From bced06a1606a2987e46b867b585474e7b0598434 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 19 Dec 2023 13:05:57 -0500
Subject: [PATCH 01/17] update the mode vintage

---
 .../processing/catch_summaries.txt                        | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/catch_summaries.txt b/stata_code/data_extraction_processing/processing/catch_summaries.txt
index 2a4d404..7a3a032 100644
--- a/stata_code/data_extraction_processing/processing/catch_summaries.txt
+++ b/stata_code/data_extraction_processing/processing/catch_summaries.txt
@@ -748,12 +748,10 @@ There were no B2's measured on Private boats, so I've set the length distributio
 
 <<dd_do:quietly>>
 
-global mode_vintage 2023_11_30
+global mode_dir "${data_main}/MRIP_${vintage_string}/mode"
 
-global mode_dir "${data_main}/MRIP_$mode_vintage/mode"
-
-use "${mode_dir}/haddock_size_mode_class_${working_year}.dta", clear
-keep if year==$working_year
+use "${mode_dir}/haddock_size_mode_class_${this_working_year}.dta", clear
+keep if year==$this_working_year
 rename lngcat inches
 sort mode year month inches
 

From 97e00f7c07e9e74d7e270455c2f9c4e73e118ad3 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 19 Dec 2023 13:11:16 -0500
Subject: [PATCH 02/17] dont round

---
 .../processing/monthly/cod_monthly_weight_ab1b2.do          | 6 +++---
 .../processing/monthly/haddock_monthly_weight_ab1b2.do      | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/monthly/cod_monthly_weight_ab1b2.do b/stata_code/data_extraction_processing/processing/monthly/cod_monthly_weight_ab1b2.do
index f19f708..429f56b 100644
--- a/stata_code/data_extraction_processing/processing/monthly/cod_monthly_weight_ab1b2.do
+++ b/stata_code/data_extraction_processing/processing/monthly/cod_monthly_weight_ab1b2.do
@@ -39,9 +39,9 @@ gen weight_per_fish= $kilotolb*$coda*((l_in_bin+.5)/$cmtoinch)^$codb
 
 
 
-gen ab1weight=round(ab1_count)*weight_per_fish
-gen b2weight=round(b2_count)*weight_per_fish
-gen b2weight_dead=round(b2_count)*weight_per_fish*discard_mortality
+gen ab1weight=ab1_count*weight_per_fish
+gen b2weight=b2_count*weight_per_fish
+gen b2weight_dead=b2_count*weight_per_fish*discard_mortality
 
 keep if year==$working_year
 
diff --git a/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do b/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do
index cff4a98..6c7e40c 100644
--- a/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do
+++ b/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do
@@ -45,14 +45,14 @@ drop if l_in_bin==0
 gen weight_per_fish= $kilotolb*$hada*((l_in_bin+.5)/$cmtoinch)^$hade
 
 
-gen ab1weight=round(ab1_count)*weight_per_fish
-gen b2weight=round(b2_count)*weight_per_fish
+gen ab1weight=ab1_count*weight_per_fish
+gen b2weight=b2_count*weight_per_fish
 
 keep if year==$working_year
 
 drop if l_in_bin==0
 
-gen b2weight_dead=round(b2_count)*weight_per_fish*discard_mortality
+gen b2weight_dead=b2_count*weight_per_fish*discard_mortality
 
 collapse (sum) ab1weight b2weight b2weight_dead ab1_count b2_count , by(year month)
 

From a1e8960300dd3a012d946bdf5dd39ec4c9339257 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 19 Dec 2023 13:13:58 -0500
Subject: [PATCH 03/17] get rid of obsolete code and drop if l_in_bin==.

---
 .../processing/monthly/process_b2_cod.do             | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/monthly/process_b2_cod.do b/stata_code/data_extraction_processing/processing/monthly/process_b2_cod.do
index 67d5ee1..3eab3f0 100644
--- a/stata_code/data_extraction_processing/processing/monthly/process_b2_cod.do
+++ b/stata_code/data_extraction_processing/processing/monthly/process_b2_cod.do
@@ -91,22 +91,12 @@ save "$my_outputdir/atlanticcod_b2_counts_$working_year.dta", replace
 
 use "$my_outputdir/cod_ab1_$working_year.dta", clear
 
-/*
-expand 2 if month==5 & year==2013
-drop if month==6 & year==2013
-
-bysort year month l_in_bin: gen mark=_n
-replace month=6 if mark==2 & year==2013 & month==5
-
-drop mark
-*/
-
 sort year month
 
 cap drop _merge
 merge m:1 year month using `claim_harvest'
 
-
+drop if l_in_bin==.
 tempvar ttt
 bysort year month: egen `ttt'=total(count)
 gen prob=count/`ttt'

From d95b93968d60e70779ec0467ac4cd24610bc3496 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 11:40:37 -0500
Subject: [PATCH 04/17] patch an extra site_id

---
 .../extraction/get_ma_allocation.do            | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/stata_code/data_extraction_processing/extraction/get_ma_allocation.do b/stata_code/data_extraction_processing/extraction/get_ma_allocation.do
index 57a0a3d..d644c4a 100644
--- a/stata_code/data_extraction_processing/extraction/get_ma_allocation.do
+++ b/stata_code/data_extraction_processing/extraction/get_ma_allocation.do
@@ -2,6 +2,18 @@
 /* read in and store the MRIP location stuff.  Put it in the file ma_site_allocation.dta */
 clear
 #delimit;
-odbc load,  exec("select site_id, stock_region_calc from recdbs.mrip_ma_site_list;") $myNEFSC_USERS_conn;
-#delimit cr
-save "${data_raw}/ma_site_allocation.dta", replace
\ No newline at end of file
+odbc load,  exec("select site_id, stock_region_calc from recdbs.mrip_ma_site_list;") $mysole_conn;
+
+/* will need to switch the connection string to $myNEFSC_USERS_conn soon */
+
+
+/* patch in the extra site_id */
+
+qui count;
+local newobs=`r(N)'+1;
+set obs `newobs';
+
+replace site_id=4434 if site_id==.;
+replace stock_region_calc="NORTH" if site_id==4434;
+
+save "${data_raw}/ma_site_allocation.dta", replace;
\ No newline at end of file

From 272f676f9567f491e2fec167dc3f9bb240d13c8b Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 11:43:48 -0500
Subject: [PATCH 05/17] data vintage update

---
 .../data_extraction_processing/processing/catch_summaries.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/catch_summaries.txt b/stata_code/data_extraction_processing/processing/catch_summaries.txt
index 7a3a032..c3b3abe 100644
--- a/stata_code/data_extraction_processing/processing/catch_summaries.txt
+++ b/stata_code/data_extraction_processing/processing/catch_summaries.txt
@@ -29,7 +29,7 @@ dyndoc "$processing_code/catch_summaries.txt", saving($my_results/catch_summarie
 <<dd_do:quietly>>
 /* If you dyndoc this right after running your MRIP data processing code, you can comment this out.*/
 do $MRIP_BLAST
-global vintage_string 2023_12_18
+global vintage_string 2024_01_02
 global my_outputdir "${data_main}/MRIP_$vintage_string/monthly"
 
 global FY_dir "${data_main}/MRIP_$vintage_string/fishing_years"
@@ -56,7 +56,7 @@ global hadd_recACL2023=610
 global cod_recACL2023=192
 
 
-global mrip_vintage "2023_12_18"
+global mrip_vintage "2024_01_02"
 
 global hadd_recACL2024=759
 global cod_recACL2024=192

From efd026fc3b275dbf42758f9ad86c948ae05c424c Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 11:44:29 -0500
Subject: [PATCH 06/17] caption and open/close updates

---
 .../processing/convert_monthly_to_annual.do   | 51 +++++++++++--------
 1 file changed, 31 insertions(+), 20 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/convert_monthly_to_annual.do b/stata_code/data_extraction_processing/processing/convert_monthly_to_annual.do
index b27f84a..2f6c845 100644
--- a/stata_code/data_extraction_processing/processing/convert_monthly_to_annual.do
+++ b/stata_code/data_extraction_processing/processing/convert_monthly_to_annual.do
@@ -47,17 +47,19 @@ save "${BLAST_DIR}/cod_catch_class_ANNUAL`yr1'.dta", replace
 replace count=count/1000
 label var count "count 1000s"
 xtline count
+xtline count if month==9 , subtitle("Averaged across all months")
 graph export "${my_images_vintage}/cod_catch_class_ANNUAL`yr1'.tif", as(tif) replace
 
-xtline count if num_fish>0
+xtline count if month==9 & num_fish>0, subtitle("Averaged across all months, no zeros")
 graph export "${my_images_vintage}/cod_catch_class_no0_ANNUAL`yr1'.tif", as(tif) replace
 
 
 bysort month: egen tc=total(count)
 gen prob=count/tc
-xtline prob
+xtline prob if month==9 , subtitle("Averaged across all months")
+
 graph export "${my_images_vintage}/cod_catch_classP_ANNUAL`yr1'.tif", as(tif) replace
-xtline prob if num_fish>0
+xtline prob if month==9 & num_fish>0, subtitle("Averaged across all months, no zeros")
 graph export "${my_images_vintage}/cod_catch_classPno0_ANNUAL`yr1'.tif", as(tif) replace
 
 
@@ -98,18 +100,21 @@ save "${BLAST_DIR}/haddock_catch_class_ANNUAL`yr1'.dta", replace
 replace count=count/1000
 label var count "count 1000s"
 xtline count
+xtline count if month==9 , subtitle("Averaged across all months")
+
 graph export "${my_images_vintage}/haddock_catch_class_ANNUAL`yr1'.tif", as(tif) replace
 
-xtline count if num_fish>0
+xtline count if month==9 & num_fish>0, subtitle("Averaged across all months, no zeros")
 graph export "${my_images_vintage}/haddock_catch_class_no0_ANNUAL`yr1'.tif", as(tif) replace
 
 
 bysort month: egen tc=total(count)
 gen prob=count/tc
-xtline prob
+xtline prob if month==9 , subtitle("Averaged across all months")
 graph export "${my_images_vintage}/haddock_catch_classP_ANNUAL`yr1'.tif", as(tif) replace
 
-xtline prob if num_fish>0
+xtline prob if month==9 & num_fish>0, subtitle("Averaged across all months, no zeros")
+
 graph export "${my_images_vintage}/haddock_catch_classPno0_ANNUAL`yr1'.tif", as(tif) replace
 
