2.3
## 41 ShrimpTrawl 2010 North4010 0.0
## 42 FixedGears 2011 North4010 5.5
## 43 HKL 2011 North4010 1.7
## 44 Pot 2011 North4010 1.2
## 45 ShrimpTrawl 2011 North4010 0.1
## 46 FixedGears 2012 North4010 7.6
## 47 HKL 2012 North4010 1.9
## 48 Pot 2012 North4010 1.6
## 49 ShrimpTrawl 2012 North4010 0.1
## 50 FixedGears 2013 North4010 9.5
## 51 HKL 2013 North4010 0.6
## 52 Pot 2013 North4010 0.2
## 53 ShrimpTrawl 2013 North4010 0.0
## 54 FixedGears 2014 North4010 6.5
## 55 HKL 2014 North4010 0.9
## 56 Pot 2014 North4010 1.5
## 57 ShrimpTrawl 2014 North4010 0.0
## 58 FixedGears 2015 North4010 10.1
## 59 HKL 2015 North4010 2.9
## 60 MidwaterTrawl 2015 North4010 6.1
## 61 Pot 2015 North4010 4.4
## 62 ShrimpTrawl 2015 North4010 0.1
## 63 BottomTrawl 2016 North4010 0.0
## 64 FixedGears 2016 North4010 8.5
## 65 HKL 2016 North4010 4.0
## 66 MidwaterTrawl 2016 North4010 0.7
## 67 Pot 2016 North4010 7.3
## 68 ShrimpTrawl 2016 North4010 0.0
## 69 BottomTrawl 2017 North4010 0.1
## 70 FixedGears 2017 North4010 9.9
## 71 HKL 2017 North4010 4.3
## 72 MidwaterTrawl 2017 North4010 2.3
## 73 Pot 2017 North4010 1.1
## 74 ShrimpTrawl 2017 North4010 0.0
## 75 BottomTrawl 2018 North4010 1.8
## 76 FixedGears 2018 North4010 8.5
## 77 HKL 2018 North4010 7.9
## 78 MidwaterTrawl 2018 North4010 2.8
## 79 Pot 2018 North4010 2.7
## 80 ShrimpTrawl 2018 North4010 0.0
## 81 BottomTrawl 2019 North4010 3.3
## 82 FixedGears 2019 North4010 8.8
## 83 HKL 2019 North4010 8.7
## 84 MidwaterTrawl 2019 North4010 1.7
## 85 Pot 2019 North4010 2.8
## 86 ShrimpTrawl 2019 North4010 0.0
## 87 BottomTrawl 2002 South4010 4.5
## 88 HKL 2002 South4010 0.2
## 89 MidwaterTrawl 2002 South4010 0.2
## 90 BottomTrawl 2003 South4010 4.5
## 91 FixedGears 2003 South4010 1.2
## 92 HKL 2003 South4010 0.3
## 93 Pot 2003 South4010 0.0
## 94 BottomTrawl 2004 South4010 9.0
## 95 FixedGears 2004 South4010 1.9
## 96 HKL 2004 South4010 0.0
## 97 Pot 2004 South4010 0.6
## 98 BottomTrawl 2005 South4010 6.9
## 99 FixedGears 2005 South4010 1.1
## 100 HKL 2005 South4010 0.1
## 101 Pot 2005 South4010 0.0
## 102 ShrimpTrawl 2005 South4010 0.0
## 103 BottomTrawl 2006 South4010 2.2
## 104 FixedGears 2006 South4010 0.6
## 105 HKL 2006 South4010 0.0
## 106 Pot 2006 South4010 1.4
## 107 BottomTrawl 2007 South4010 9.4
## 108 FixedGears 2007 South4010 0.6
## 109 HKL 2007 South4010 0.0
## 110 Pot 2007 South4010 0.7
## 111 BottomTrawl 2008 South4010 5.7
## 112 FixedGears 2008 South4010 0.4
## 113 HKL 2008 South4010 0.0
## 114 Pot 2008 South4010 0.2
## 115 BottomTrawl 2009 South4010 10.8
## 116 FixedGears 2009 South4010 0.6
## 117 Pot 2009 South4010 0.1
## 118 BottomTrawl 2010 South4010 2.3
## 119 FixedGears 2010 South4010 0.7
## 120 Pot 2010 South4010 0.2
## 121 BottomTrawl 2011 South4010 0.0
## 122 FixedGears 2011 South4010 1.0
## 123 HKL 2011 South4010 0.2
## 124 Pot 2011 South4010 0.0
## 125 FixedGears 2012 South4010 1.5
## 126 HKL 2012 South4010 0.3
## 127 Pot 2012 South4010 0.0
## 128 BottomTrawl 2013 South4010 0.0
## 129 FixedGears 2013 South4010 1.9
## 130 Pot 2013 South4010 