| version | year | type | age | area | location | metric | value | var_mod | date_time |
|---|---|---|---|---|---|---|---|---|---|
| 2 | NA | Conservation limits | _ | coun_England_Wales | _ | Mean | 209010700.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Finland | _ | Mean | 104278220.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_France | _ | Mean | 55156800.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Gulf | _ | Mean | 248680000.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Iceland_NE | _ | Mean | 23889096.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Iceland_SW | _ | Mean | 51693269.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Ireland | _ | Mean | 710711690.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Labrador | _ | Mean | 243660000.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Newfoundland | _ | Mean | 267780000.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Northern_Ireland | _ | Mean | 93800000.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Norway | _ | Mean | 444064979.75 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Quebec | _ | Mean | 50380000.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Russia | _ | Mean | 357856550.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Scotia Fundy | _ | Mean | 224140000.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Scotland | _ | Mean | 561073322.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_Sweden | _ | Mean | 13997100.00 | cons_lim | 2022-08-18 08:37:30 |
| 2 | NA | Conservation limits | _ | coun_US | _ | Mean | 435369000.00 | cons_lim | 2022-08-18 08:37:30 |
| 1 | NA | Demographic transitions | Mixed | Atlantic | _ | Coefficient of variation | 0.01 | CV_dummy | 2020-11-24 18:32:04 |
| 1 | NA | Homewater catches | Mixed | Atlantic | _ | Coefficient of variation | 0.05 | CV_hw | 2020-11-24 18:32:04 |
| 1 | NA | Natural mortality rate | Mixed | Atlantic | _ | Coefficient of variation | 0.03 | CV_M | 2020-11-24 18:32:04 |
The following working document is just a technical analysis of the WGNAS database (and further its graphical interface) (ICES 2024). It uses different sources, ICES vocabulary, the stock annex (ICES 2021), to analyse the structure of the wgnas database before integrating in a single database (wgnas, wgbast, wgeel) in the DIASPARA project. This document does not engage the WGNAS it’s just a technical analysis, to try to get how this works. This document is listed as a task there : https://github.com/DIASPARAproject/WP3_migdb/issues/11
Main database structure
When loading the first lines of the db, it really looks as following :
Area
We first analyse the types of area that are found in the database. These are the possible geographical locations.
| area |
|---|
| LB fishery |
| LB/SPM/swNF fishery |
| neNF fishery |
| FAR fishery |
| GLD fishery |
| area |
|---|
| coun_Gulf |
| coun_Ireland |
| coun_Finland |
| coun_Scotland |
| coun_Russia |
| coun_Norway |
| coun_Northern_Ireland |
| coun_Iceland_SW |
| coun_Iceland_NE |
| coun_US |
| coun_Scotia Fundy |
| coun_England_Wales |
| coun_Labrador |
| coun_Newfoundland |
| coun_Sweden |
| coun_Quebec |
| coun_France |
| area |
|---|
| GF |
| NO_SW |
| SW |
| NEC |
| NAC |
| NO_NO |
| US |
| RU_RP |
| FR |
| IC_NE |
| IR |
| Atlantic |
| QC |
| NI_FO |
| FI |
| RU_KB |
| NF |
| IC_SW |
| NO_SE |
| SC_EA |
| NO_MI |
| LB |
| RU_AK |
| EW |
| SF |
| SC_WE |
| NI_FB |
| RU_KW |
The latter table (Table 2 (c)) is by default, so Atlantic, NEC and NAC are included. Having a label in a reference table and a geom to associate to those labels would be very usefull.
Location
Locations corresponding to fisheries
| location |
|---|
| Bef. Fisheries |
| Bef. Gld fisheries |
| Aft. First fisheries |
| Aft. Second fisheries |
| Aft. Gld fisheries |
| Return aft. Second fishery |
| Gld fisheries |
| Return aft. First fishery |
| location |
|---|
| GLD - by NAC SU |
| _ |
| FAR - by SU |
| GLD - by NEC SU |
| delayed spawners |
| additional |
| GLD - by cplx |
| location |
|---|
| NO_SW |
| SW |
| NO_NO |
| US |
| RU_RP |
| FR |
| IC_NE |
| IR |
| QC |
| NI_FO |
| FI |
| RU_KB |
| NF |
| IC_SW |
| NO_SE |
| SC_EA |
| NO_MI |
| LB |
| RU_AK |
| EW |
| SF |
| SC_WE |
| NI_FB |
| RU_KW |
| GF |
Here we search for locations related to fisheries.
QUESTION TO WGNAS
- Is there some gis reference for these fishing areas
- Would it possible to use ICES areas there or would this reporting correspond to different boundaries ?
Locations corresponding to fisheries
| GLD - by NAC SU |
|---|
| p_C8_2_NAC_gld_mu |
| _ |
|---|
| theta6_surv |
| log_N9_sd |
| N |
| nSm |
| CV_N1_pr |
| CV_M |
| log_N6_sd |
| theta6_delSp |
| p_smolt_pr |
| min_log_N9 |
| Stocking_2SW |
| date_begin |
| date_end_hindcast |
| log_C6_mu |
| p_smolt |
| log_N6_mu |
| eggs |
| CV_theta1 |
| N_NEC |
| log_C6_sd |
| max_log_N9 |
| CV_dummy |
| log_C9_sd |
| log_C9_mu |
| log_N9_mu |
| E_M |
| theta9_surv |
| E_theta1_pr |
| cons_lim |
| prop_female |
| E_theta1 |
| N_Sample |
| CV_hw |
| N_NAC |
| mu_N1_pr |
| date_end |
| theta9_delSp |
| N_Sample_sm |
| FAR - by SU |
|---|
| p_C8_NEC_3_far_mu |
| p_C5_NEC_1_far_mu |
| p_C8_NEC_1_far_mu |
| GLD - by NEC SU |
|---|
| p_C8_2_NEC_gld_mu |
| delayed spawners |
|---|
| log_C9_delSp_sd |
| log_C6_delSp_mu |
| log_C6_delSp_sd |
| log_C9_delSp_mu |
| additional |
|---|
| log_C9_sup_mu |
| log_C9_sup_sd |
| log_C6_sup_sd |
| log_C6_sup_mu |
| GLD - by cplx |
|---|
| p_C8_2_NECNAC_gld_mu |
Some values have been deprecated and are present in the database archive but not in the main database.