 /*******************END HADDOCK **************************************/
@@ -166,14 +171,14 @@ save "${BLAST_DIR}/cod_size_class_ANNUAL`yr1'.dta", replace
 
 replace count=count/1000
 label var count "count 1000s"
-xtline count, xline($cmin)
+xtline count if month==9, xline($cmin) subtitle("Averaged across all months")
 graph export  "${my_images_vintage}/cod_size_class_ANNUAL`yr1'.tif", as(tif) replace
 
 
 
 bysort month: egen tc=total(count)
 gen prob=count/tc
-xtline prob, xline($cmin)
+xtline prob if month==9, xline($cmin) subtitle("Averaged across all months")
 graph export "${my_images_vintage}/cod_size_classP_ANNUAL`yr1'.tif", as(tif) replace
 
 
@@ -188,27 +193,26 @@ keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,
 replace fishing_year=`yr1'
 
 
-gen open=inlist(month,4,9,10)
+gen open=inlist(month,9,10)
 collapse (sum) count, by(lngcat fishing_year open)
 preserve
 keep if open==1
-expand 3, gen(o1)
+expand 2, gen(o1)
 sort fishing_year  lngcat
 
-gen month=4 if o1==0
+gen month=9 if o1==0
 sort fishing_year lngcat o1
-bysort fishing_year lngcat: replace month=_n+7 if o1==1
+bysort fishing_year lngcat: replace month=_n+8 if o1==1
 tempfile open
 drop o1
 save `open', replace
 restore
 
 keep if open==0
-expand 9, gen(cl)
+expand 10, gen(cl)
 sort fishing_year lngcat cl
 bysort fishing_year lngcat: gen month=_n 
-bysort fishing_year lngcat: replace month=_n+1 if month>=4
-bysort fishing_year lngcat: replace month=_n+3 if month>=9
+bysort fishing_year lngcat: replace month=_n+2 if month>=9
 
 
 append using `open'
@@ -221,18 +225,25 @@ save "${BLAST_DIR}/cod_size_class_OPEN_SPLIT`yr1'.dta", replace
 
 xtset month lng
 
+bysort month: egen tc=total(count)
 
 
 replace count=count/1000
 label var count "count 1000s"
-xtline count, xline($cmin)
-graph export  "${my_images_vintage}/cod_size_class_OPEN_SPLIT`yr1'.tif", as(tif) replace
 
+gen open="open"
+replace open="closed" if month==8
+xtline count if inlist(month,8,9), xline($cmin) i(open) t(lng)
+
+graph export  "${my_images_vintage}/cod_size_class_OPEN_SPLIT`yr1'.tif", as(tif) replace
 
 
+cap drop tc
 bysort month: egen tc=total(count)
 gen prob=count/tc
-xtline prob, xline($cmin)
+
+xtline prob if inlist(month,8,9), xline($cmin) i(open) t(lng)
+
 graph export "${my_images_vintage}/cod_size_classP_OPEN_SPLIT`yr1'.tif", as(tif) replace
 
 
@@ -270,13 +281,13 @@ save "${BLAST_DIR}/haddock_size_class_ANNUAL`yr1'.dta", replace
 
 replace count=count/1000
 label var count "count 1000s"
-xtline count, xline($hmin)
+xtline count if month==9, xline($hmin) subtitle("Averaged across all months")
 graph export  "${my_images_vintage}/haddock_size_class_ANNUAL`yr1'.tif", as(tif) replace
 
 
 
 bysort month: egen tc=total(count)
 gen prob=count/tc
-xtline prob, xline($hmin)
+xtline prob if month==9, xline($hmin) subtitle("Averaged across all months")
 graph export "${my_images_vintage}/haddock_size_classP_ANNUAL`yr1'.tif", as(tif) replace
 

From cc4f1aa83f8b29453f215ee68cba71f251ee323b Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 11:45:29 -0500
Subject: [PATCH 07/17] compute mortality.

---
 .../processing/catch_summaries.txt            | 250 +++++++++++++++++-
 1 file changed, 247 insertions(+), 3 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/catch_summaries.txt b/stata_code/data_extraction_processing/processing/catch_summaries.txt
index c3b3abe..43cec1a 100644
--- a/stata_code/data_extraction_processing/processing/catch_summaries.txt
+++ b/stata_code/data_extraction_processing/processing/catch_summaries.txt
@@ -19,7 +19,9 @@ global working_data "${project_dir}/working_data"
 global output_dir "${project_dir}/output"
 global this_working_year 2023
 global last_year = $this_working_year - 1
-global two_years = $this_working_year - 2  
+global two_years = $this_working_year - 2 
+global BLAST_DIR "${BLAST_root}/cod_haddock_fy2024/source_data/mrip"
+ 
 dyndoc "$processing_code/catch_summaries.txt", saving($my_results/catch_summaries_${this_working_year}.html) replace
 
  ---> 
@@ -31,11 +33,44 @@ dyndoc "$processing_code/catch_summaries.txt", saving($my_results/catch_summarie
 do $MRIP_BLAST
 global vintage_string 2024_01_02
 global my_outputdir "${data_main}/MRIP_$vintage_string/monthly"
-
 global FY_dir "${data_main}/MRIP_$vintage_string/fishing_years"
+global BLAST_DIR "${BLAST_root}/cod_haddock_fy2024/source_data/mrip"
 local my_common1 "atlanticcod"
 local my_common2 "haddock"
 
+
+
+/* Here are some parameters */
+global mt_to_kilo=1000
+global kilo_to_lbs=2.20462262
+global cm_to_inch=0.39370787
+global mortality_release=0.15
+
+
+
+/* l-W is updated to be consistent with PDB 
+These are the length-weight relationships for Cod and Haddock
+GOM Cod Formula:
+Wlive (kg) = 0.000005132·L(fork cm)3.1625 (p < 0.0001, n=4890)
+
+http://www.nefsc.noaa.gov/publications/crd/crd0903/
+Haddock Weight length formula 
+Annual: Wlive (kg) = 0.000009298·L(fork cm)3.0205 (p < 0.0001, n=4890)
+GROUNDFISH ASSESSMENT UPDATES 2012 page 181
+
+Fork length and total length are equivalentfor haddock and haddock*/
+
+
+global cod_lwa 0.000005132
+global cod_lwb 3.1625
+global had_lwa 0.000009298
+global had_lwe 3.0205
+global lngcat_offset_cod 0.5
+global lngcat_offset_haddock 0.5
+
+
+
+
 /*global this_working_year = 2023 */
 global last_year = $this_working_year - 1
 global two_years = $this_working_year - 2  
@@ -483,7 +518,7 @@ list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_
 <</dd_do>>
 ~~~~
 
-
+These weights are computed using the monthly length distributions from MRIP. That data is a little thin.
 
 
 ~~~~
@@ -527,6 +562,86 @@ format ab1_count b2_count %10.0fc
 
 keep if year==$this_working_year
 <</dd_do>>
+
+
+<<dd_do>>
+list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_per_fish, abbreviate(16) sum(ab1mt b2mt b2dead_mt  ab1_count b2_count)
+<</dd_do>>
+~~~~
+
+
+
+### These weights are computed using the annual length distribution of catch
+
+~~~~
+<<dd_do:quietly>>
+
+
+
+/* load in total catch */
+
+
+
+use "${BLAST_DIR}/cod_size_class_ANNUAL${this_working_year}.dta", replace
+/*lngcat fishing_year count month*/
+drop fishing_year
+
+bysort month: egen t=total(count)
+gen prob=count/t
+keep month lngcat prob
+
+tempfile lengths
+save `lengths'
+
+
+
+
+use ${data_main}/MRIP_${vintage_string}\monthly\atlanticcod_catch_${this_working_year}.dta
+gen landings=claim+harvest
+keep year month landings release
+destring month, replace
+merge 1:m month using `lengths', keep(1 3)
+
+
+gen count_release=prob*release
+gen count_landings=prob*landings
+
+
+collapse (sum) count_release count_landings, by(year month lngcat)
+/* compute weights */
+
+
+/* l_in_bin from MRIP is length of catch, rounded down to the nearest inch */
+
+gen weight_per_fish= $kilo_to_lbs*$cod_lwa*((lngcat+.5)/$cm_to_inch)^$cod_lwb
+gen landed_weight=weight_per_fish*count_landings
+gen released_weight=weight_per_fish*count_release
+
+collapse (sum) count_release count_landings landed_weight released_weight, by(year month)
+
+
+gen ab1_lbs_per_fish=landed_weight /count_landings 
+gen b2_lbs_per_fish=released_weight/count_release 
+
+
+replace landed_weight=landed_weight/($mt_to_kilo*$kilo_to_lbs)
+replace released_weight=released_weight/($mt_to_kilo*$kilo_to_lbs)
+rename landed_weight ab1mt 
+rename released_weight b2mt 
+
+rename count_landings ab1_count 
+rename count_release  b2_count 
+
+gen b2dead_mt=b2mt*$mortality_release
+
+format ab1_lbs_per_fish b2_lbs_per_fish %4.3fc
+
+
+format ab1_count b2_count %10.0fc
+
+format b2mt ab1mt b2dead_mt %6.1fc
+
+<</dd_do>>
 <<dd_do>>
 
 list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_per_fish, abbreviate(16) sum(ab1mt b2mt b2dead_mt  ab1_count b2_count)
@@ -536,6 +651,20 @@ list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_
 
 
 
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 Catch Statistics for Haddock  
 ===============================================================
 
