wgbast database description

DIASPARA WP3.2 working document

Technical analysis of the wgbast database
Author

Briand Cédric, Oliviero Jules, Helminen Jani

Published

28-12-2024

The following working document is just a technical analysis of the WGBAST database. It uses different sources, ICES vocabulary, the stock annex (ICES 2021), to analyse the structure of the wgbast database before assessing whether we could integrate it in a single database (wgnas, wgbast, wgeel) in the DIASPARA project. This document does not engage the WGBAST it’s to try to get how this works. At this stage answers were kindly provided by Tapani. This document is listed as a task there github link to diaspara

Spatial units

River stock

“river stock” correspond salmon that belongs to a particular river. In most cases, river stocks most likely correspond to biological populations which lend support for this level of division from a conservation genetic perspective. However, it should be noted that some larger rivers may harbour several salmon subpopulations that are genetically separated spatially and/or temporally (Lind et al. 2015) (ICES 2021).

Salmon population

According to the results of Säisä et al. (2005), there are three main groups of salmon populations in the Baltic Sea: 1) Gulf of Bothnia populations, 2) populations in southern Sweden, and 3) eastern populations (Gulf of Finland and eastern Main Basin). These groups or lineages are assumed to mirror three distinct post-glacial colonization events. About 5% of the total genetic diversity of the Baltic salmon is explained by differences between rivers within groups, whereas 6% is explained by differences between the lineages (Säisä et al., 2005) (ICES 2021).

Assessment units within the Baltic Sea area

Within the Baltic Sea area, currently six different assessment units (AUs) have been established (Figure A.1.1.1). The grouping of rivers within an assessment unit is based on management objectives and biological and genetic characteristics of the river stocks contained in a unit. The partition of rivers into assessment units needs to make sense from a management perspective. River stocks of a particular unit are believed to exhibit similar migration patterns at sea. It can therefore be assumed that they are subjected to the same sea fisheries, experience the same exploitation rates and are affected by management of sea fisheries in the same way. In addition, the genetic variability between river stocks of an assessment unit is smaller than the genetic variability between river stocks of different units (see above). Although the rivers of assessment units 5 and 6 are relatively small in terms of their production capacity compared with rivers in the other assessment units, they are very important from a conservation perspective because of their unique genetic background. The six assessment units in the Baltic Sea consist of:

  • 1 ) Northeastern Bothnian Bay river stocks, starting at Perhonjoki up till the river Råneälven.
  • 2 ) Western Bothnian Bay river stocks, starting at Lögdeälven up to Luleälven.
  • 3 ) Bothnian Sea river stocks, from Dalälven up to Gideälven and from Paimionjoki up to Kyrönjoki.
  • 4 ) Western Main Basin river stocks, i.e. southeastern part of Sweden.
  • 5 ) Eastern Main Basin river stocks, i.e. rivers in Estonia, Latvia and Lithuania.
  • 6 ) Gulf of Finland river stocks. Wild river stocks belonging to each assessment unit are listed in the next section(ICES 2021).
Figure 1: Grouping of salmon river stocks in six assessment units in the Baltic Sea. The genetic variability between river stocks of an assessment unit is smaller than the genetic variability between river stocks of different units. In addition, the river stocks of a particular unit exhibit similar migration patterns. Wild salmon rivers (dark blue), mixed salmon rivers (light blue), reared salmon rivers (red), river stretches not accessible for salmon (grey). (source wgbast stock annex)

QUESTION WGBAST

Could we have access to a gis of this map (river type) to create the referentials in WP3.1 habitat

ANSWER WGBAST

Jānis Bajinskis has produced this map

TODO

Contact Janis

ICES vocab linked with catchments in the Baltic.