Values present in database_archive but not in database for version column :
[1] 3 4
Values present in database_archive but not in database for year column :
[1] 51 52
Values present in database_archive but not in database for area column :
[1] "NEAC"
Values present in database_archive but not in database for location column :
[1] "main"| var_mod | location_count |
|---|---|
| CV_M | 1 |
| CV_N1_pr | 1 |
| CV_dummy | 1 |
| CV_hw | 1 |
| CV_theta1 | 1 |
| E_M | 1 |
| E_theta1 | 1 |
| E_theta1_pr | 1 |
| N | 1 |
| N_NAC | 1 |
| N_NEC | 1 |
| N_Sample | 1 |
| N_Sample_sm | 1 |
| Stocking_2SW | 1 |
| cons_lim | 1 |
| date_begin | 1 |
| date_end | 1 |
| date_end_hindcast | 1 |
| deltat5_1 | 1 |
| deltat5_2 | 1 |
| deltat8_1 | 1 |
| deltat8_2 | 1 |
| deltat8_2_1 | 1 |
| deltat8_2_2 | 1 |
| eggs | 1 |
| log_C5_NAC_1_lbnf_mu | 1 |
| log_C5_NAC_1_lbnf_sd | 1 |
| log_C5_NAC_2_lbnf_lab_mu | 1 |
| log_C5_NAC_2_lbnf_lab_sd | 1 |
| log_C5_NAC_2_lbnf_oth_mu | 1 |
| log_C5_NAC_2_lbnf_oth_sd | 1 |
| log_C5_NEC_1_far_mu | 1 |
| log_C5_NEC_1_far_sd | 1 |
| log_C6_delSp_mu | 1 |
| log_C6_delSp_sd | 1 |
| log_C6_mu | 1 |
| log_C6_sd | 1 |
| log_C6_sup_mu | 1 |
| log_C6_sup_sd | 1 |
| log_C8_2_gld_tot_mu | 1 |
| log_C8_2_gld_tot_sd | 1 |
| log_C8_NAC_1_lbnf_mu | 1 |
| log_C8_NAC_1_lbnf_sd | 1 |
| log_C8_NAC_3_lbnf_mu | 1 |
| log_C8_NAC_3_lbnf_sd | 1 |
| log_C8_NAC_4_lbnf_lab_mu | 1 |
| log_C8_NAC_4_lbnf_lab_sd | 1 |
| log_C8_NAC_4_lbnf_oth_mu | 1 |
| log_C8_NAC_4_lbnf_oth_sd | 1 |
| log_C8_NEC_1_far_mu | 1 |
| log_C8_NEC_1_far_sd | 1 |
| log_C8_NEC_3_far_mu | 1 |
| log_C8_NEC_3_far_sd | 1 |
| log_C9_delSp_mu | 1 |
| log_C9_delSp_sd | 1 |
| log_C9_mu | 1 |
| log_C9_sd | 1 |
| log_C9_sup_mu | 1 |
| log_C9_sup_sd | 1 |
| log_N6_mu | 1 |
| log_N6_sd | 1 |
| log_N9_mu | 1 |
| log_N9_sd | 1 |
| max_log_N9 | 1 |
| min_log_N9 | 1 |
| mu_N1_pr | 1 |
| nSm | 1 |
| omega | 25 |
| p_C5_NEC_1_far_mu | 1 |
| p_C8_2_NAC_gld_mu | 1 |
| p_C8_2_NECNAC_gld_mu | 1 |
| p_C8_2_NEC_gld_mu | 1 |
| p_C8_NEC_1_far_mu | 1 |
| p_C8_NEC_3_far_mu | 1 |
| p_smolt | 1 |
| p_smolt_pr | 1 |
| prop_female | 1 |
| theta6_delSp | 1 |
| theta6_surv | 1 |
| theta9_delSp | 1 |
| theta9_surv | 1 |
So in the end, only omega has 25 locations, and in this case the location corresponds to area. This means we can get rid of the location column. For omega we can keep it,; so we can add a column with a foreign key to area in the parameters table where priors will be stored.
Sea age
Salmon mature at various sea ages, typically returning to freshwater to spawn after one to three years at sea, but also sometimes at older sea ages; this varies widely between populations. Those salmon that return after one year at sea are referred to as one-sea-winter (1SW) salmon, or grilse, with older fish categorised as 2SW, 3SW, etc. In practice, however, for management purposes these older sea age fish are typically aggregated and collectively referred to as multi-sea-winter (MSW) salmon. The sea age when salmon become sexually mature depends on genetics as well as growing conditions in the sea, and possibly freshwater, although the precise proximate factors initiating homeward migration are unknown (Hansen and Quinn, 1998). The sea age of Atlantic salmon is important in the context of stock definition since these different groups of fish have different migration routes, return at different times and are differentially exploited in fisheries. Thus, for example, it is only potential MSW salmon that are exploited in the distant water salmon fishery that operates off the west coast of Greenland (ICES 2021).