@@ -707,6 +836,121 @@ list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_
 ~~~~
 
 
+
+
+
+### These weights are computed using the annual length distribution of catch
+
+~~~~
+<<dd_do:quietly>>
+
+
+
+/* load in total catch */
+
+
+
+use "${BLAST_DIR}/haddock_size_class_ANNUAL${this_working_year}.dta", replace
+/*lngcat fishing_year count month*/
+drop fishing_year
+
+bysort month: egen t=total(count)
+gen prob=count/t
+keep month lngcat prob
+
+tempfile lengths
+save `lengths'
+
+
+
+
+use ${data_main}/MRIP_${vintage_string}\monthly\haddock_catch_${this_working_year}.dta
+gen landings=claim+harvest
+keep year month landings release
+destring month, replace
+merge 1:m month using `lengths', keep(1 3)
+
+
+gen count_release=prob*release
+gen count_landings=prob*landings
+
+
+collapse (sum) count_release count_landings, by(year month lngcat)
+/* compute weights */
+
+
+
+gen discard_mortality=.113 if month<=6 & lngcat>=20
+replace discard_mortality=.459 if month>6 & lngcat>=20
+
+replace discard_mortality=.321 if month<=6 & lngcat<20
+replace discard_mortality=.742 if month>6 & lngcat<20
+
+
+
+
+
+
+
+/* l_in_bin from MRIP is length of catch, rounded down to the nearest inch */
+
+gen weight_per_fish= $kilo_to_lbs*$had_lwa*((lngcat+.5)/$cm_to_inch)^$had_lwe
+gen landed_weight=weight_per_fish*count_landings
+gen released_weight=weight_per_fish*count_release
+
+gen b2dead_weight=weight_per_fish*discard_mortality*count_release
+
+gen b2dead_count=discard_mortality*count_release
+
+collapse (sum) count_release count_landings landed_weight released_weight b2dead_count b2dead_weight, by(year month)
+
+
+gen ab1_lbs_per_fish=landed_weight /count_landings 
+gen b2_lbs_per_fish=released_weight/count_release 
+
+
+replace landed_weight=landed_weight/($mt_to_kilo*$kilo_to_lbs)
+replace released_weight=released_weight/($mt_to_kilo*$kilo_to_lbs)
+replace b2dead_weight=b2dead_weight/($mt_to_kilo*$kilo_to_lbs)
+
+
+rename landed_weight ab1mt 
+rename released_weight b2mt 
+
+rename count_landings ab1_count 
+rename count_release  b2_count 
+
+
+format ab1_lbs_per_fish b2_lbs_per_fish %4.3fc
+
+format ab1_count b2_count b2dead_count %10.0fc
+
+format b2mt ab1mt b2dead_weight %6.1fc
+
+<</dd_do>>
+<<dd_do>>
+
+list year month ab1mt b2mt b2dead_weight ab1_count b2_count b2dead_count, abbreviate(16) sum(ab1mt b2mt b2dead_weight ab1_count b2_count b2dead_count)
+<</dd_do>>
+~~~~
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 Length distributions for haddock landed. Just the Fish in the 15-19" range. There were no B2's measured on Private boats, so this assumes the B2's on private boats is similar to the B2s on ForHire and Charter vessels.
 
 

From ac810b3858d288006616aafe3300923c7ef2db2d Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:25:51 -0500
Subject: [PATCH 08/17] unweighted for cod

---
 .../processing/annual/b2_length_freqs_by_year_gom.do       | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_year_gom.do b/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_year_gom.do
index aeb712d..e31b8e2 100644
--- a/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_year_gom.do
+++ b/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_year_gom.do
@@ -167,6 +167,13 @@ replace l_in_bin=0 if strmatch(common_dom, "Z")==1
 sort year w2 strat_id psu_id id_code
 svyset psu_id [pweight= wp_size], strata(var_id) singleunit(certainty)
 
+
+/* use unweighted for atlantic cod lengths */
+if "$my_common"=="atlanticcod"{
+	svyset psu_id, strata(var_id) singleunit(certainty)
+}
+ 
+ 
  
 local myv l_in_bin
 

From d1475e5e7026a574d3a2b82c7dacbcb86f1ba6c8 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:26:19 -0500
Subject: [PATCH 09/17] adjust discard mortalities

---
 .../processing/catch_summaries.txt            | 21 +++++++++++--------
 .../monthly/haddock_monthly_weight_ab1b2.do   | 18 ++++++++++++----
 2 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/catch_summaries.txt b/stata_code/data_extraction_processing/processing/catch_summaries.txt
index 43cec1a..3dfe548 100644
--- a/stata_code/data_extraction_processing/processing/catch_summaries.txt
+++ b/stata_code/data_extraction_processing/processing/catch_summaries.txt
@@ -879,15 +879,18 @@ collapse (sum) count_release count_landings, by(year month lngcat)
 /* compute weights */
 
 
-
-gen discard_mortality=.113 if month<=6 & lngcat>=20
-replace discard_mortality=.459 if month>6 & lngcat>=20
-
-replace discard_mortality=.321 if month<=6 & lngcat<20
-replace discard_mortality=.742 if month>6 & lngcat<20
-
-
-
+/*
+Spring (waves 1, 2, 3) small (<50cm, <=19inches) 0.321
+Spring (waves 1, 2, 3) large (>=50cm, >19inches) 0.113
+Fall (waves 4, 5, 6) small (<50cm, <=19inches) 0.742
+Fall (waves 4, 5, 6) large (>=50cm, >19inches) 0.459
+*/
+
+gen discard_mortality=.113 if month<=6 & lngcat>19
+replace discard_mortality=.459 if month>6 & lngcat>19
+
+replace discard_mortality=.321 if month<=6 & lngcat<=19
+replace discard_mortality=.742 if month>6 & lngcat<=19
 
 
 
diff --git a/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do b/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do
index 6c7e40c..8df5eb6 100644
--- a/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do
+++ b/stata_code/data_extraction_processing/processing/monthly/haddock_monthly_weight_ab1b2.do
@@ -1,10 +1,20 @@
 use "${data_main}/MRIP_${vintage_string}/monthly/haddock_b2_counts_${working_year}.dta", clear
 
-gen discard_mortality=.113 if month<=6 & l_in_bin>=20
-replace discard_mortality=.459 if month>6 & l_in_bin>=20
+gen discard_mortality=.113 if month<=6 & l_in_bin>19
+replace discard_mortality=.459 if month>6 & l_in_bin>19
 
-replace discard_mortality=.321 if month<=6 & l_in_bin<20
-replace discard_mortality=.742 if month>6 & l_in_bin<20
+replace discard_mortality=.321 if month<=6 & l_in_bin<=19
+replace discard_mortality=.742 if month>6 & l_in_bin<=19
+
+
+
+
+/*
+Spring (waves 1, 2, 3) small (<50cm, <=19inches) 0.321
+Spring (waves 1, 2, 3) large (>=50cm, >19inches) 0.113
+Fall (waves 4, 5, 6) small (<50cm, <=19inches) 0.742
+Fall (waves 4, 5, 6) large (>=50cm, >19inches) 0.459
+*/
 
 tempfile b2_adj
 save `b2_adj', replace

From 73dae0a6f6cec846e170c6cd1f46461576caef9b Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:26:56 -0500
Subject: [PATCH 10/17] unweighted for cod

---
 .../processing/annual/length_freqs_by_year_gom.do   | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/annual/length_freqs_by_year_gom.do b/stata_code/data_extraction_processing/processing/annual/length_freqs_by_year_gom.do
index e0609bc..bbc789b 100644
--- a/stata_code/data_extraction_processing/processing/annual/length_freqs_by_year_gom.do
+++ b/stata_code/data_extraction_processing/processing/annual/length_freqs_by_year_gom.do
@@ -131,16 +131,17 @@ replace area_s="GOM" if st==23 | st==33
 replace area_s="GOM" if st==25 & strmatch(stock_region_calc,"NORTH")
 replace area_s="GBS" if st==25 & strmatch(stock_region_calc,"SOUTH")
 
- /* classify catch into the things I care about (common==$mycommon) and things I don't care about "ZZZZZZZZ" use the id_code*/
+ /* classify catch into the things I care about (common==$mycommon) and things I don't care about "ZZZZZZZZ" */
  gen common_dom="Z"
 if strmatch("$my_common","atlanticcod")==1{
-  replace common_dom="COD" if strmatch(sp_code,"8791030402")
+  replace common_dom="C" if strmatch(sp_code,"8791030402")
  }
  
  if strmatch("$my_common","haddock")==1{
-  replace common_dom="HAD" if strmatch(sp_code,"8791031301")
+  replace common_dom="H" if strmatch(sp_code,"8791031301")
  }
 
+
  
 tostring wave, gen(w2)
 tostring year, gen(year2)
@@ -177,6 +178,12 @@ replace l_in_bin=0 if strmatch(common_dom, "Z")==1
 sort year2 area_s w2 strat_id psu_id id_code common_dom
 svyset psu_id [pweight= wp_size], strata(var_id) singleunit(certainty)
 
+/* use unweighted for atlantic cod lengths */
+if "$my_common"=="atlanticcod"{
+	svyset psu_id, strata(var_id) singleunit(certainty)
+}
+
+
  
 local myv l_in_bin
 

From d881b963f3a27a69acda5e3ea7044d93bd7b7277 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:27:25 -0500
Subject: [PATCH 11/17] tidyup

---
 .../annual/cod_haddock_directed_trips_annual.do          | 6 +++---
 .../processing/annual/domain_cod_annual_catch_totals.do  | 6 +++---
 .../annual/domain_haddock_annual_catch_totals.do         | 9 ++++-----
 3 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/annual/cod_haddock_directed_trips_annual.do b/stata_code/data_extraction_processing/processing/annual/cod_haddock_directed_trips_annual.do
index 90dc469..583052b 100644
--- a/stata_code/data_extraction_processing/processing/annual/cod_haddock_directed_trips_annual.do
+++ b/stata_code/data_extraction_processing/processing/annual/cod_haddock_directed_trips_annual.do
@@ -201,10 +201,12 @@ svyset psu_id [pweight= wp_int], strata(var_id) singleunit(certainty)
 preserve
 sort  my_dom_id  year strat_id psu_id id_code
 local myvariables dtrip
-local i=1
+local i=0
 /* total with over(<overvar>) requires a numeric variable */
 
 foreach var of local myvariables{
+	local ++i 
+
 	svy: total `var', over(my_dom_id)
 	
 	mat b`i'=e(b)'
@@ -213,9 +215,7 @@ foreach var of local myvariables{
 	mat sub`i'=vecdiag(V)'
 	mat colnames sub`i'=variance
 
-	local ++i 
 }
-local --i
 sort my_dom_id year 
 duplicates drop my_dom_id, force
 keep my_dom_id year area_s month dom_id
diff --git a/stata_code/data_extraction_processing/processing/annual/domain_cod_annual_catch_totals.do b/stata_code/data_extraction_processing/processing/annual/domain_cod_annual_catch_totals.do
index 84b3fd1..59080a6 100644
--- a/stata_code/data_extraction_processing/processing/annual/domain_cod_annual_catch_totals.do
+++ b/stata_code/data_extraction_processing/processing/annual/domain_cod_annual_catch_totals.do
@@ -133,7 +133,7 @@ svyset psu_id [pweight= wp_catch], strata(var_id) singleunit(certainty)
 
  
 local myvariables tot_cat claim harvest release
-local i=1
+local i=0
 /* total with over(<overvar>) requires a numeric variable
 
 
@@ -141,15 +141,15 @@ local i=1
  */
 
 foreach var of local myvariables{
+	local ++i 
+
 	svy: total `var', over(my_dom_id)
 	
 	mat b`i'=e(b)'
 	mat colnames b`i'=`var'
 	mat V=e(V)
 
-	local ++i 
 }
-local --i
 sort year my_dom_id
 duplicates drop my_dom_id, force
 keep my_dom_id year area_s month common_dom
diff --git a/stata_code/data_extraction_processing/processing/annual/domain_haddock_annual_catch_totals.do b/stata_code/data_extraction_processing/processing/annual/domain_haddock_annual_catch_totals.do
index 2d9fe13..fcfef85 100644
--- a/stata_code/data_extraction_processing/processing/annual/domain_haddock_annual_catch_totals.do
+++ b/stata_code/data_extraction_processing/processing/annual/domain_haddock_annual_catch_totals.do
@@ -15,7 +15,7 @@ local my_common $species2
 
 
 tempfile tl1 cl1
-
+clear
 foreach file in $triplist{
 	append using ${data_raw}/`file'
 }
@@ -81,7 +81,7 @@ replace common=subinstr(lower(common)," ","",.)
 save `cl1'
 
 use `tl1'
-merge 1:m year strat_id psu_id id_code using `cl1', keep(3)
+merge 1:m year wave strat_id psu_id id_code using `cl1', keep(3)
 drop _merge
 /*ONLY keep trips for which there was catch>0 */
 
@@ -138,7 +138,7 @@ svyset psu_id [pweight= wp_catch], strata(var_id) singleunit(certainty)
 
  
 local myvariables tot_cat claim harvest release
-local i=1
+local i=0
 
 
 /* total with over(<overvar>) requires a numeric variable 
@@ -146,15 +146,14 @@ local i=1
 */
 
 foreach var of local myvariables{
+	local ++i 
 	svy: total `var', over(my_dom_id)
 	
 	mat b`i'=e(b)'
 	mat colnames b`i'=`var'
 	mat V=e(V)
 
-	local ++i 
 }
-local --i
 sort year my_dom_id
 duplicates drop my_dom_id, force
 keep my_dom_id year area_s month common_dom

From 8a057aa79c85c74c87b0ad19520d65e584a672ef Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:28:35 -0500
Subject: [PATCH 12/17] add global

---
 .../processing/batch_file_to_process_annual_mrip_data.do         | 1 +
 1 file changed, 1 insertion(+)

diff --git a/stata_code/data_extraction_processing/processing/batch_file_to_process_annual_mrip_data.do b/stata_code/data_extraction_processing/processing/batch_file_to_process_annual_mrip_data.do
index 9a4fb00..2ba3a07 100644
--- a/stata_code/data_extraction_processing/processing/batch_file_to_process_annual_mrip_data.do
+++ b/stata_code/data_extraction_processing/processing/batch_file_to_process_annual_mrip_data.do
@@ -43,6 +43,7 @@ global working_year  2019
 global working_year  2020
 global working_year  2021
 global working_year  2022
+global working_year  2023
 
 local year $working_year
 global wavelist 1 2 3 4 5 6

From 6d5650a5a51e225919830e1f77f3a729a7bf1964 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:29:38 -0500