types <- icesVocab::getCodeTypeList()
types[grep('river', tolower(types$Description)),]
                                    GUID                 Key
463 7823c0a9-eeba-4766-9823-4578026786d2 RiversAndCatchments
                            Description
463 National Rivers and Catchment Areas
                                                                                    LongDescription
463 Codes for fresh water bodies as defined by national authorities, preceeded by the country code.
      Modified
463 2023-09-21
RiversAndCatchments <- icesVocab::getCodeList('RiversAndCatchments')
nrow(RiversAndCatchments)
[1] 729
kable(RiversAndCatchments[1:10,]) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
kable(RiversAndCatchments[is.na(RiversAndCatchments$key),]) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
Table 1: = ICES Vocab for River and Catchments (RiversAndCatchments)
(a) RiverAndCatchments, 10 first lines
GUID Key Description LongDescription Modified Deprecated
58e80ffa-4f0f-41f8-8c2e-5b4f485d4852 DK0100 Pissebæk NA 2023-07-11 FALSE
491a52c2-a2f4-487d-a009-fd43f16a05a8 DK0101 Møllebæk ved Vang NA 2023-07-11 FALSE
874181b9-e3d0-4282-a9ab-0ad77371ffba DK0101a Askebæk NA 2023-07-11 FALSE
0cb3f7c1-e541-4da2-8f38-6879e1faac64 DK0106 Ormebæk NA 2023-07-11 FALSE
92823a74-dd64-4b62-b970-da0f783975af DK0107 Onsbæk NA 2023-07-11 FALSE
b8d456d6-1b36-4d5a-9a1c-afea66393979 DK0110 Risebæk NA 2023-07-11 FALSE
3bf70f6a-305f-46fc-9761-e7a2f9fe3a61 DK0113 Hullebæk NA 2023-07-11 FALSE
a25f0904-fe7c-4ed8-8862-d651817277ab DK0117 Munkebæk NA 2023-07-11 FALSE
4f914977-11ed-4529-90ba-6959caeef57d DK0117a Stangebæk NA 2023-07-11 FALSE
98ac4f1d-2220-4c40-a27b-3e8f9a4ae292 DK0118 Melå NA 2023-07-11 FALSE
(b) This row has a problem
GUID Key Description LongDescription Modified Deprecated
NA NA NA NA NA NA
:---- :--- :----------- :--------------- :-------- :----------
ICES

Note the url in this table (Table 1): https://opendata-download.smhi.se/svar/SVAR_Basprodukter_2016_6.pdf is no longer accessed anywhere

It does not seems as if there is a hierarchy in these geographic units.

ICES

Just for information there is a line with NA ?

TODO

We’ll have to reconcile this table with GIS, we have to if there is a GIS map somewhere in ICES.

TODO

link ICES codes in our referential (which will be a map polygon in postgis).

NOTE

River stock, assessment units and rivers align with the envisioned db hierachical structure for spatial data.

Category of rivers

Table 2: Classification criteria for wild, mixed, reared and potential salmon rivers in the Baltic Sea (ICES 2021)
Category of salmon river Management plan for salmon stock in the river Releases Criteria for wild smolt production
Wild Self-sustaining No continuous releases >90% of total smolt prod.
Mixed Not self-sustaining at these production levels Releases occur 10–90% of total smolt prod.
Reared Not self-sustaining Releases occur <10% of total smolt prod.
Potential leading to category wild Lead to self-sustaining river stock Releases occur during re-establishment Long-term >90% wild smolt prod.
Potential leading to category mixed Not self-sustaining river stock Releases occur Long-term 10–90% wild smolt prod.

QUESTION WGBAST

The rivers are stored in the db, but these details (Table 2) might vary within one basin (see Figure 1), maybe this information should be stored alongside the referential as a separate table assessing the category of river but also including a period, as the status might change over time ?