| n | age |
|---|---|
| 26 | 0SW |
| 1525 | 1FW |
| 14687 | 1SW |
| 212 | 1SW immature |
| 212 | 1SW mature |
| 1007 | 1SW maturing |
| 1007 | 1SW not maturing |
| 1325 | 1SW post-return |
| 1525 | 2FW |
| 18868 | 2SW |
| 1325 | 2SW post-return |
| 1525 | 3FW |
| 1525 | 4FW |
| 1525 | 5FW |
| 1525 | 6FW |
| 57 | Mixed |
| 649 | _ |
| 1551 | eggs |
| n | age | var_mod |
|---|---|---|
| 17 | _ | cons_lim |
| 1 | _ | date_begin |
| 1 | _ | date_end |
| 1 | _ | date_end_hindcast |
| 1 | _ | N |
| 1 | _ | N_NAC |
| 1 | _ | N_NEC |
| 1 | _ | nSm |
| 625 | _ | omega |
| n | age | var_mod |
|---|---|---|
| 25 | 0SW | mu_N1_pr |
| 1 | 0SW | N_Sample_sm |
| 1325 | 1FW | p_smolt |
| 200 | 1FW | p_smolt_pr |
| 25 | 1SW | deltat5_1 |
| 25 | 1SW | deltat5_2 |
| 1325 | 1SW | eggs |
| 53 | 1SW | log_C5_NAC_2_lbnf_lab_mu |
| 53 | 1SW | log_C5_NAC_2_lbnf_lab_sd |
| 53 | 1SW | log_C5_NAC_2_lbnf_oth_mu |
| 53 | 1SW | log_C5_NAC_2_lbnf_oth_sd |
| 1325 | 1SW | log_C6_delSp_mu |
| 1325 | 1SW | log_C6_delSp_sd |
| 1325 | 1SW | log_C6_mu |
| 1325 | 1SW | log_C6_sd |
| 1250 | 1SW | log_C6_sup_mu |
| 1250 | 1SW | log_C6_sup_sd |
| 1325 | 1SW | log_N6_mu |
| 1325 | 1SW | log_N6_sd |
| 1325 | 1SW | prop_female |
| 1325 | 1SW | theta6_delSp |
| 53 | 1SW immature | log_C8_NAC_1_lbnf_mu |
| 53 | 1SW immature | log_C8_NAC_1_lbnf_sd |
| 53 | 1SW immature | log_C8_NEC_1_far_mu |
| 53 | 1SW immature | log_C8_NEC_1_far_sd |
| 53 | 1SW mature | log_C5_NAC_1_lbnf_mu |
| 53 | 1SW mature | log_C5_NAC_1_lbnf_sd |
| 53 | 1SW mature | log_C5_NEC_1_far_mu |
| 53 | 1SW mature | log_C5_NEC_1_far_sd |
| 1007 | 1SW maturing | p_C5_NEC_1_far_mu |
| 1007 | 1SW not maturing | p_C8_NEC_1_far_mu |
| 1325 | 1SW post-return | theta6_surv |
| 1325 | 2FW | p_smolt |
| 200 | 2FW | p_smolt_pr |
| 25 | 2SW | deltat8_1 |
| 25 | 2SW | deltat8_2 |
| 25 | 2SW | deltat8_2_1 |
| 25 | 2SW | deltat8_2_2 |
| 1325 | 2SW | eggs |
| 53 | 2SW | log_C8_2_gld_tot_mu |
| 53 | 2SW | log_C8_2_gld_tot_sd |
| 53 | 2SW | log_C8_NAC_3_lbnf_mu |
| 53 | 2SW | log_C8_NAC_3_lbnf_sd |
| 53 | 2SW | log_C8_NAC_4_lbnf_lab_mu |
| 53 | 2SW | log_C8_NAC_4_lbnf_lab_sd |
| 53 | 2SW | log_C8_NAC_4_lbnf_oth_mu |
| 53 | 2SW | log_C8_NAC_4_lbnf_oth_sd |
| 53 | 2SW | log_C8_NEC_3_far_mu |
| 53 | 2SW | log_C8_NEC_3_far_sd |
| 1325 | 2SW | log_C9_delSp_mu |
| 1325 | 2SW | log_C9_delSp_sd |
| 1325 | 2SW | log_C9_mu |
| 1325 | 2SW | log_C9_sd |
| 1250 | 2SW | log_C9_sup_mu |
| 1250 | 2SW | log_C9_sup_sd |
| 1325 | 2SW | log_N9_mu |
| 1325 | 2SW | log_N9_sd |
| 25 | 2SW | max_log_N9 |
| 25 | 2SW | min_log_N9 |
| 318 | 2SW | p_C8_2_NAC_gld_mu |
| 1007 | 2SW | p_C8_2_NEC_gld_mu |
| 106 | 2SW | p_C8_2_NECNAC_gld_mu |
| 1007 | 2SW | p_C8_NEC_3_far_mu |
| 1325 | 2SW | prop_female |
| 1325 | 2SW | Stocking_2SW |
| 1325 | 2SW | theta9_delSp |
| 1325 | 2SW post-return | theta9_surv |
| 1325 | 3FW | p_smolt |