Subject: [PATCH 13/17] split by open and closed periods

---
 .../b2_length_freqs_by_Open_Close_gom.do      | 243 ++++++++++++++++
 .../domain_cod_Open_Close_catch_totals.do     | 182 ++++++++++++
 .../domain_haddock_Open_Close_catch_totals.do | 184 ++++++++++++
 .../annual/length_freqs_by_Open_Close_gom.do  | 250 +++++++++++++++++
 .../annual/process_b2_cod_OpenClose.do        |  93 +++++++
 .../annual/process_b2_haddock_OpenClose.do    |  94 +++++++
 ...tch_file_to_process_OpenClose_mrip_data.do | 263 ++++++++++++++++++
 7 files changed, 1309 insertions(+)
 create mode 100644 stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_Open_Close_gom.do
 create mode 100644 stata_code/data_extraction_processing/processing/annual/domain_cod_Open_Close_catch_totals.do
 create mode 100644 stata_code/data_extraction_processing/processing/annual/domain_haddock_Open_Close_catch_totals.do
 create mode 100644 stata_code/data_extraction_processing/processing/annual/length_freqs_by_Open_Close_gom.do
 create mode 100644 stata_code/data_extraction_processing/processing/annual/process_b2_cod_OpenClose.do
 create mode 100644 stata_code/data_extraction_processing/processing/annual/process_b2_haddock_OpenClose.do
 create mode 100644 stata_code/data_extraction_processing/processing/batch_file_to_process_OpenClose_mrip_data.do

diff --git a/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_Open_Close_gom.do b/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_Open_Close_gom.do
new file mode 100644
index 0000000..4573ecb
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/b2_length_freqs_by_Open_Close_gom.do
@@ -0,0 +1,243 @@
+/* This is a file that produces a dataset that contains #of fish encountered per trip.
+This is a port of Scott's "cod_domain_length_freqs_by_wave_gom_2013.sas"
+
+This is a template program for estimating length frequencies
+using the MRIP public-use datasets.
+
+The program is setup to use information in the trip_yyyyw
+dataset to define custom domains.  The length frequencies are
+estimated within the domains by merging the trip information onto
+the size_yyyyw datasets.
+
+Required input datasets:
+ trip_yyyyw
+ size_yyyyw
+
+
+It looks like we also need to port cod_domain_length_freqs_b2_by_wave_gom_2013 as well 
+
+There will be one output per variable and year in working directory:
+"$my_common`myv'_b2_OpenClose_$working_year.dta"
+
+
+
+*/
+
+/* General strategy 
+COMPUTE totals and std deviations for cod catch
+
+ */
+ clear
+ mata: mata clear
+
+
+
+
+tempfile tl1 sl1
+
+foreach file in $triplist{
+	append using ${data_raw}/`file'
+}
+capture drop $drop_conditional
+
+
+replace var_id=strat_id if strmatch(var_id,"")
+sort year strat_id psu_id id_code
+/*  Deal with new variable names in the transition period  
+
+  */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+}
+save `tl1'
+clear
+
+
+foreach file in $b2list{
+	append using ${data_raw}/`file'
+}
+cap drop $drop_conditional
+/*  Deal with new variable names in the transition period    */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+
+}
+
+	capture confirm variable wp_catch_chts
+	if _rc==0{
+		drop wp_catch
+		rename wp_catch_chts wp_catch
+		else{
+		}
+
+}
+
+sort year strat_id psu_id id_code
+replace common=subinstr(lower(common)," ","",.)
+save `sl1'
+
+use `tl1'
+merge 1:m year strat_id psu_id id_code using `sl1', keep(1 3)
+drop _merge
+keep if year==$working_year
+/* THIS IS THE END OF THE DATA MERGING CODE */
+
+
+ /* ensure that domain is sub_reg=4 (New England), relevant states (MA, NH, ME), mode_fx =123, 457 */
+ keep if sub_reg==4
+ keep if st==23 | st==33 |st==25
+
+/*This is the "full" mrip data */
+tempfile tc1
+save `tc1'
+
+/*classify as GOM or GB based on the ma_site_allocation.dta file */
+rename intsite site_id
+sort site_id
+
+
+merge m:1 site_id using "${data_raw}/ma_site_allocation.dta", keepusing(stock_region_calc)
+rename  site_id intsite
+drop if _merge==2
+drop _merge
+
+/*classify into GOM or GBS */
+gen str3 area_s="OTH"
+
+replace area_s="GOM" if st==23 | st==33
+replace area_s="GOM" if st==25 & strmatch(stock_region_calc,"NORTH")
+replace area_s="GBS" if st==25 & strmatch(stock_region_calc,"SOUTH")
+
+ /* classify catch into the things I care about (common==$mycommon) and things I don't care about "ZZZZZZZZ" */
+ gen common_dom="Z"
+if strmatch("$my_common","atlanticcod")==1{
+  replace common_dom="C" if strmatch(sp_code,"8791030402")
+ }
+ 
+ if strmatch("$my_common","haddock")==1{
+  replace common_dom="H" if strmatch(sp_code,"8791031301")
+ }
+
+ 
+
+ 
+tostring wave, gen(w2)
+tostring year, gen(year2)
+
+destring month, gen(mymo)
+drop month
+tostring mymo, gen(month)
+drop mymo
+
+tostring year, gen(myy)
+
+
+
+
+/* l_in_bin already defined
+gen l_in_bin=floor(lngth*0.03937) */
+
+/* this might speed things up if I re-classify all length=0 for the species I don't care about */
+replace l_in_bin=0 if strmatch(common_dom, "Z")==1
+
+
+sort year w2 strat_id psu_id id_code
+
+
+/* use unweighted for atlantic cod lengths */
+if "$my_common"=="atlanticcod"{
+	svyset psu_id, strata(var_id) singleunit(certainty)
+	gen open=inlist(month,"9","10")
+
+}
+if "$my_common"=="haddock"{
+	svyset psu_id [pweight= wp_size], strata(var_id) singleunit(certainty)
+	gen open=!inlist(month,"3")
+
+}
+
+tostring open, gen(myo)
+
+gen my_dom_id_string=common_dom+"_"+area_s+"_"+myo
+
+ 
+ 
+local myv l_in_bin
+
+	svy: tab `myv' my_dom_id_string, count
+	/*save some stuff  
+	matrix of proportions, row names, column names, estimate of total population size*/
+	mat eP=e(Prop)
+	mat eR=e(Row)'
+	mat eC=e(Col)
+	local PopN=e(N_pop)
+
+	local mycolnames: colnames(eC)
+	mat colnames eP=`mycolnames'
+	
+	clear
+	/*read the eP into a dataset and convert proportion of population into numbers*/
+	svmat eP, names(col)
+	foreach var of varlist *{
+		replace `var'=`var'*`PopN'
+	}
+	/*read in the "row" */
+	svmat eR
+	order eR
+	rename eR `myv'
+	
+
+	
+	keep `myv' *GOM*
+	drop *Z_*
+	gen year=$working_year
+	
+	
+	qui desc
+	
+	foreach var of varlist *GOM*{
+	tokenize `var', parse("_")
+	rename `var' `3'_`5'
+	}
+	reshape long GOM_, i(year l_in_bin) j(oo)
+	rename GOM_ count
+	gen str6 open="OPEN" if oo==1
+	replace open="CLOSED" if oo==0
+	
+	sort year open l_in_bin
+	order year open l_in_bin
+	drop oo
+	
+		
+	save "$my_outputdir/$my_common`myv'_b2_OpenClose_${working_year}.dta", replace
+
+
+
+
+
+
+
diff --git a/stata_code/data_extraction_processing/processing/annual/domain_cod_Open_Close_catch_totals.do b/stata_code/data_extraction_processing/processing/annual/domain_cod_Open_Close_catch_totals.do
new file mode 100644
index 0000000..099d3ab
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/domain_cod_Open_Close_catch_totals.do
@@ -0,0 +1,182 @@
+/* This is a file that produces data on a, b1, b2, and other top-level catch statistics by wave
+
+This is a port of Scott's sas code
+
+*/
+version 12.1
+
+/* General strategy 
+COMPUTE totals and std deviations for cod catch
+
+ */
+ mata: mata clear
+
+local my_common $species1
+tempfile tl1 cl1
+
+clear
+foreach file in $triplist{
+	append using ${data_raw}/`file'
+}
+capture drop $drop_conditional
+
+sort year strat_id psu_id id_code
+/*  Deal with new variable names in the transition period  
+
+  */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+}
+save `tl1'
+
+clear
+
+foreach file in $catchlist{
+	append using ${data_raw}/`file'
+}
+cap drop $drop_conditional
+replace var_id=strat_id if strmatch(var_id,"")
+replace wp_catch=wp_int if wp_catch==.
+/*  Deal with new variable names in the transition period    */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+
+}
+
+	capture confirm variable wp_catch_chts
+	if _rc==0{
+		drop wp_catch
+		rename wp_catch_chts wp_catch
+		else{
+		}
+
+}
+sort year strat_id psu_id id_code
+replace common=subinstr(lower(common)," ","",.)
+save `cl1'
+use `tl1'
+merge 1:m year wave strat_id psu_id id_code using `cl1', keep(3)
+drop _merge
+
+/* THIS IS THE END OF THE DATA MERGING CODE */
+
+
+/* ensure that domain is sub_reg=4 (New England), relevant states (MA, NH, ME), mode_fx =123, 457 */
+* keep if inlist(sub_reg,4,5)
+* keep if st==23 | st==33 |st==25
+
+/*This is the "full" mrip data */
+tempfile tc1
+save `tc1'
+
+/*classify as GOM or GB based on the ma_site_allocation.dta file */
+rename intsite site_id
+sort site_id
+
+
+merge m:1 site_id using "${data_raw}/ma_site_allocation.dta", keepusing(stock_region_calc)
+rename  site_id intsite
+drop if _merge==2
+drop _merge
+
+/*classify into GOM or GBS */
+gen str3 area_s="OTH"
+
+replace area_s="GBS" if  inlist(sub_reg,5 ,6 ,7) | inlist(st,9, 44)
+replace area_s="GOM" if st==23 | st==33
+replace area_s="GOM" if st==25 & strmatch(stock_region_calc,"NORTH")
+replace area_s="GBS" if st==25 & strmatch(stock_region_calc,"SOUTH")
+
+ /* classify catch into the things I care about (common==$mycommon) and things I don't care about "ZZZZZZZZ" */
+ gen common_dom="zzzzzz"
+ replace common_dom=common if strmatch(common, "`my_common'") 
+ 
+ 
+tostring wave, gen(w2)
+tostring year, gen(year2)
+tostring year, gen(myy)
+
+
+
+gen open=inlist(month,"09","10")
+tostring open, gen(myo)
+
+gen my_dom_id_string=year2+"_"+myo+"_"+area_s+"_"+myy+"_"+common_dom
+
+replace my_dom_id_string=ltrim(rtrim(my_dom_id_string))
+encode my_dom_id_string, gen(my_dom_id)
+replace wp_catch=0 if wp_catch<=0
+sort year my_dom_id
+
+
+
+svyset psu_id [pweight= wp_catch], strata(var_id) singleunit(certainty)
+
+ 
+local myvariables tot_cat claim harvest release
+local i=0
+/* total with over(<overvar>) requires a numeric variable
+
+
+
+ */
+
+foreach var of local myvariables{
+	local ++i 
+
+	svy: total `var', over(my_dom_id)
+	
+	mat b`i'=e(b)'
+	mat colnames b`i'=`var'
+	mat V=e(V)
+
+}
+sort year my_dom_id
+duplicates drop my_dom_id, force
+keep my_dom_id year area_s month common_dom
+
+foreach j of numlist 1/`i'{
+	svmat b`j', names(col)
+}
+
+drop if strmatch(common_dom,"zzzzzz")
+keep if strmatch(area_s,"GOM")
+sort year area_s month common_dom
+drop month
+decode my_dom_id, gen(my_dom_id_string)
+split my_dom_id_string, gen(stub) parse("_")
+
+
+	gen str6 open="OPEN" if stub2=="1"
+	replace open="CLOSED" if stub2=="0"
+	drop stub*
+
+
+save "$my_outputdir/`my_common'_catch_OpenClose_$working_year.dta", replace
+
+
+
diff --git a/stata_code/data_extraction_processing/processing/annual/domain_haddock_Open_Close_catch_totals.do b/stata_code/data_extraction_processing/processing/annual/domain_haddock_Open_Close_catch_totals.do
new file mode 100644
index 0000000..5f9f09d
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/domain_haddock_Open_Close_catch_totals.do
@@ -0,0 +1,184 @@
+/* This is a file that produces data on a, b1, b2, and other top-level catch statistics by wave
+
+This is a port of Scott's sas code
+
+*/
+version 12.1
+
+/* General strategy 
+COMPUTE totals and std deviations for cod catch
+
+ */
+ mata: mata clear
+
+local my_common $species2
+
+
+tempfile tl1 cl1
+
+clear
+foreach file in $triplist{
+	append using ${data_raw}/`file'
+}
+capture drop $drop_conditional
+
+sort year strat_id psu_id id_code
+/*  Deal with new variable names in the transition period  
+
+  */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+}
+save `tl1'
+clear
+
+
+foreach file in $catchlist{
+	append using ${data_raw}/`file'
+}
+cap drop $drop_conditional
+replace var_id=strat_id if strmatch(var_id,"")
+replace wp_catch=wp_int if wp_catch==.
+/*  Deal with new variable names in the transition period    */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+
+}
+
+	capture confirm variable wp_catch_chts
+	if _rc==0{
+		drop wp_catch
+		rename wp_catch_chts wp_catch
+		else{
+		}
+
+}
+sort year strat_id psu_id id_code
+replace common=subinstr(lower(common)," ","",.)
+save `cl1'
+
+use `tl1'
+merge 1:m year wave strat_id psu_id id_code using `cl1', keep(3)
+drop _merge
+/*ONLY keep trips for which there was catch>0 */
+
+
+/* THIS IS THE END OF THE DATA MERGING CODE */
+
+
+/* ensure that domain is sub_reg=4 (New England), relevant states (MA, NH, ME), mode_fx =123, 457 */
+* keep if inlist(sub_reg,4,5)
+* keep if st==23 | st==33 |st==25
+
+/*This is the "full" mrip data */
+tempfile tc1
+save `tc1'
+
+/*classify as GOM or GB based on the ma_site_allocation.dta file */
+rename intsite site_id
+sort site_id
+
+
+merge m:1 site_id using "${data_raw}/ma_site_allocation.dta", keepusing(stock_region_calc)
+rename  site_id intsite
+drop if _merge==2
+drop _merge
+
+/*classify into GOM or GBS */
+gen str3 area_s="OTH"
+
+replace area_s="GBS" if  inlist(sub_reg,5 ,6 ,7) | inlist(st,9, 44)
+replace area_s="GOM" if st==23 | st==33