part I - Fishery

Figure 2: Catches of salmon in % of TAC in 1993-2023. For years 1993–1997 (1993–1998 for Gulf of Finland) it is not possible to divide the total reported catch into commercial and recreational catches. (source (ICES 2024))
Data summary
Name Piped data
Number of rows 17728
Number of columns 23
_______________________
Column type frequency:
character 17
numeric 6
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
species 0 1.00 2 7 0 4 0
country 0 1.00 2 2 0 9 0
tp_type 0 1.00 2 5 0 6 0
sub_div 12 1.00 2 5 0 15 0
sub_div2 0 1.00 1 5 0 5 0
sub_div3 0 1.00 1 5 0 8 0
fishery 170 0.99 1 1 0 3 0
f_type 368 0.98 3 5 0 7 0
gear 901 0.95 2 3 0 8 0
w_type 876 0.95 3 3 0 6 0
n_type 1000 0.94 3 3 0 6 0
river 15960 0.10 4 18 0 61 0
notes 15616 0.12 2 184 0 257 0
w_ci 17661 0.00 1 16 0 34 0
n_ci 17573 0.01 1 13 0 74 0
gear2 13523 0.24 2 3 0 11 0
subdiv_ic 17674 0.00 9 11 0 4 0

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
year 0 1.00 2012.29 7.98 1972 2008.00 2013.00 2018.0 2023 ▁▁▁▆▇
time_period 0 1.00 4.06 3.83 0 1.00 3.00 7.0 12 ▇▂▂▂▂
effort 11243 0.37 10060.26 42629.13 0 68.00 572.00 3200.0 798450 ▇▁▁▁▁
weight 394 0.98 7.91 50.75 0 0.03 0.18 1.2 1372 ▇▁▁▁▁
numb 3326 0.81 1408.76 14320.71 0 8.00 49.00 267.0 741985 ▇▁▁▁▁
hyr 8310 0.53 1.51 0.50 1 1.00 2.00 2.0 2 ▇▁▁▁▇

Year

unique(catchdb$year)
 [1] 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986
[16] 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
[31] 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
[46] 2017 2018 2019 2020 2021 2022 2023

Other timeperiod

table(catchdb$time_period, catchdb$tp_type) %>%
 kable() %>%
  kable_styling(bootstrap_options = c("striped", "hover"))
Table 3: = Table of timpe periods in the wgbast db
HYR MON MONTH QTR Year YR
0 0 0 0 0 64 4110
1 1325 678 0 195 0 0
2 1239 682 0 243 0 1
3 0 854 0 231 0 0
4 0 921 0 301 0 0
5 0 1016 1 0 0 0
6 0 866 4 0 0 0
7 0 864 4 0 0 0
8 0 882 4 0 0 0
9 0 921 0 0 0 0
10 0 780 0 0 0 0
11 0 827 0 0 0 0
12 0 715 0 0 0 0

There are 0 and 0 NA values for tp_type.

NOTE

HYR and QTR are half of year and quarter

QUESTION WGBAST

Could you confirm that MON and MONTH are the same values, same for Year and YR ?

ANSWER WGBAST

  • Yup, MON=MONTH and Year=YR
TODO

Add constraint according to tp_type. Also add a not null constraint.

Country

Two letter country codes.

unique(catchdb$country)
[1] "DE" "DK" "PL" "RU" "FI" "SE" "EE" "LT" "LV"