| 200 | 3FW | p_smolt_pr |
| 1325 | 4FW | p_smolt |
| 200 | 4FW | p_smolt_pr |
| 1325 | 5FW | p_smolt |
| 200 | 5FW | p_smolt_pr |
| 1325 | 6FW | p_smolt |
| 200 | 6FW | p_smolt_pr |
| 1 | eggs | CV_N1_pr |
| 25 | eggs | CV_theta1 |
| 1325 | eggs | E_theta1 |
| 200 | eggs | E_theta1_pr |
| 1 | Mixed | CV_dummy |
| 1 | Mixed | CV_hw |
| 1 | Mixed | CV_M |
| 1 | Mixed | E_M |
| 53 | Mixed | N_Sample |
| age | age2 | var_mod |
|---|---|---|
| 1SW | 2SW | eggs |
| 2SW | 1SW | eggs |
| 2FW | 6FW | p_smolt |
| 2FW | 1FW | p_smolt |
| 2FW | 3FW | p_smolt |
| 2FW | 4FW | p_smolt |
| 2FW | 5FW | p_smolt |
| 6FW | 2FW | p_smolt |
| 6FW | 1FW | p_smolt |
| 6FW | 3FW | p_smolt |
| 6FW | 4FW | p_smolt |
| 6FW | 5FW | p_smolt |
| 1FW | 2FW | p_smolt |
| 1FW | 6FW | p_smolt |
| 1FW | 3FW | p_smolt |
| 1FW | 4FW | p_smolt |
| 1FW | 5FW | p_smolt |
| 3FW | 2FW | p_smolt |
| 3FW | 6FW | p_smolt |
| 3FW | 1FW | p_smolt |
| 3FW | 4FW | p_smolt |
| 3FW | 5FW | p_smolt |
| 4FW | 2FW | p_smolt |
| 4FW | 6FW | p_smolt |
| 4FW | 1FW | p_smolt |
| 4FW | 3FW | p_smolt |
| 4FW | 5FW | p_smolt |
| 5FW | 2FW | p_smolt |
| 5FW | 6FW | p_smolt |
| 5FW | 1FW | p_smolt |
| 5FW | 3FW | p_smolt |
| 5FW | 4FW | p_smolt |
| 1FW | 2FW | p_smolt_pr |
| 1FW | 3FW | p_smolt_pr |
| 1FW | 4FW | p_smolt_pr |
| 1FW | 5FW | p_smolt_pr |
| 1FW | 6FW | p_smolt_pr |
| 2FW | 1FW | p_smolt_pr |
| 2FW | 3FW | p_smolt_pr |
| 2FW | 4FW | p_smolt_pr |
| 2FW | 5FW | p_smolt_pr |
| 2FW | 6FW | p_smolt_pr |
| 3FW | 1FW | p_smolt_pr |
| 3FW | 2FW | p_smolt_pr |
| 3FW | 4FW | p_smolt_pr |
| 3FW | 5FW | p_smolt_pr |
| 3FW | 6FW | p_smolt_pr |
| 4FW | 1FW | p_smolt_pr |
| 4FW | 2FW | p_smolt_pr |
| 4FW | 3FW | p_smolt_pr |
| 4FW | 5FW | p_smolt_pr |
| 4FW | 6FW | p_smolt_pr |
| 5FW | 1FW | p_smolt_pr |
| 5FW | 2FW | p_smolt_pr |
| 5FW | 3FW | p_smolt_pr |
| 5FW | 4FW | p_smolt_pr |
| 5FW | 6FW | p_smolt_pr |
| 6FW | 1FW | p_smolt_pr |
| 6FW | 2FW | p_smolt_pr |
| 6FW | 3FW | p_smolt_pr |
| 6FW | 4FW | p_smolt_pr |
| 6FW | 5FW | p_smolt_pr |
| 2SW | 1SW | prop_female |
| 1SW | 2SW | prop_female |
NOTE
Only eggs, p_smolt, p_smolt_pr and prop_female need an age, the other is contained in the name of the variable.
NOTE
So the age also covers information on maturity but the only time it is really used outside from the metadata (eggs, smolt, prop_female) the maturity is not necessary.
QUESTION TO WGNAS
- Why is
omeganot mixed ? - Would it not make more sense to store
2SWasMSW(multi-sea-winter) ? So in the referential have1SW 2SW 3SW… how many ? and thenMSW?
| n | life_stage |
|---|---|
| 103 | Adult |
| 1 | Adults |
| 13 | Eggs |
| 1 | Multiple |
| 2 | Non mature |
| 5 | PFA |
| 20 | Smolts |
| 21 | Spawners |
| 8 | _ |
NOTE
get rid of Adults replace with Adult.
NOTE
get rid of Multiple there is only one instance.
NOTE
Now there is the PFA, which is fine, but not really a stage.