+replace area_s="GOM" if st==25 & strmatch(stock_region_calc,"NORTH")
+replace area_s="GBS" if st==25 & strmatch(stock_region_calc,"SOUTH")
+
+ /* classify catch into the things I care about (common==$mycommon) and things I don't care about "ZZZZZZZZ" */
+ gen common_dom="zzzzzz"
+ replace common_dom=common if strmatch(common, "`my_common'") 
+ 
+ 
+tostring wave, gen(w2)
+tostring year, gen(year2)
+tostring year, gen(myy)
+
+
+
+gen open=!inlist(month,"03")
+tostring open, gen(myo)
+
+gen my_dom_id_string=year2+"_"+myo+"_"+area_s+"_"+myy+"_"+common_dom
+
+replace my_dom_id_string=ltrim(rtrim(my_dom_id_string))
+encode my_dom_id_string, gen(my_dom_id)
+replace wp_catch=0 if wp_catch<=0
+sort year my_dom_id
+svyset psu_id [pweight= wp_int], strata(strat_id) singleunit(certainty)
+/*svyset psu_id [pweight= wp_int], strata(strat_id) singleunit(certainty) */
+
+
+svyset psu_id [pweight= wp_catch], strata(var_id) singleunit(certainty)
+
+ 
+local myvariables tot_cat claim harvest release
+local i=0
+
+
+/* total with over(<overvar>) requires a numeric variable 
+
+*/
+
+foreach var of local myvariables{
+	local ++i 
+	svy: total `var', over(my_dom_id)
+	
+	mat b`i'=e(b)'
+	mat colnames b`i'=`var'
+	mat V=e(V)
+
+}
+sort year my_dom_id
+duplicates drop my_dom_id, force
+keep my_dom_id year area_s month common_dom
+
+foreach j of numlist 1/`i'{
+	svmat b`j', names(col)
+}
+
+drop if strmatch(common_dom,"zzzzzz")
+keep if strmatch(area_s,"GOM")
+sort year area_s month common_dom
+drop month
+decode my_dom_id, gen(my_dom_id_string)
+split my_dom_id_string, gen(stub) parse("_")
+
+
+	gen str6 open="OPEN" if stub2=="1"
+	replace open="CLOSED" if stub2=="0"
+	drop stub*
+
+
+save "$my_outputdir/`my_common'_catch_OpenClose_$working_year.dta", replace
diff --git a/stata_code/data_extraction_processing/processing/annual/length_freqs_by_Open_Close_gom.do b/stata_code/data_extraction_processing/processing/annual/length_freqs_by_Open_Close_gom.do
new file mode 100644
index 0000000..2ccb2d9
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/length_freqs_by_Open_Close_gom.do
@@ -0,0 +1,250 @@
+ /* This is a file that produces a dataset that contains #of fish encountered per trip.
+This is a port of Scott's "cod_domain_length_freqs_by_wave_gom_2013.sas"
+
+This is a template program for estimating length frequencies
+using the MRIP public-use datasets.
+
+The program is setup to use information in the trip_yyyyw
+dataset to define custom domains.  The length frequencies are
+estimated within the domains by merging the trip information onto
+the size_yyyyw datasets.
+
+Required input datasets:
+ trip_yyyyw
+ size_yyyyw
+
+
+It looks like we also need to port cod_domain_length_freqs_b2_by_wave_gom_2013 as well 
+
+There will be one output per variable and year in working directory:
+"$my_common`myv'_a1b1$working_year.dta"
+
+
+
+*/
+
+/* General strategy 
+COMPUTE totals and std deviations for cod catch
+
+ */
+ clear
+
+ mata: mata clear
+
+tempfile tl1 sl1
+
+foreach file in $triplist{
+	append using ${data_raw}/`file'
+}
+capture drop $drop_conditional
+
+replace var_id=strat_id if strmatch(var_id,"")
+sort year strat_id psu_id id_code
+/*  Deal with new variable names in the transition period  
+
+  */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+}
+save `tl1'
+clear
+
+ 
+foreach file in $sizelist{
+	append using ${data_raw}/`file'
+}
+cap drop $drop_conditional
+/*  Deal with new variable names in the transition period    */
+
+	capture confirm variable wp_int_chts
+	if _rc==0{
+		drop wp_int
+		rename wp_int_chts wp_int
+		else{
+		}
+}
+	capture confirm variable wp_size_chts
+	if _rc==0{
+		drop wp_size
+		rename wp_size_chts wp_size
+		else{
+		}
+
+}
+
+	capture confirm variable wp_catch_chts
+	if _rc==0{
+		drop wp_catch
+		rename wp_catch_chts wp_catch
+		else{
+		}
+
+}
+
+sort year strat_id psu_id id_code
+replace var_id=strat_id if strmatch(var_id,"")
+
+replace common=subinstr(lower(common)," ","",.)
+save `sl1'
+
+use `tl1'
+merge 1:m year strat_id psu_id id_code using `sl1', keep(1 3)
+drop _merge
+keep if year==$working_year
+/* THIS IS THE END OF THE DATA MERGING CODE */
+
+
+ /* ensure that domain is sub_reg=4 (New England), relevant states (MA, NH, ME), mode_fx =123, 457 */
+ keep if sub_reg==4
+ keep if st==23 | st==33 |st==25
+
+/*This is the "full" mrip data */
+tempfile tc1
+save `tc1'
+
+/*classify as GOM or GB based on the ma_site_allocation.dta file */
+rename intsite site_id
+sort site_id
+
+
+merge m:1 site_id using "${data_raw}/ma_site_allocation.dta", keepusing(stock_region_calc)
+rename  site_id intsite
+drop if _merge==2
+drop _merge
+
+/*classify into GOM or GBS */
+gen str3 area_s="OTH"
+
+replace area_s="GOM" if st==23 | st==33
+replace area_s="GOM" if st==25 & strmatch(stock_region_calc,"NORTH")
+replace area_s="GBS" if st==25 & strmatch(stock_region_calc,"SOUTH")
+
+ /* classify catch into the things I care about (common==$mycommon) and things I don't care about "ZZZZZZZZ" */
+ gen common_dom="Z"
+if strmatch("$my_common","atlanticcod")==1{
+  replace common_dom="C" if strmatch(sp_code,"8791030402")
+ }
+ 
+ if strmatch("$my_common","haddock")==1{
+  replace common_dom="H" if strmatch(sp_code,"8791031301")
+ }
+
+ 
+
+ 
+tostring wave, gen(w2)
+tostring year, gen(year2)
+
+destring month, gen(mymo)
+drop month
+tostring mymo, gen(month)
+drop mymo
+
+tostring year, gen(myy)
+
+
+
+
+/* l_in_bin already defined
+gen l_in_bin=floor(lngth*0.03937) */
+
+/* this might speed things up if I re-classify all length=0 for the species I don't care about */
+replace l_in_bin=0 if strmatch(common_dom, "Z")==1
+
+
+sort year w2 strat_id psu_id id_code
+
+
+
+
+
+
+pause
+
+
+
+
+/* use unweighted for atlantic cod lengths */
+if "$my_common"=="atlanticcod"{
+	svyset psu_id, strata(var_id) singleunit(certainty)
+	gen open=inlist(month,"9","10")
+
+}
+if "$my_common"=="haddock"{
+	svyset psu_id [pweight= wp_size], strata(var_id) singleunit(certainty)
+	gen open=!inlist(month,"3")
+
+}
+
+tostring open, gen(myo)
+
+gen my_dom_id_string=common_dom+"_"+area_s+"_"+myo
+
+ 
+ 
+local myv l_in_bin
+
+	svy: tab `myv' my_dom_id_string, count
+	/*save some stuff  
+	matrix of proportions, row names, column names, estimate of total population size*/
+	mat eP=e(Prop)
+	mat eR=e(Row)'
+	mat eC=e(Col)
+	local PopN=e(N_pop)
+
+	local mycolnames: colnames(eC)
+	mat colnames eP=`mycolnames'
+	
+	clear
+	/*read the eP into a dataset and convert proportion of population into numbers*/
+	svmat eP, names(col)
+	foreach var of varlist *{
+		replace `var'=`var'*`PopN'
+	}
+	/*read in the "row" */
+	svmat eR
+	order eR
+	rename eR `myv'
+	
+
+	
+	keep `myv' *GOM*
+	drop *Z_*
+	gen year=$working_year
+	
+	
+	qui desc
+	
+	foreach var of varlist *GOM*{
+	tokenize `var', parse("_")
+	rename `var' `3'_`5'
+	}
+	reshape long GOM_, i(year l_in_bin) j(oo)
+	rename GOM_ count
+	gen str6 open="OPEN" if oo==1
+	replace open="CLOSED" if oo==0
+	
+	sort year open l_in_bin
+	order year open l_in_bin
+	drop oo
+	
+		
+	save "$my_outputdir/$my_common`myv'_a1b1_OpenClose_${working_year}.dta", replace
+
+clear
+
+
+
+
diff --git a/stata_code/data_extraction_processing/processing/annual/process_b2_cod_OpenClose.do b/stata_code/data_extraction_processing/processing/annual/process_b2_cod_OpenClose.do
new file mode 100644
index 0000000..0040ccd
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/process_b2_cod_OpenClose.do
@@ -0,0 +1,93 @@
+
+
+/* in order to get the right distribution of lengths, you have to multiply the B2 length proportions by the number of B2's in each year.  You have to multiply the A+B1 length proportions by the number of A+B1's in a year.
+
+Then you have to add these up. 
+*/
+
+
+/* process the b2 cod */
+use  "$my_outputdir/atlanticcod_landings_OpenClose_$working_year.dta", clear
+gen ab1=landings
+keep year open ab1
+tempfile claim_harvest
+sort year 
+save `claim_harvest'
+
+use "$my_outputdir/atlanticcod_landings_OpenClose_$working_year.dta", clear
+rename b2 release
+keep year open release
+tempfile cm
+sort year 
+save `cm'
+
+
+
+use "$my_outputdir/cod_b2_OpenClose_$working_year.dta", clear
+
+sort year 
+merge m:1 year open using `cm'
+replace release=0 if release==.
+drop _merge
+
+
+tempvar tt
+bysort year open : egen `tt'=total(count)
+gen prob=count/`tt'
+
+gen b2_count=prob*release
+
+keep year open l_in_bin b2_count
+
+sort year open l_in_bin
+/* save */
+save "$my_outputdir/atlanticcod_b2_counts_OpenClose_$working_year.dta", replace
+
+
+
+
+use "$my_outputdir/cod_ab1_OpenClose_$working_year.dta", clear
+
+
+sort year 
+
+cap drop _merge
+merge m:1 year open using `claim_harvest'
+
+
+tempvar ttt
+bysort year open : egen `ttt'=total(count)
+gen prob=count/`ttt'
+
+gen ab1_count=prob*ab1
+
+keep year open l_in_bin ab1_count
+
+sort year open  l_in_bin
+
+merge 1:1 year open l_in_bin using  "$my_outputdir/atlanticcod_b2_counts_OpenClose_$working_year.dta"
+replace ab1_count=0 if ab1_count==.
+replace b2_count=0 if b2_count==.
+gen countnumbersoffish=round(ab1_count+b2_count)
+tempfile tth1
+save `tth1'
+
+keep year open l_in_bin countnumbersoffish ab1_count b2_count
+ 
+rename l_in_bin lngcatinches
+sort year open lngcatinches
+
+label var lngcatinches "length in inches"
+
+
+
+save "$my_outputdir/cod_size_class_OpenClose_$working_year.dta", replace
+
+/* compute the numbers of sub-legal fish retained
+use `tt1', clear
+keep year  l_in_bin ab1_count countnumbers
+
+save "$my_outputdir/cod_sublegals_annual_$working_year.dta", replace */
+
+
+
diff --git a/stata_code/data_extraction_processing/processing/annual/process_b2_haddock_OpenClose.do b/stata_code/data_extraction_processing/processing/annual/process_b2_haddock_OpenClose.do
new file mode 100644
index 0000000..4e82c65
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/process_b2_haddock_OpenClose.do
@@ -0,0 +1,94 @@
+
+
+/* in order to get the right distribution of lengths, you have to multiply the B2 length proportions by the number of B2's in each year.  You have to multiply the A+B1 length proportions by the number of A+B1's in a year.
+
+Then you have to add these up. 
+*/
+
+
+/* process the b2 haddock */
+use  "$my_outputdir/haddock_landings_OpenClose_$working_year.dta", clear
+gen ab1=landings
+keep year open ab1
+tempfile claim_harvest
+sort year 
+save `claim_harvest'
+
+use  "$my_outputdir/haddock_landings_OpenClose_$working_year.dta", clear
+rename b2 release
+keep year open release
+tempfile cm
+sort year 
+save `cm'
+
+use "$my_outputdir/haddock_b2_OpenClose_$working_year.dta", clear
+
+
+sort year 
+merge m:1 year open using `cm'
+replace release=0 if release==.
+drop _merge
+
+
+tempvar tt
+bysort year open : egen `tt'=total(count)
+gen prob=count/`tt'
+
+gen b2_count=prob*release
+
+keep year open l_in_bin b2_count
+
+sort year open l_in_bin
+/* save */
+save  "$my_outputdir/haddock_b2_counts_OpenClose_$working_year.dta", replace
+
+
+
+
+use  "$my_outputdir/haddock_ab1_OpenClose_$working_year.dta", clear
+
+
+sort year 
+
+cap drop _merge
+merge m:1 year open using `claim_harvest'
+
+
+tempvar ttt
+bysort year open : egen `ttt'=total(count)
+gen prob=count/`ttt'
+
+gen ab1_count=prob*ab1
+
+keep year open l_in_bin ab1_count
+
+sort year open  l_in_bin
+
+merge 1:1 year open l_in_bin using  "$my_outputdir/haddock_b2_counts_OpenClose_$working_year.dta"
+replace ab1_count=0 if ab1_count==.
+replace b2_count=0 if b2_count==.
+gen countnumbersoffish=round(ab1_count+b2_count)
+tempfile tth1
+save `tth1'
+
+keep year open l_in_bin countnumbersoffish ab1_count b2_count
+ 
+rename l_in_bin lngcatinches
+sort year open lngcatinches
+
+label var lngcatinches "length in inches"
+
+save  "$my_outputdir/haddock_size_class_OpenClose_$working_year.dta", replace
+
+
+/* compute the numbers of sub-legal fish retained
+use `tth1', clear
+keep year  l_in_bin ab1_count countnumbers
+
+save  "$my_outputdir/haddock_sublegals_annual_$working_year.dta", replace */
+
+
+
+
+
+
diff --git a/stata_code/data_extraction_processing/processing/batch_file_to_process_OpenClose_mrip_data.do b/stata_code/data_extraction_processing/processing/batch_file_to_process_OpenClose_mrip_data.do
new file mode 100644
index 0000000..615d0a0
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/batch_file_to_process_OpenClose_mrip_data.do
@@ -0,0 +1,263 @@
+/* 
+This probably isn't doing everything we need it to do
+
+Need to read in the 2b95 landings.  Doesn't loop over years
+
+we probably won' use this anymore
+
+
+
+
+This is just a little helper file that calls all the yearly files and stacks the wave-level data into single datasets 
+It also aggregates everything into the proper format for the recreational bioeconomic model 