Species

table(catchdb$species, useNA="ifany",dnn = "species") %>%
 kable() %>%
 kable_styling(bootstrap_options = c("striped", "hover"))
catchdb[catchdb$species=="NA",]%>%
 head(2) %>%
 kable() %>%
  kable_styling(bootstrap_options = c("striped", "hover")) 
catchdb[catchdb$species=="SAL&TRS",]%>%
 head(2) %>%
 kable() %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
Table 4: Species in wgbast catch database
(a) Table of Species numbers
species Freq
NA 11
SAL 8915
SAL&TRS 6
TRS 8796
(b) First two entries where species = NA
species country year time_period tp_type sub_div sub_div2 sub_div3 fishery f_type gear effort weight w_type numb n_type river notes w_ci n_ci gear2 subdiv_ic hyr
NA EE 2021 0 Year 28 22-31 200 C SEAL FYK NA NA NA 9 LOG NA NUMB states the number of occasions when seal damage was reported by commercial fishermen (SAL and TRS are combined) NA NA NA NA NA
NA EE 2021 0 Year 28 22-31 200 C SEAL MIS NA NA NA 33 LOG NA NUMB states the number of occasions when seal damage was reported by commercial fishermen (SAL and TRS are combined) NA NA NA NA NA
(c) First two entries where species = SAL&TRS
species country year time_period tp_type sub_div sub_div2 sub_div3 fishery f_type gear effort weight w_type numb n_type river notes w_ci n_ci gear2 subdiv_ic hyr
SAL&TRS EE 2023 0 YR 28 22-31 200 C SEAL FYK NA NA NA 2 LOG NA NUMB states the number of occasions when seal damage was reported by commercial fishermen (SAL and TRS are combined) NA NA NA NA NA
SAL&TRS EE 2023 0 YR 28 22-31 200 C SEAL GNS NA NA NA 66 LOG NA NUMB states the number of occasions when seal damage was reported by commercial fishermen (SAL and TRS are combined) NA NA NA NA NA

QUESTION WGBAST : species

Some ‘NA’ are character (11 rows) (Table 4) for EE. This is for seal damage. Is there a need for this ? It’s not reported the same way every year ?

ANSWER WGBAST

  • Estonia cannot distinguish whether seal damaged catch is SAL or TRS. Split to the species could base on expert elicitation but has remained undone.

Catch habitat

Countries participating in the Baltic salmon fishery are asked to deliver catch data of salmon and sea trout. Catches are given by economic zone, ICES subdivision, as well as type of fishery separated by offshore, coastal and river (ICES 2021).

Catches are divided into four different fishing area categories: River (R), Coastal (C), Open sea (O) and Sea (S). Sea (S) is only used when it is not possible to separate between coast and open sea. There is no standardized way of distributing sea catches into either of the two WGBAST fishing area categories Coast (C) or Open sea (O). For the commercial fisheries, a majority of the countries divide the commercial landings on fishing area depending on which gear that has been used, where longlines and driftnets are categorised as open sea (O) and trapnets as coastal (C) (ICES 2021).

Exceptions:

  • In Latvia, the distribution is depending on how the catches are reported into the official catch statistics. Here catches from vessels carrying EU logbook are categorised as open sea (O), whereas catches from vessels reporting in the national logbook system are categorised as coastal (C). Latvian vessels that are active 2 nautical miles (NM) or more off the coast are obliged to use EU logbook.

  • In Lithuania, catches outside territorial water, i.e. 12 NM or more from the coast, are categorised as open sea (O). Inside this border catches are categorised as coastal (C).

  • In Poland, length of the vessel defines if the catch is coastal (C) or open sea (O). Catches from vessels 10 meters or less are coastal (C) and catches from vessels longer than 10 meters are categorised as open sea (O).

Latvia and Lithuania are the only two countries directly using the actual geographical position when categorising the catches as either coastal (C) or open sea (O). For the recreational fisheries, all countries define trolling as open sea (O) whereas catches from other gears are defined as coastal (C) (ICES 2021).

Table 5: Habitat and fishery
(a) Habitat type in column `fishery` in wgbast catch database. Rows correspond to the values in sub_div, columns to habitat type
C O R NA
200 108 412 50 14
21 3 0 0 0
22 105 428 0 64
22-32 6 0 0 0
23 76 436 0 0
24 407 954 2 80
25 665 1296 118 0
26 854 1086 190 0
27 426 161 54 0
28 1933 351 320 0
29 1167 123 38 0
30 1138 112 530 0
300 110 51 51 0
31 955 7 980 0
32 1375 212 268 0
NA 0 0 0 12
(b) Contingency table for `sub_div`and `sub_div2` including NA
0 21 22-31 22-32 32
200 0 0 584 0 0
21 0 3 0 0 0
22 0 0 597 0 0
22-32 0 0 0 6 0
23 0 0 512 0 0
24 0 0 1443 0 0
25 0 0 2079 0 0
26 0 0 2130 0 0
27 0 0 641 0 0
28 0 0 2603 0 1
29 0 0 1327 0 1
30 0 0 1780 0 0
300 0 0 212 0 0
31 0 0 1942 0 0
32 0 0 0 0 1855
NA 12 0 0 0 0
(c) Contingency table for `sub_div2`and `sub_div3` including NA
0 200 21 22-32 30 300 31 32
0 12 0 0 0 0 0 0 0
21 0 0 3 0 0 0 0 0
22-31 0 11916 0 0 54 3783 97 0
22-32 0 0 0 6 0 0 0 0
32 0 0 0 0 0 0 0 1857
Figure 3: Double dekker plot showing the importance of habitat type per species and subdivision. Cell importance according to the number of rows