0.1
## 131 BottomTrawl 2014 South4010 0.0
## 132 FixedGears 2014 South4010 1.6
## 133 HKL 2014 South4010 0.1
## 134 Pot 2014 South4010 0.0
## 135 BottomTrawl 2015 South4010 1.4
## 136 FixedGears 2015 South4010 2.5
## 137 HKL 2015 South4010 1.1
## 138 Pot 2015 South4010 0.0
## 139 BottomTrawl 2016 South4010 2.9
## 140 FixedGears 2016 South4010 0.8
## 141 HKL 2016 South4010 0.2
## 142 Pot 2016 South4010 0.1
## 143 ShrimpTrawl 2016 South4010 0.0
## 144 BottomTrawl 2017 South4010 3.1
## 145 FixedGears 2017 South4010 1.3
## 146 HKL 2017 South4010 0.3
## 147 Pot 2017 South4010 0.1
## 148 ShrimpTrawl 2017 South4010 0.1
## 149 BottomTrawl 2018 South4010 16.2
## 150 FixedGears 2018 South4010 1.0
## 151 HKL 2018 South4010 0.1
## 152 Pot 2018 South4010 0.1
## 153 ShrimpTrawl 2018 South4010 0.1
## 154 BottomTrawl 2019 South4010 7.9
## 155 FixedGears 2019 South4010 1.5
## 156 HKL 2019 South4010 0.3
## 157 Pot 2019 South4010 0.2
## 158 ShrimpTrawl 2019 South4010 0.0
# non-catch-shares after 2011
aggregate(info_ncs$Observed_DISCARD.MTS[info_ncs$ryear >= 2011] +
info_ncs$Observed_RETAINED.MTS[info_ncs$ryear >= 2011],
FUN = sum, by = list(info_ncs$gear2[info_ncs$ryear >= 2011]))
## Group.1 x
## 1 BottomTrawl 36.78862
## 2 FixedGears 88.25765
## 3 HKL 35.33838
## 4 MidwaterTrawl 13.65291
## 5 Pot 23.61832
# conclusion: ignore shrimp trawl
info_ncs <- info_ncs[info_ncs$gear2 != "ShrimpTrawl",]
# after 2011, bottom trawl in non-catch-shares is very small compared to catch-shares
# run function to combine discard rates
disc_rate_N_TW <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "North4010",
gears = c("BottomTrawl", "MidwaterTrawl"),
fleet = 1,
min_cv = 0.05)
disc_rate_S_TW <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "South4010",
gears = c("BottomTrawl", "MidwaterTrawl"),
fleet = 1,
min_cv = 0.05)
disc_rate_N_FG <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "North4010",
gears = c("FixedGears", "HKL", "Pot"),
fleet = 2,
min_cv = 0.05)
disc_rate_S_FG <-
discard_rates_combined(info_ncs = info_ncs,
info_cs = info_cs,
info_em = info_em,
Area = "South4010",
gears = c("FixedGears", "HKL", "Pot"),
fleet = 2,
min_cv = 0.05)
# remove 2002 from disc_rate_S_FG because it represents on the HKL fleet with few trips
# and no observed discards
disc_rate_S_FG <- disc_rate_S_FG[disc_rate_S_FG$Yr > 2002,]
# combine the tables into a single table
data_discard_rates_WCGOP <-
rbind(data.frame(disc_rate_N_TW, Area = "North", Gear = "TW"),
data.frame(disc_rate_S_TW, Area = "South", Gear = "TW"),
data.frame(disc_rate_N_FG, Area = "North", Gear = "FG"),
data.frame(disc_rate_S_FG, Area = "South", Gear = "FG"))
rownames(data_discard_rates_WCGOP) <- 1:nrow(data_discard_rates_WCGOP)
#+ setup_usethis, echo = FALSE
# add .rda file
usethis::use_data(data_discard_rates_WCGOP, overwrite = TRUE)
#+ cleanup
rm(file_index_orbs)
rm(info_ncs)
rm(info_cs)
rm(info_em)
rm(disc_rate_N_TW)
rm(disc_rate_S_TW)
rm(disc_rate_N_FG)
rm(disc_rate_S_FG)
rm(data_discard_rates_WCGOP)
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.