+It's quite awesome.
+
+
+Running survey commands on multiple years takes a very long time. 
+
+In order to do a data update, you will need to:
+
+1. run the copy_over_raw_mrip.do to copy and convert the sas7bdat files to dta. 
+
+2. Run get_ma_allocation to get Recreation sites for MA (NORTH SOUTH) and 
+
+3. Change the working year to the most recent year.
+
+	CHECK for missing waves in the "ab1_lengths", catch totals, catch frequencies.
+ */
+
+ 
+global my_outputdir "${data_main}/MRIP_$vintage_string/annual"
+capture mkdir "$my_outputdir"
+ 
+/*Set up the catchlist, triplist, and b2list global macros. These hold the filenames that are needed to figure out the catch, length-frequency, trips, and other things.*/
+
+
+
+/********************************************************************************/
+/********************************************************************************/
+/* Use these to control the years and species for which the MRIP data is polled/queried*/
+/********************************************************************************/
+/********************************************************************************/
+global working_year  2019
+global working_year  2020
+global working_year  2021
+global working_year  2022
+global working_year  2023
+
+local year $working_year
+global wavelist 1 2 3 4 5 6
+global species1 "atlanticcod"
+global species2 "haddock"
+/*this is dumb, but I'm too lazy to replace everything that referred to these local/globals */
+
+
+
+/*catchlist -- this assembles then names of files that are needed in the catchlist */
+/*Check to see if the file exists */	/* If the file exists, add the filename to the list if there are observations */
+
+
+global catchlist: dir "${data_raw}" files "catch_$working_year*.dta" 
+global triplist: dir "${data_raw}" files "trip_$working_year*.dta" 
+global b2list: dir "${data_raw}" files "size_b2_$working_year*.dta" 
+global sizelist: dir "${data_raw}" files "size_$working_year*.dta" 
+
+
+/* catch frequencies per trip*/
+
+/* need to drop 
+id_code=="1757420210428005" from the sizelist, triplist, and catchlist. This is a trip that took place inshore in 2020 that caught 2 fish that were probably not cod
+
+
+id_code="1792820210410001" should be dropped from the triplist catchlist when computing targeted trips. 
+	
+no changes to triplist or b2list
+
+The syntax will be to set up a global and then do 
+cap drop $drop_conditional after loading in the catchlist or sizelist files
+
+		If we don't need to drop anything, the capture will swallow the error term.
+		And if we do, the code will drop the appropriate rows.
+*/
+
+global drop_conditional 
+
+
+/* catch totals  -- these are done for all 3 years at once*/
+
+global my_common "atlanticcod"
+
+	
+	if "$my_common"=="atlanticcod"{
+	   global drop_conditional `"if id_code=="1757420210428005"  "'
+	}
+	else {
+    global drop_conditional 
+	}
+
+do "${processing_code}/annual/domain_cod_Open_Close_catch_totals.do"
+
+use "$my_outputdir/atlanticcod_catch_OpenClose_$working_year.dta", clear
+keep year open tot_cat claim harvest release
+rename claim a
+rename harvest b1
+rename release b2
+rename tot_cat tot_catch
+gen landings=a+b1
+save "$my_outputdir/atlanticcod_landings_OpenClose_$working_year.dta", replace
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+global my_common "haddock"
+	
+	if "$my_common"=="atlanticcod"{
+	   global drop_conditional `"if id_code=="1757420210428005"  "'
+	}
+	else {
+    global drop_conditional 
+	}
+
+
+do "${processing_code}/annual/domain_haddock_Open_Close_catch_totals.do"
+
+
+use "$my_outputdir/haddock_catch_OpenClose_$working_year.dta", clear
+keep year open tot_cat claim harvest release
+rename claim a
+rename harvest b1
+rename release b2
+rename tot_cat tot_catch
+gen landings=a+b1
+save "$my_outputdir/haddock_landings_OpenClose_$working_year.dta", replace
+
+
+
+
+
+clear
+
+/* length frequencies */
+
+
+
+foreach sp in atlanticcod haddock{
+	global my_common `sp'
+	
+		
+	if "$my_common"=="atlanticcod"{
+	   global drop_conditional `"if id_code=="1757420210428005"  "'
+	}
+	else {
+    global drop_conditional 
+	}
+
+
+	do "${processing_code}/annual/length_freqs_by_Open_Close_gom.do"
+
+	clear
+}
+
+/*stack together multiple, cleanup extras and delete */
+local cod_wave_ab1: dir "$my_outputdir" files "atlanticcodl_in_bin_a1b1_OpenClose*.dta"
+
+foreach file of local cod_wave_ab1{
+	clear
+	append using ${my_outputdir}/`file'
+	! rm ${my_outputdir}/`file'
+}
+save "$my_outputdir/cod_ab1_OpenClose_$working_year.dta", replace
+
+
+/*stack together multiple, cleanup extras and delete */
+local haddock_wave_ab1: dir "$my_outputdir" files "haddockl_in_bin_a1b1_OpenClose*.dta"
+
+foreach file of local haddock_wave_ab1{
+	clear
+
+	append using ${my_outputdir}/`file'
+	! rm ${my_outputdir}/`file'
+}
+save "$my_outputdir/haddock_ab1_OpenClose_$working_year.dta", replace
+
+
+/* B2 length frequencies per wave*/
+foreach sp in atlanticcod haddock{
+	global my_common `sp'
+	
+		
+	if "$my_common"=="atlanticcod"{
+	   global drop_conditional `"if id_code=="1757420210428005"  "'
+	}
+	else {
+    global drop_conditional 
+	}
+
+
+	do "${processing_code}/annual/b2_length_freqs_by_Open_Close_gom.do"
+
+	
+}
+
+/*stack these into a single dataset */
+clear
+local cod_wave_b2: dir "$my_outputdir" files "atlanticcodl_in_bin_b2_OpenClose*.dta"
+local haddock_wave_b2: dir "$my_outputdir" files "haddockl_in_bin_b2_OpenClose*.dta"
+
+clear
+foreach file of local cod_wave_b2{
+	
+	append using ${my_outputdir}/`file'
+	! rm ${my_outputdir}/`file'
+}
+
+
+save "$my_outputdir/cod_b2_OpenClose_$working_year.dta", replace
+	clear
+foreach file of local haddock_wave_b2{
+
+	append using ${my_outputdir}/`file'
+	! rm ${my_outputdir}/`file'
+}
+
+save "$my_outputdir/haddock_b2_OpenClose_$working_year.dta", replace
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+/*need to edit both of these to point to "annual" data files
+I think the haddock one wokrs, just need to pull over the changes to the cod one.
+*/
+/* join the b2 length data with the total number of released to get the length distribution for the number of fish released */
+
+do "${processing_code}/annual/process_b2_haddock_OpenClose.do"
+do "${processing_code}/annual/process_b2_cod_OpenClose.do"
+
+
+
+
+global drop_conditional `"if id_code=="1792820210410001"  "'

From 453ab54a5384b1323a4e8e447ce6aafeb843b8e3 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:30:21 -0500
Subject: [PATCH 14/17] add OpenClose to wrapper

---
 .../processing/process_wrapper.do             | 21 ++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/process_wrapper.do b/stata_code/data_extraction_processing/processing/process_wrapper.do
index 56cc0af..a6ebdf3 100644
--- a/stata_code/data_extraction_processing/processing/process_wrapper.do
+++ b/stata_code/data_extraction_processing/processing/process_wrapper.do
@@ -30,9 +30,7 @@ global BLAST_DIR "${BLAST_root}/cod_haddock_fy2024/source_data/mrip"
 
 
 
-/*this computes calendar year estimates, which you don't really use
-do "$processing_code/batch_file_to_process_annual_mrip_data.do"
- */
+
  
  
 /*this computes monthly estimates*/
@@ -66,6 +64,23 @@ do "$processing_code/monthly/joint_catch_frequencies.do"
 
 /* Write to a html file.*/
 
+
+
+/*this computes calendar year estimates, which you don't really use */
+do "$processing_code/batch_file_to_process_annual_mrip_data.do"
+
+
+
+
+/*this computes calendar year estimates, which you don't really use */
+do "$processing_code/batch_file_to_process_OpenClose_mrip_data.do"
+
+
+
+
+
+
+
 global this_working_year 2023
 dyndoc "$processing_code/catch_summaries.txt", saving($my_results/catch_summaries_${this_working_year}.html) replace
 

From bd3d931c888ce5487a01cafdcddd6293485d55c6 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 15:30:36 -0500
Subject: [PATCH 15/17] re-extract ma site allocaiton

---
 stata_code/data_extraction_processing/extraction_wrapper.do | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stata_code/data_extraction_processing/extraction_wrapper.do b/stata_code/data_extraction_processing/extraction_wrapper.do
index 897ede3..7929201 100644
--- a/stata_code/data_extraction_processing/extraction_wrapper.do
+++ b/stata_code/data_extraction_processing/extraction_wrapper.do
@@ -1,7 +1,7 @@
 /* after running do $BLAST_MRIP */
 /* get the mass location data from oracle */
 
-*do ${extraction_code}/get_ma_allocation.do
+do ${extraction_code}/get_ma_allocation.do
 
 
 /* copying over partial years of data */

From e958cc271fcf5a4823498960648b9cefb72b41b4 Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 16:20:01 -0500
Subject: [PATCH 16/17] compute weights iwith the open-close length
 distributions

---
 .../annual/cod_weights_using_OpenClose.do     | 80 +++++++++++++++++++
 .../processing/catch_summaries.txt            | 76 ++----------------
 .../processing/process_wrapper.do             | 16 ++++
 3 files changed, 102 insertions(+), 70 deletions(-)
 create mode 100644 stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do

diff --git a/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do b/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do
new file mode 100644
index 0000000..3923925
--- /dev/null
+++ b/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do
@@ -0,0 +1,80 @@
+
+
+global cod_lwa 0.000005132
+global cod_lwb 3.1625
+global had_lwa 0.000009298
+global had_lwe 3.0205
+global lngcat_offset_cod 0.5
+global lngcat_offset_haddock 0.5
+global mt_to_kilo=1000
+global kilo_to_lbs=2.20462262
+global cm_to_inch=0.39370787
+global mortality_release=0.15
+
+
+
+
+
+use "$my_outputdir/cod_size_class_OpenClose_$this_working_year.dta" if open=="OPEN", clear
+expand 2 , gen(mark)
+gen month=9
+replace month=10 if mark==1
+
+drop mark
+tempfile open
+save `open'
+
+
+use "$my_outputdir/cod_size_class_OpenClose_$this_working_year.dta" if open=="CLOSED", clear
+expand 12
+bysort year open lngcat: gen month=_n
+drop if inlist(month,9,10)
+
+append using `open'
+
+drop count
+bysort year month open: egen tab1=total(ab1_count)
+bysort year month open: egen tb2=total(b2_count)
+
+gen prob_ab1=ab1_count/tab1
+gen prob_b2=b2_count/tb2
+
+
+keep year month open lngcat prob*
+
+tempfile lengths
+save `lengths', replace
+
+
+use "${monthlydir}\atlanticcod_catch_$this_working_year.dta", clear
+gen ab1=claim+harvest
+rename release b2
+
+gen str6 open="OPEN" if inlist(month,"09","10")
+replace open="CLOSED" if open==""
+destring month, replace
+keep year month ab1 b2 open
+merge 1:m year month open using `lengths', keep(1 3)
+gen ab1_count=ab1*prob_ab1
+gen b2_count=b2*prob_b2
+keep year month lngcat open ab1_count b2_count
+sort year month open lngcat
+
+
+gen weight_per_fish= $kilo_to_lbs*$cod_lwa*((lngcat+.5)/$cm_to_inch)^$cod_lwb
+gen ab1mt=weight_per_fish*ab1_count/($mt_to_kilo*$kilo_to_lbs)
+gen b2mt=weight_per_fish*b2_count/($mt_to_kilo*$kilo_to_lbs)
+
+
+
+collapse (sum) ab1_count b2_count ab1mt b2mt ,  by(year month)
+
+gen b2dead_mt=b2mt*$mortality_release
+
+format ab1_count b2_count %10.0fc
+
+format b2mt ab1mt b2dead_mt %6.1fc
+
+save "$my_outputdir\atlanticcod_weights_OpenClose_${this_working_year}.dta", replace
+
+
diff --git a/stata_code/data_extraction_processing/processing/catch_summaries.txt b/stata_code/data_extraction_processing/processing/catch_summaries.txt
index 3dfe548..93fd671 100644
--- a/stata_code/data_extraction_processing/processing/catch_summaries.txt
+++ b/stata_code/data_extraction_processing/processing/catch_summaries.txt
@@ -16,6 +16,7 @@ if strmatch("$user","minyangWin"){
 /* setup directories */
 global code_dir "${project_dir}/stata_code"
 global working_data "${project_dir}/working_data"
+global my_annualdir "${data_main}/MRIP_$vintage_string/annual"
 global output_dir "${project_dir}/output"
 global this_working_year 2023
 global last_year = $this_working_year - 1
@@ -33,6 +34,7 @@ dyndoc "$processing_code/catch_summaries.txt", saving($my_results/catch_summarie
 do $MRIP_BLAST
 global vintage_string 2024_01_02
 global my_outputdir "${data_main}/MRIP_$vintage_string/monthly"
+global my_annualdir "${data_main}/MRIP_$vintage_string/annual"
 global FY_dir "${data_main}/MRIP_$vintage_string/fishing_years"
 global BLAST_DIR "${BLAST_root}/cod_haddock_fy2024/source_data/mrip"
 local my_common1 "atlanticcod"
@@ -571,80 +573,14 @@ list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_
 
 
 
-### These weights are computed using the annual length distribution of catch
+### These weights are computed using the length distribution of catch for the Open and Closed periods separately
 