The values for habitat are : O, C, R, NA there are 170 NA values in the database. 200=MainB(22-29); 300=GoB(30-31). :::{.callout-note appearance=“simple”} ## TODO Create geographical grouping of areas + use ICES subdiv3 :::

QUESTION WGBAST : habitat

  • In the stock annex there is a mention to sea S but it does not seem to be present in the database ?
  • The name of the column fisheryis not very explicit, would the use of habitat_type be more in line with data ?
  • Can you confirm that 200 is 22-31 and not 22-29, and that 300 is 30-31 ?

ANSWER WGBAST

In the stock annex there is an old notation. Today we use “O” (open sea) instead of “S”.

The best match for fishery habitat in ICES vocabulary seems to be WLTYP.

WLTYP <- icesVocab::getCodeList('WLTYP')
kable(WLTYP, caption = "Water type (for stations)") %>% 
kable_styling(bootstrap_options = c("striped", "hover", "condensed")) 
Table 6
Water type (for stations)
GUID Key Description LongDescription Modified Deprecated
9388a49e-4a5f-46b3-9b7b-8dcfb03e7b6f BP Beach - peri-urban according to UNEP MARLIN litter protocol 2021-12-10 FALSE
a6e1119b-3bcc-4b0a-8053-f8f7a86f0053 BR Beach - rural according to UNEP MARLIN litter protocol 2019-01-17 FALSE
53708e1d-d3c6-47a7-a0ee-1c70e6fa7f9b BU Beach - urban according to UNEP MARLIN litter protocol 2024-08-26 FALSE
86d9897d-6adc-430e-a689-f321b75cadcc C WFD Coastal water NA 2024-12-05 FALSE
0a28de1c-018a-4841-b3a3-a68e01c81cd5 CE Coastal water (Estuary) NA 2024-08-26 FALSE
85a228c9-9033-4f97-accf-4968db78a90a CF Coastal water (Fjord) NA 2024-11-28 FALSE
e57989c4-a3f9-4560-9460-60dce3a26185 CR Coastal water (River) NA 2024-05-31 FALSE
eb979616-8b95-4c1b-92e8-b5f8d8bf1b96 FW Fresh water NA 2022-08-19 FALSE
c557dc19-27b9-46b6-a164-d7d8d4f55738 L Land station NA 2024-11-07 FALSE
5b3da387-3b2b-47c4-9967-c3161f533207 LK Lake NA 2022-11-01 FALSE
b51355b0-b905-4b4e-ab12-98d9b47d7752 MC Marine water (coast) Marine water within 4 nm from the baseline. 2024-06-18 FALSE
a75522ef-5e4a-4e2d-8550-38091cb6c994 MO Marine water (open sea) NA 2024-12-05 FALSE
913ae617-a160-4687-a62c-8923c6762c4f NA Not applicable NA 2022-08-19 FALSE
1c792737-6f55-422a-b709-88af2d78c4ea T WFD Transitional water - implies reduced salinity NA 2023-11-29 FALSE
4f85f72f-c2f0-41c7-b966-c80c897b80d7 TT Transitional water (Tidal) - significant tide and reduced salinity NA 2024-09-10 FALSE

ICES vocabulary for water types (stations)

QUESTION ICES : vocabulary for habitat

Should we use this vocabulary for catch habitat ?