Developmental stage
We first start by looking at the possible reference tables in ICES corresponding to both maturity and stage. Currently we have to store information about the sea age (0SW, 1SW, 2SW, ...,MSW) , the freshwater age (1FW 2FW 3FW 4FW ...). The maturity could be stored in the metadata as it seems to be linked always with parameters. Currently in wgnas we have maturity : immature, mature, not maturing and post return. In the metadata we have egg, smolts, spawner, adults
| GUID | Key | Description | LongDescription | Modified | |
|---|---|---|---|---|---|
| 30 | 76fab5ff-5f3e-4488-8167-17d360f47c35 | STAGE | Developmental Stage of Specimens | NA | 2024-10-22 |
| 216 | dcc61865-822a-47a4-a740-a85a5702d0c5 | TS_DevStage | Development stage or maturity | NA | 2024-04-11 |
| 324 | eac72d6a-219e-42a7-99b3-f50ac258b607 | DevScale | Scale applied for reporting developmental stages | At present, the codetype targets the Eggs and Larvae surveys | 2023-09-21 |
| 325 | d943050b-a4e3-4508-b0ca-10b298f308f5 | DevStage | Developmental stage codes | NA | 2023-09-21 |
| 427 | 2e045807-14b1-48b0-bb2e-43967cec51e7 | POFStaging | Stages of POF (description to be updated) | NA | 2023-09-21 |
| 449 | 8b86cce6-b742-4865-986c-13932874d9df | LifeStage | Life stage based on plumage (birds) | NA | 2023-09-21 |
| 466 | 14cbcbfe-f084-40a8-80e3-052e69b06334 | DigestionStage | Digestion stage of stomach content. | Visual-based assessment of digestion stage, in relation to diet studies. | 2023-09-21 |
| GUID | Key | Description | LongDescription | Modified | Deprecated |
|---|---|---|---|---|---|
| 7c946d9d-fe30-48fa-a19d-54e72a4160da | -9 | Missing Value | NA | 2024-04-04 | FALSE |
| 0da7235e-9a5f-471f-8685-cdcceb3259c0 | 1 | Juvenile/Immature (4-stage scale) | NA | 2024-04-04 | FALSE |
| 781f7cd8-2e68-4590-9124-f9d936e31f52 | 2 | Maturing (4-stage scale) | NA | 2024-04-04 | FALSE |
| ebb2258d-81fd-47d0-8383-7bfe88af82cd | 3 | Spawning (4-stage scale) | NA | 2024-04-04 | FALSE |
| 5e364aed-fe87-494e-81ff-195c6363f191 | 4 | Spent (4-stage scale) | NA | 2024-04-04 | FALSE |
| 02c6638c-9a7d-49d1-b06f-942ee5d95a39 | 5 | Resting/Skip of spawning (4-stage scale, additional option) | NA | 2024-04-04 | FALSE |
| 37d204b2-f8a6-48cd-a244-728ab4010111 | 51 | Immature (5 stage scale) | NA | 2024-04-04 | FALSE |
| 46d154b0-61f7-414a-b1d1-4275839afdfe | 52 | Developing/Resting (5-stage scale) | NA | 2024-04-04 | FALSE |
| 54992917-0bbd-4dd6-8044-32bb70754279 | 53 | Pre-spawning ((5-stage scale) | NA | 2024-04-04 | FALSE |
| 4146842c-eb45-49cd-8674-8d69ee6b81c1 | 54 | Spawning (5-stage scale) | NA | 2024-04-04 | FALSE |
| 52a5be9c-c656-496f-adba-b6af23ba88a3 | 55 | Post-spawning (5-stage scale) | NA | 2024-04-04 | FALSE |
| 17e59dde-46b3-4764-80f1-01e1134c8ba0 | 6 | Abnormal (4-stage scale, additional option) | NA | 2024-04-04 | FALSE |
| 9dab155a-95e6-4dcc-adaf-c8b67febbb60 | 61 | Juvenile/Immature (6-stage scale) | NA | 2024-04-04 | FALSE |
| 32e854ae-0e44-4523-855d-92b8bccdabbe | 62 | Maturing (6-stage scale) | NA | 2024-04-04 | FALSE |
| 85c79865-4505-4b6e-96bb-37e5a18b9c95 | 63 | Spawning (6-stage scale) | NA | 2024-04-04 | FALSE |
| 2637e1c0-8dba-4da8-beba-7c865acfd7b4 | 64 | Spent (6-stage scale) | NA | 2024-04-04 | FALSE |
| f682c57c-f70e-4c1b-859c-ab77f865c3f6 | 65 | Resting/Skip of spawning (6-stage scale) | NA | 2024-04-04 | FALSE |
| 8165075c-ae3b-49e4-b8ed-0dad8f215e78 | 66 | Abnormal (6-stage scale) | NA | 2024-04-04 | FALSE |
| a25f81c6-91af-47fe-b2a1-6f76a8643ac3 | A | Immature | NA | 2024-04-04 | FALSE |
| 62b08142-2f9d-4b8c-b53f-d9bce26b1c35 | B | Developing | NA | 2024-04-04 | FALSE |
| 4b4643bd-0255-42bc-a473-0b936492ae9f | Ba | Developing, but functionally immature (first-time developer) | NA | 2024-04-04 | FALSE |
| 5fb2d514-c4f0-4911-8eb4-f4e9c692041d | Bb | Developing and functionally mature | NA | 2024-04-04 | FALSE |
| 1ad95503-f3e6-46a6-997f-eefcba1c9bd7 | Be | Berried (crustaceans) | Used to be "B", changed to leave code for maturity scale SMSF | 2024-04-04 | FALSE |
| c5e12291-673e-4ad2-b7b8-6f2adf52ec21 | C | Spawning | NA | 2024-04-04 | FALSE |
| a9bc29b4-4ee3-4b1b-bf31-76d58170d75e | Ca | Actively spawning | NA | 2024-04-04 | FALSE |
| 8d8784d6-9795-43c0-927b-f404a18f3491 | Cb | Spawning capable | NA | 2024-04-04 | FALSE |
| 5af75fd2-06df-4d60-a843-2a3977cd6e5c | D | Regressing / Regenerating | NA | 2024-04-04 | FALSE |
| c11149a2-e084-4af0-b737-4d41d59d3943 | Da | Regressing | NA | 2024-04-04 | FALSE |
| ecb4cdea-3ac1-42cd-a279-c9b20e360999 | Db | Regenerating | NA | 2024-04-04 | FALSE |