 ~~~~
-<<dd_do:quietly>>
-
-
-
-/* load in total catch */
-
-
-
-use "${BLAST_DIR}/cod_size_class_ANNUAL${this_working_year}.dta", replace
-/*lngcat fishing_year count month*/
-drop fishing_year
-
-bysort month: egen t=total(count)
-gen prob=count/t
-keep month lngcat prob
-
-tempfile lengths
-save `lengths'
-
-
-
-
-use ${data_main}/MRIP_${vintage_string}\monthly\atlanticcod_catch_${this_working_year}.dta
-gen landings=claim+harvest
-keep year month landings release
-destring month, replace
-merge 1:m month using `lengths', keep(1 3)
-
-
-gen count_release=prob*release
-gen count_landings=prob*landings
-
-
-collapse (sum) count_release count_landings, by(year month lngcat)
-/* compute weights */
-
-
-/* l_in_bin from MRIP is length of catch, rounded down to the nearest inch */
-
-gen weight_per_fish= $kilo_to_lbs*$cod_lwa*((lngcat+.5)/$cm_to_inch)^$cod_lwb
-gen landed_weight=weight_per_fish*count_landings
-gen released_weight=weight_per_fish*count_release
-
-collapse (sum) count_release count_landings landed_weight released_weight, by(year month)
-
-
-gen ab1_lbs_per_fish=landed_weight /count_landings 
-gen b2_lbs_per_fish=released_weight/count_release 
-
-
-replace landed_weight=landed_weight/($mt_to_kilo*$kilo_to_lbs)
-replace released_weight=released_weight/($mt_to_kilo*$kilo_to_lbs)
-rename landed_weight ab1mt 
-rename released_weight b2mt 
-
-rename count_landings ab1_count 
-rename count_release  b2_count 
-
-gen b2dead_mt=b2mt*$mortality_release
-
-format ab1_lbs_per_fish b2_lbs_per_fish %4.3fc
-
-
-format ab1_count b2_count %10.0fc
-
-format b2mt ab1mt b2dead_mt %6.1fc
-
-<</dd_do>>
 <<dd_do>>
 