ANSWER WGBAST

I agree, we could use ICES vocabulary for catch habitat (i.e MO, MC, C and CR/FW)

QUESTION WGBAST: 4 nm from the baseline ?

Currently the definition in ICES vocab is WFD coastal water (C) or MC (Marine water (coast)) Marine water within 4 nm from the baseline. It seems that there are country difference in the interpretation of coastal or marine 2 10 12, so what do we choose ?

ANSWER WGBAST

In the WGBAST thinking we have only one coastal water category independently from the distance to the baseline. All trapnet fishing is considered coastal even though fishing sites may varies from very close to shoreline out to beyond base line. At the Finnish coast baseline goes far out at sea in some places.

NOTE WGBAST

Currently subdivisions are used but for some historical data it is not possible to separate ICES subdivisions, so for these historical data these data are lumped together.

Catches type

Catches are further classified as commercial, recreational, discard, and seal damage (ICES 2021). The excel tables gives more types than the stock annex : commercial=COMM, recreational=RECR, discard=DISC, sealdamage=SEAL, unreported=UNRP, ALV=released alive back in water.

Table 7: Frequency of catches classification f_type in the database.
f_type Freq
ALV 537
BMS 77
BROOD 39
COMM 12920
DISC 334
RECR 2473
SEAL 980
NA 368

QUESTION WGBAST: what are ‘BMS’ and ‘BROOD’ ?

There is a difference between the stock annex, the excel table and the database. The stock annex lists four types COMM, RECR, DISC and SEAL. The excel also describes ALV, UNRP which does not exist. The db has two additional types BROOD and BMS which are reported neither in the stock annex nor in the excel table. These correspond to very few lines. Do you want to keep those values? Do you agree that UNRP should not be in the excel description ?

ANSWER WGBAST

The Stock annex seems to miss part of catch categories. * BROOD means broodstock fishery and BMS is catch of undersized salmon (below minimum landing size, landing obligation). * ALV is caught fish that has been releases back to sea/river alive. UNRP is unreported catch. * At some point intention was to include unreported catch estimates to the catch data but has not realised so far. Might be OK to drop from the excel description.

NOTE

There are 368 NA values for f_type.

Source of fishery data

Logbooks provide primary information on catches taken on board the vessels, where real count and weight estimates are normally difficult to obtain. The catch statistics in different countries are obtained by combination of data included in logbooks, landing declarations, first sales notes and fisheries companies catch reports. From 2005 EU type logbooks were implemented in the new member states Latvia, Estonia, Poland and Lithuania (ICES 2021).

In the excel table the possible values are indicated as : logbook=LOG, extrapolated=EXT, estimated=EST, expert evaluation=EXP.

The ICES vocab DataSourceOfScientificWeight seems to provide the closest match with these data, however it lacks extrapolated, estimated.

Table 8: Catches according to source of capture and outcome f_type in the WGNAS fisheries database.
(a) Frequency of each type in the database including NA
n_type Freq
EST 944
EXP 28
EXT 335
EXV 1295
GST 9
LOG 14117
NA 1000
(b) Contingency table for `n_type`and `f_type`including NA
ALV BMS BROOD COMM DISC RECR SEAL NA
EST 118 0 0 82 0 742 0 2
EXP 0 0 0 0 0 28 0 0
EXT 0 0 0 196 0 48 91 0
EXV 391 0 0 15 14 873 2 0
GST 0 0 0 1 0 8 0 0
LOG 28 73 39 12101 315 655 882 24
NA 0 4 0 525 5 119 5 342
Table 9: ICES vocabulary for DataSourceOfScientificWeight.
DataSourceOfScientificWeight table
GUID Key Description LongDescription Modified Deprecated
7eb92e58-87b0-4f61-9a3f-54c07aaaa3f1 Combcd Combination of census data Combination of census data 2021-12-22 FALSE
7c5c1d9d-7e4a-4006-b5db-f6ecbf0ceba0 ExpertEval Expert evaluation NA 2022-06-28 FALSE
8495beb2-2e75-47c8-ba42-d2deb881df6e Logb Logbook Logbook 2021-12-22 FALSE
4b90937e-f2cc-4656-b6fe-41e7e22f21ff Othdf Other declarative forms Other declarative forms 2021-12-22 FALSE
d25929d1-c40c-4bd9-abe0-346955226e8f Saln Sales notes Sales notes 2021-12-22 FALSE
fc49c8ea-85b5-4b99-aafe-741ee4a6998f Sampld Sampling data Sampling data 2021-12-22 FALSE