| a1cf8684-f842-4f2f-9912-aefefea6d9d3 | E | Omitted spawning | NA | 2024-04-04 | FALSE |
| 1dce569f-2d2d-43a9-8041-d90950ade023 | Eg | Elasmobranch egg | Used to be "E", changed it to use the code for maturity scale SMSF | 2024-04-04 | FALSE |
| 1736cf72-fbca-4389-868d-e996159664e3 | F | Abnormal | NA | 2024-04-04 | FALSE |
| 429ad685-ee68-4781-84eb-90f0cd8f0634 | I | Immature / National BITS scale step | NA | 2024-04-04 | FALSE |
| ad5c19e1-3c59-4bd6-b001-f1cfbcab0b6d | II | National BITS scale step | NA | 2020-06-03 | FALSE |
| 595124ad-a831-4ce0-ba88-26fb4183022c | III | National BITS scale step | NA | 2020-06-03 | FALSE |
| 52e89979-b100-4cee-93c9-206d132a4c2a | IV | National BITS scale step | NA | 2024-04-04 | FALSE |
| 60f82148-71f3-4f0f-98c1-a6cd59918f25 | IX | National BITS scale step | NA | 2024-04-04 | FALSE |
| 9ddbe93e-b920-46fc-8f0d-b1bc94cacace | M | Mature | NA | 2024-04-04 | FALSE |
| 4b9a6671-aae4-4731-8a20-6bfa6764cc9c | R1_1 | Immature | IMARES RIVO 4 scale code for Immature used before 2000 for cod, haddock, whiting, Norway pout and saithe | 2024-04-04 | FALSE |
| 542d1576-cb99-42b4-a046-c5af124c7812 | R1_2 | Maturing | IMARES RIVO 4 scale code for Maturing, used before 2000 for cod, haddock, whiting, Norway pout and saithe | 2024-04-04 | FALSE |
| e5dba8d3-daf0-49b7-9a5e-0deaeae94591 | R1_3 | Spawning | IMARES RIVO 4 scale used before 2000 for Spawning, for cod, haddock, whiting, Norway pout and saithe | 2024-04-04 | FALSE |
| 35caf0f4-b23e-4114-b004-53ceed7dc5ae | R1_4 | Spent | IMARES PIVO 4 scale code for Spent, used before 2000 for cod, haddock, whiting, Norway pout and saithe | 2024-04-04 | FALSE |
| cc410273-2714-4253-bfa6-fadd39e83099 | R2_2 | Immature | IMARES RIVO new 4 scale code for Immature, used from 2000 til 1-1-2011, for all species | 2024-04-04 | FALSE |
| 24e63a36-bbcc-422e-9b42-1938d816574c | R2_4 | Maturing | IMARES RIVO new 4 scale code for Maturing, used between 2000 and 1-1-2011, for all species | 2024-04-04 | FALSE |
| 6024da49-355d-41e0-9c35-91c92133adef | R2_6 | Spawning | IMARES RIVO new 4 scale for Spawning, used between 2001 and 1-1-2011, for all species | 2024-04-04 | FALSE |
| 8f5b8ad1-f335-487a-bb17-58936b4bae8b | R2_8 | Spent/Recovering | IMARES RIVO new 4 scale code for Spent/Recovering, used between 2001 and 1-1-2011, for all species | 2024-04-04 | FALSE |
| 193d1307-7594-4e61-bddb-5ed722448fc1 | RF1 | Immature redfish | NA | 2024-04-04 | FALSE |
| 2bd20b2d-41f7-4ce4-944c-c124c2ee25bc | RF2 | Maturing_mature redfish | NA | 2024-04-04 | FALSE |
| 34288e8c-0586-48e9-bce9-2ea62580d278 | RF3 | Mature_fertilized redfish | NA | 2024-04-04 | FALSE |
| 8891c3b8-f440-4eca-8cb9-32c3f544cb82 | RF4 | Parturition redfish | NA | 2024-04-04 | FALSE |
| 94165bd1-2c96-485e-92f7-f8fdbec294d0 | RF5 | Postspawning redfish | NA | 2024-04-04 | FALSE |
| b725388b-288c-4895-819e-029e9625d0a4 | RF6 | Recovery redfish | NA | 2024-04-04 | FALSE |
| add7abf9-c812-4073-afd5-6168efc473da | S1 | Immature (6-stage scale) | NA | 2024-04-04 | FALSE |
| d94cc258-cf59-41df-8e12-e917b8c8753d | S2 | Maturing (6-stage scale) | NA | 2024-04-04 | FALSE |
| ab5a79b8-c948-41d0-ba0e-2d048c9c2d65 | S3 | Pre-spawning (6-stage scale) | NA | 2024-04-04 | FALSE |
| 185d00c7-b55b-4b6f-ad48-bc02494e7c3e | S4 | Spawning (6-stage scale) | NA | 2024-04-04 | FALSE |
| d7b6f253-9fa6-41bb-96ff-4e4ee3440858 | S5 | Post-partial spawning (6-stage scale) | NA | 2024-04-04 | FALSE |
| 2fad9d30-d07a-4ffb-b665-1bd687131d5b | S6 | Spent/Recovery (6-stage scale) | NA | 2024-04-04 | FALSE |
| 7d6b8aeb-1019-410c-9377-e03dd45bb06c | V | National BITS scale step | NA | 2020-06-03 | FALSE |
| 61f27c0b-f86f-4d44-b1fc-e695a071ff76 | VI | National BITS scale step | NA | 2024-04-04 | FALSE |
| 94bbebde-ffe9-41e9-b0d8-d712018b81e6 | VII | National BITS scale step | NA | 2024-04-04 | FALSE |
| 304ebd7a-7749-4b94-b155-301e786d8f6a | VIII | National BITS scale step | NA | 2024-04-04 | FALSE |
| 39a755c5-f830-49f0-8ca1-d1ea31989843 | X | National BITS scale step | NA | 2024-04-04 | FALSE |
| GUID | Key | Description | LongDescription | Modified | Deprecated |
|---|---|---|---|---|---|
| 16f8c30a-b724-4636-bd78-0a9a1776039e | -9 | No information | NA | 2024-04-04 | FALSE |
| c1566f6d-c099-44c3-bd39-222fe4c033de | B | Berried | NA | 2024-04-04 | FALSE |
| 0424ae90-03aa-4e73-8cda-e8745d0b8158 | E | Egg | NA | 2024-04-04 | FALSE |
| 3ea553fe-66cf-47ff-b4ff-eb83d1c28643 | J | Juvenile | NA | 2024-04-04 | FALSE |
QUESTION TO ICES
Does it make sense to use a code outside from its scope (I seems to me that yes). If so can we use the TS_DevStage and add values in it and propose definitions ?
