code changes needed to pick up wave 5 data.

stata_code/data_extraction_processing/extraction_wrapper.do

@@ -14,7 +14,7 @@ do ${extraction_code}/copy_over_raw_mrip.do
 
 /* copying over partial years of data */
 global yearlist 2023(1)2023
-*global wavelist 1(1)5
-global wavelist 1(1)4
+global wavelist 1(1)5
+*global wavelist 1(1)4
 
 do ${extraction_code}/copy_over_raw_mrip.do

stata_code/data_extraction_processing/processing/catch_summaries.txt

@@ -29,8 +29,9 @@ 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 $MRIP_BLAST
-global vintage_string 2023_11_08
+global vintage_string 2023_12_18
 global my_outputdir "${data_main}/MRIP_$vintage_string/monthly"
+global mode_dir "${data_main}/MRIP_${vintage_string}/mode"
 
 global FY_dir "${data_main}/MRIP_$vintage_string/fishing_years"
 local my_common1 "atlanticcod"
@@ -746,9 +747,7 @@ 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 "${data_main}/MRIP_$mode_vintage/mode"
 
 use "${mode_dir}/haddock_size_mode_class_${working_year}.dta", clear
 keep if year==$working_year

stata_code/data_extraction_processing/processing/convert_monthly_to_annual.do

@@ -29,7 +29,9 @@ use ${stacked_month}/monthly_cod_catch_class.dta, replace
 
 
 
-keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12))
+/*keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,9,10,11,12))*/
+keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12)) 
+
 replace fishing_year=`yr1'
 /* annual totals */
 collapse (sum) count, by(tot_cat fishing_year)
@@ -76,9 +78,8 @@ graph export "${my_images_vintage}/cod_catch_classPno0_ANNUAL`yr1'.tif", as(tif)
 /*Load in the stacked monthly catch class distributions*/
 use ${stacked_month}/monthly_haddock_catch_class.dta, replace
 
-
-
-keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12))
+/*keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,9,10,11,12))*/
+keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12)) 
 replace fishing_year=`yr1'
 /* annual totals */
 collapse (sum) count, by(tot_cat fishing_year)
@@ -146,9 +147,9 @@ graph export "${my_images_vintage}/haddock_catch_classPno0_ANNUAL`yr1'.tif", as(
 
 /*read in the size class distributions. Keep just the relevant FY. Collapse*/
 use ${stacked_month}/monthly_cod_size_class.dta, replace
+/*keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,9,10,11,12))*/
+keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12)) 
 
-
-keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12))
 replace fishing_year=`yr1'
 collapse (sum) count, by(lngcat fishing_year)
 
@@ -184,11 +185,13 @@ graph export "${my_images_vintage}/cod_size_classP_ANNUAL`yr1'.tif", as(tif) rep
 use ${stacked_month}/monthly_cod_size_class.dta, replace
 
 
-keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12))
+/*keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,9,10,11,12))*/
+keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12)) 
+
 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
@@ -251,7 +254,8 @@ graph export "${my_images_vintage}/cod_size_classP_OPEN_SPLIT`yr1'.tif", as(tif)
 use ${stacked_month}/monthly_haddock_size_class.dta, replace
 
 
-keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12))
+/*keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,9,10,11,12))*/
+keep if fishing_year==`yr1' | (fishing_year==`lastyr' & inlist(month,1,2,3,4,11,12)) 
 replace fishing_year=`yr1'
 
 collapse (sum) count, by(lngcat fishing_year)