QUESTION / ANSWERS WGBAST

  • Could you provide definitions of extrapolated and estimated. ?

Need to come back to this later on

Yes, they are the same.

All GST -values should be updated as “expert evaluated”.

  • The source of fishery data might partially correspond to the vocab dataSourceOfScientificWeight (Table 9). At least there is a Logbook, Expert evaluation, any idea if something in this vocab might correspond to extrapolated or estimated ?

The “Combcd” might do best for these.

  • Do you want to allow NA values there ?

No, I don’t think so. Better to give a value from vocab here.

  • Would you treat things differently if tables for Baltic TRUTTA and SALMON were separated ?

No, not to my understanding

NOTE

w_typeand n_type source of data are similar and will be treated in the same column in the database There are 876 NA values for w_type.

Table 10: Catches according to data source for weight w_type in the WGNAS fisheries database.
(a) Frequency of each type datasource for weight in the database including NA
w_type Freq
EST 893
EXP 28
EXT 495
EXV 1218
GST 30
LOG 14188
NA 876
(b) Contingency table for `n_type`and `w_type`including NA
EST EXP EXT EXV GST LOG NA
EST 679 0 2 8 18 181 56
EXP 0 28 0 0 0 0 0
EXT 2 0 256 0 0 75 2
EXV 51 0 0 1210 0 0 34
GST 1 0 0 0 8 0 0
LOG 106 0 237 0 0 13704 70
NA 54 0 0 0 4 228 714

gear

TODO analyse gear according to ftype

Part II. Electrofishing and river data

The data are read from the WGBAST_2024_Young_fish xlsx file. This file has two sheets. The number of young fish is the number of fish released in water (stocking), and the smolt corresponds to smolts counts.

smolts <- readxl::read_xlsx(file.path(datawd, "WGBAST_2024_Young_fish_26-02-2024.xlsx"), sheet = "number of wild smolts")
young_fish <- readxl::read_xlsx(file.path(datawd, "WGBAST_2024_Young_fish_26-02-2024.xlsx"), sheet = "numb of young fish")
smolts <- janitor::clean_names(smolts)
young_fish <- janitor::clean_names(young_fish)

smolts %>%skim()
Data summary
Name Piped data
Number of rows 2478
Number of columns 16
_______________________
Column type frequency:
character 11
numeric 5
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
species 0 1.00 3 3 0 2 0
country 0 1.00 2 2 0 7 0
sub_div 0 1.00 2 8 0 11 0
sub_div2 0 1.00 2 8 0 26 0
sub_div3 0 1.00 2 8 0 27 0
river 26 0.99 3 14 0 117 0
age 2470 0.00 7 7 0 1 0
origin 0 1.00 1 1 0 1 0
river_category 1091 0.56 4 5 0 2 0
the_most_probable_number_of_smolts 80 0.97 1 21 0 998 0
notes 1697 0.32 4 67 0 27 0