There seem to be a correspondence between the 4 stage scale and the maturity
| Stage wgnas | stage (4 scale ICES) | table |
|---|---|---|
| eggs | Egg | TS_DevStage |
| smolt | ||
| immature | Immature (6-stage scale) | TS_MATURITY |
| Non mature (metadata) | Immature (6-stage scale) | TS_MATURITY |
| PFA | see question below | |
| mature | Maturing (6-stage scale) ? | TS_MATURITY |
| mature | Pre-spawning (6-stage scale) ? | TS_MATURITY |
| not maturing | Resting/Skip of spawning (4-stage scale, additional option) | TS_MATURITY |
| spawner (metadata table) | Spawning (6-stage scale) | TS_MATURITY |
| post-return | Post-spawning (5-stage scale) | TS_MATURITY |
QUESTION TO WGNAS
- Is the correspondence mature / maturing correct or is it pre -spawing?
- Is the correspondence OK. Do we really need
PFAstage or could we just describe it in the metadata ?
QUESTION TO ICES
Could we add smolt and PFA (pre fisheries abundance) somewhere ?
Metric
The metric are linked with coefficients, they don’t need to be stored in the main db
| n | metric |
|---|---|
| 50 | Bound |
| 29 | Coefficient of variation |
| 679 | Hyperparameter |
| 7 | Index |
| 38278 | Mean |
| 11033 | Standard deviation |
| n | metric |
|---|---|
| 2 | Bound |
| 5 | Coefficient of variation |
| 75 | Estimate |
| 6 | Hyperparameter |
| 7 | Index |
| 60 | Mean |
| 2 | Precision |
| 17 | Standard deviation |
There is a problem of correspondence between the database and metadata, detailed below :
| var_mod | metric_metadata | metric_database |
|---|---|---|
| NA | NA | NA |
| :------- | :--------------- | :--------------- |
| var_mod | metric_metadata | metric_database |
|---|---|---|
| tau_theta4 | Precision | NA |
| C5_NEC_1_tot | Estimate | NA |
| C6_hw | Estimate | NA |
| C5_NAC_1 | Estimate | NA |
| h6_hw_delSp | Estimate | NA |
| C9_hw | Estimate | NA |
| p_C8_2_NECNAC | Estimate | NA |
| C5_NAC_2_lab | Estimate | NA |
| C8_NAC_4_lab | Estimate | NA |
| N9 | Estimate | NA |
| theta1_ddp | Estimate | NA |
| h9_hw_delSp | Estimate | NA |
| tau_theta3 | Precision | NA |
| C5_NAC_2 | Estimate | NA |
| N8_1 | Estimate | NA |
| p_C8_NEC_1 | Estimate | NA |
| logit_theta3_pr | Estimate | NA |
| h5_NEC_1 | Estimate | NA |
| N5 | Estimate | NA |
| logN8 | Estimate | NA |
| N7 | Estimate | NA |
| C8_NEC_1 | Estimate | NA |
| h8_NEC_1 | Estimate | NA |
| logit_theta4 | Estimate | NA |
| h8_NEC_3 | Estimate | NA |
| theta3_pr | Estimate | NA |
| p_C5_NEC_1 | Estimate | NA |
| C5_NAC_2_other | Estimate | NA |
| h8_NAC_4 | Estimate | NA |
| C8_NEC_3 | Estimate | NA |
| C8_NEC_1_tot | Estimate | NA |
| logN2 | Estimate | NA |
| theta1 | Estimate | NA |
| theta4 | Estimate | NA |
| C8_2 | Estimate | NA |
| C5_NAC_1_tot | Estimate | NA |
| C8_NAC_3 | Estimate | NA |
| logit_theta3 | Estimate | NA |
| C8_2_comp | Estimate | NA |
| p_smolt_gamma | Estimate | NA |
| h5_NAC_1 | Estimate | NA |
| N4 | Estimate | NA |
| C8_NAC_1 | Estimate | NA |
| h8_NAC_4_lab | Estimate | NA |
| C8_NAC_4 | Estimate | NA |
| C6_hw_delSp | Estimate | NA |
| h8_NAC_1 | Estimate | NA |
| p_C8_2_NAC | Estimate | NA |
| C9_hw_delSp | Estimate | NA |
| N10 | Estimate | NA |
| C8_NEC_3_tot | Estimate | NA |
| h8_NAC_4_other | Estimate | NA |
| h6_hw | Estimate | NA |
| logN4 | Estimate | NA |
| h8_2 | Estimate | NA |
| N3 | Estimate | NA |
| p_smolt_stoch | Estimate | NA |
| theta8_2 | Estimate | NA |
| theta3 | Estimate | NA |
| N3_tot | Estimate | NA |
| N6 | Estimate | NA |
| h9_hw | Estimate | NA |
| C8_NAC_1_tot | Estimate | NA |
| h5_NAC_2 | Estimate | NA |
| C8_NAC_3_tot | Estimate | NA |
| log_N9_pr | Estimate | NA |
| p_C8_NEC_3 | Estimate | NA |
| h8_NAC_3 | Estimate | NA |
| N1 | Estimate | NA |
| logN5 | Estimate | NA |
| N1_pr | Estimate | NA |
| N3_pr | Estimate | NA |
| p_C8_2_NEC | Estimate | NA |
| C8_2_tot | Estimate | NA |
| C5_NEC_1 | Estimate | NA |
| C8_NAC_4_other | Estimate | NA |
| N8_2 | Estimate | NA |
Metadata
| type_object |
|---|
| single_value |
| array |
| matrix |
| vector |
| nimble |
|---|
| Data_nimble |
| Const_nimble |
| other |
| Output |
| model_stage |
|---|
| Fit |
| other |
| First year |
| type |
|---|
| Origin distribution in sea catches |
| Maturation rate |
| Homewater catches |
| Conservation limits |
| Number of years |
| Initialization first year |
| Returns |
| Abundance |
| High seas harvest rates |
| Smolt age structure |
| Time spent at sea |
| Sex ratio |
| Number of SU |
| Number of smolt ages |