-list year month ab1mt b2mt b2dead_mt ab1_count b2_count ab1_lbs_per_fish b2_lbs_per_fish, abbreviate(16) sum(ab1mt b2mt b2dead_mt  ab1_count b2_count)
+/* load in total catch */
+use "${my_annualdir}/atlanticcod_weights_OpenClose_${this_working_year}.dta", replace
+list year month ab1mt b2mt b2dead_mt ab1_count b2_count, abbreviate(16) sum(ab1mt b2mt b2dead_mt  ab1_count b2_count)
 <</dd_do>>
 ~~~~
 
diff --git a/stata_code/data_extraction_processing/processing/process_wrapper.do b/stata_code/data_extraction_processing/processing/process_wrapper.do
index a6ebdf3..5434468 100644
--- a/stata_code/data_extraction_processing/processing/process_wrapper.do
+++ b/stata_code/data_extraction_processing/processing/process_wrapper.do
@@ -78,6 +78,22 @@ do "$processing_code/batch_file_to_process_OpenClose_mrip_data.do"
 
 
 
+/*apply Open/Close distributions to the monthly catches */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
 
 

From 104948e4ab9a77601b8336708e3a70ef4e427c0b Mon Sep 17 00:00:00 2001
From: Min-Yang Lee <Min-Yang.Lee@noaa.gov>
Date: Tue, 2 Jan 2024 16:29:12 -0500
Subject: [PATCH 17/17] finish code to compute weights using the Open and Close
 periods

---
 .../processing/annual/cod_weights_using_OpenClose.do      | 8 ++++----
 .../processing/process_wrapper.do                         | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do b/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do
index 3923925..763bf13 100644
--- a/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do
+++ b/stata_code/data_extraction_processing/processing/annual/cod_weights_using_OpenClose.do
@@ -15,7 +15,7 @@ global mortality_release=0.15
 
 
 
-use "$my_outputdir/cod_size_class_OpenClose_$this_working_year.dta" if open=="OPEN", clear
+use "$annual/cod_size_class_OpenClose_$this_working_year.dta" if open=="OPEN", clear
 expand 2 , gen(mark)
 gen month=9
 replace month=10 if mark==1
@@ -25,7 +25,7 @@ tempfile open
 save `open'
 
 
-use "$my_outputdir/cod_size_class_OpenClose_$this_working_year.dta" if open=="CLOSED", clear
+use "$annual/cod_size_class_OpenClose_$this_working_year.dta" if open=="CLOSED", clear
 expand 12
 bysort year open lngcat: gen month=_n
 drop if inlist(month,9,10)
@@ -73,8 +73,8 @@ gen b2dead_mt=b2mt*$mortality_release
 
 format ab1_count b2_count %10.0fc
 
-format b2mt ab1mt b2dead_mt %6.1fc
+format b2mt ab1mt b2dead_mt %6.2fc
 
-save "$my_outputdir\atlanticcod_weights_OpenClose_${this_working_year}.dta", replace
+save "$annual\atlanticcod_weights_OpenClose_${this_working_year}.dta", replace
 
 
diff --git a/stata_code/data_extraction_processing/processing/process_wrapper.do b/stata_code/data_extraction_processing/processing/process_wrapper.do
index 5434468..500a424 100644
--- a/stata_code/data_extraction_processing/processing/process_wrapper.do
+++ b/stata_code/data_extraction_processing/processing/process_wrapper.do
@@ -82,7 +82,7 @@ do "$processing_code/batch_file_to_process_OpenClose_mrip_data.do"
 
 
 
-
+do "$processing_code/annual/cod_weights_using_OpenClose.do"