| River harvest rates |
| Stocking |
| First year |
| Survival rate |
| Proportion of delayed individuals |
| Sea catches |
| Demographic transitions |
| Fecundity rate |
| Natural mortality rate |
| Prior hyperparameter |
| locations |
|---|
| NF fisheries |
| Bef. Fisheries |
| _ |
| GLD - by NAC SU |
| FAR - by SU |
| Aft. FAR fisheries |
| Bef. Gld fisheries |
| Bef. FAR fisheries |
| LB/SPM fisheries in Lb |
| LB/SPM fisheries out. Lb |
| Aft. First fisheries |
| Btw. GLD - NF/LB fisheries |
| Aft. NF/LB fisheries |
| Btw. NF/LB - GLD fisheries |
| NF/LB fisheries |
| Aft. Second fisheries |
| Aft. Gld fisheries |
| Btw. FAR - GLD fisheries |
| NF/LB/SPM fisheries |
| GLD - by NEC SU |
| Btw. GLD - FAR fisheries |
| Return aft. Second fishery |
| LB/SPM fisheries tot |
| Return aft. First fishery |
| Gld fisheries |
| Bef. NF/LB fisheries |
| FAR fisheries |
| GLD - by cplx |
| GLD fisheries |
| fishery |
|---|
| LB fishery |
| LB/SPM/swNF fishery |
| neNF fishery |
| FAR fishery |
| neNF |
| NA |
| delayed spawners |
| GLD fishery |
| _ |
| main |
| LB-LB/SPM/swNF fishery |
| metric |
|---|
| Estimate |
| Index |
| Bound |
| Hyperparameter |
| Standard deviation |
| Coefficient of variation |
| Precision |
| Mean |
| status |
|---|
| other |
| parameter_estimate |
| derived_quantity |
| parameter_constant |
| data |
| environment |
|---|
| Transition |
| Multiple |
| River |
| Sea |
| _ |
| life_stage |
|---|
| Adult |
| Spawners |
| PFA |
| Eggs |
| Non mature |
| _ |
| Smolts |
| Adults |
| Multiple |
| complex |
|---|
| Multiple |
| NEC |
| NAC |
| _ |
| ages |
|---|
| 0SW |
| 1SW |
| 1SW mature |
| _ |
| Mixed |
| Multiple |
| 2SW post-return |
| 1SW post-return |
| eggs |
| 1SW immature |
| 2SW |
Hierarchical structure of the database
The database could start with the simplest structure, with a basic table corresponding to all data. Then three tables could be created, one per species. This is to allow querying the different tables independently. From these species tables, three different tables could be produced, one for data, one for parameters outputs, one for parameters priors. The tables could have a different format, meaning maybe parameter does not have stage (only if this simplifies further development). Data should have stage because eel data need stage. The stage can be easily pulled up with a joining of the metadata table.
From these three table on could envisage the creation of specific table for working groups. Meaning one table for eel (wgeel), one table for salmon (wgnas), one table for salmon (wgbast), and one table for trutta (wgtrutta).
Referential tables
Similarly, referential tables could be created with a mother table from which specific (or wg specific) tables would inherit. This would make the setting up of consistent foreign key more easy. For instance wgbast could reference different age class than wgnas, and the stage would be completely different between wgeel and wgnas reference daughter tables. Some of these referential table would be common between species (e.g. source from ICES vocab, which corresponds to working group or accession events (datacalls)).
Unicity constraints
Another important point to add (at least to the salmoglob database) is unicity constraint. As some values would be null, creating unicity constraints with indexes would be necessary. These allow to have different levels of constraints for instance the unicity would be defined for : (year, age, area, parameter) (year, age, parameter) (year, area, parameter) (year, parameter)
One of the table will have to contain twice the area it will have to be treated separately. (year, area, area, parameter)
Other comments.
Currently stage in metadata not consistent, replicates information about maturity but not always. The lack of consistency in the metadata is not a problem as this table refers to the model.
Additional values about maturity, stage, can be stored in the metadata table.
There is a discrepancy between data in the historical dataset and the current, so we need to create additional parameters for the historical database and this will need to be checked.
References
ICES. 2021. “Stock Annex: Salmon (Salmo Salar) in Northeast Atlantic.” ICES Stock Annexes. https://doi.org/10.17895/ICES.PUB.18622037.V1.
———. 2024. “The Second ICES/NASCO Workshop on Salmon Mortality at Sea (WKSalmon2; Outputs from 2022 Meeting).” ICES Scientific Reports. https://doi.org/10.17895/ICES.PUB.22560790.