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
year 0 1.00 2010.39 8.16 1987.0 2005.00 2011.00 2017.00 2025.00 ▁▂▆▇▅
assessment_unit 0 1.00 4.58 1.55 1.0 4.00 5.00 6.00 6.00 ▃▁▁▇▆
min_numb_of_wild_smolts 1551 0.37 45.70 197.56 0.0 0.10 1.00 11.65 1667.17 ▇▁▁▁▁
max_numb_of_wild_smolts 1550 0.37 138.01 401.20 0.1 3.66 11.93 54.84 3002.33 ▇▁▁▁▁
n_type 952 0.62 3.47 1.15 1.0 3.00 3.00 4.00 8.00 ▁▇▆▁▁
young_fish %>%skim()
Data summary
Name Piped data
Number of rows 7714
Number of columns 15
_______________________
Column type frequency:
character 7
logical 3
numeric 5
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
species 0 1.00 3 3 0 2 0
country 0 1.00 2 2 0 10 0
sub_div2 0 1.00 2 5 0 2 0
river 1654 0.79 2 26 0 333 0
age 0 1.00 2 8 0 12 0
origin 9 1.00 1 1 0 1 0
notes 6235 0.19 2 187 0 272 0

Variable type: logical

skim_variable n_missing complete_rate mean count
min_numb_of_wild_smolts 7714 0 NaN :
max_numb_of_wild_smolts 7714 0 NaN :
n_type 7714 0 NaN :

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
year 0 1 2007.13 9.83 1984 2000 2008.0 2015.0 2022 ▂▅▅▇▇
assessment_unit 1 1 3.96 1.71 1 3 5.0 5.0 6 ▅▃▃▇▅
sub_div 24 1 30.23 17.55 22 26 29.0 31.0 200 ▇▁▁▁▁
sub_div3 0 1 206.05 88.02 32 200 200.0 300.0 300 ▂▁▁▇▅
the_most_probable_number_of_smolts 20 1 83.85 195.67 0 5 19.5 70.8 4500 ▇▁▁▁▁
sy <- bind_rows(
smolts %>% 
mutate(
  tab="smolts",
  the_most_probable_number_of_smolts = as.numeric(the_most_probable_number_of_smolts),
),
young_fish %>% 
mutate(
  tab = "young_fish",
  sub_div = as.character(sub_div),
  sub_div3 = as.character(sub_div3),
  min_numb_of_wild_smolts = as.numeric(min_numb_of_wild_smolts),
  max_numb_of_wild_smolts = as.numeric(max_numb_of_wild_smolts),
  n_type = as.numeric(n_type)
))
save(sy, file= "data/sy.Rdata")
NOTE WGBAST

R1168C15 3,4 (probably two values….) probably need correction

Electrofishing data are obtained along with smolt counts at rivers Tornionjoki, Simojoki, Åbyälven, Rickleån, Sävarån, Ume/Vindelälven, Öreälven and Lögdeälven (Assessment unit 1-3), Mörrumsån, Emån and Testeboån (AU 4) to estimate smolt production based on parr density in electrofishing.

  • Annual number of sampling sites electrofished
  • Estimated density of age 0+
  • 1+
  • >1+ parr.

The number of sampling sites is used as a measure of precision of the parr density.

Question WGBAST

  • There must be a dataset of electrofishing somewhere. This should be part of the template db on electrofishing, can we have access ?
  • Would it be usefull to start from a full db of electrofishing data ?

ANSWER WGBAST

There is an input dataset for the river model. This has been compiled from the national data set for 17 rivers (that are included in the full life history model at present). In other words that dataset is missing AU5-6 rivers, which parr densities and the corresponding smolt production estimates are presented in the WGBAST report tables only. Atso knows more about this.

Yes, I think this would be good. Would it be possible to apply same data construction for SAL, TRS and EEL ?

Yes we think so and will try

Species

Table 11: Frequencies of species type in the young fish and smolt database.
smolts young_fish
SAL 1391 2883
TRS 1087 4831

Country

Table 12: Countries in the young fish and smolt database.
smolts young_fish
DE 0 337
DK 72 302
EE 266 345
EU 0 15
FI 110 3100
LT 429 1098
LV 541 378
PL 0 954
RU 538 154
SE 522 1031

Time

Table 13: Number of values per year and sheet in the database
smolts young_fish
1984 0 13
1985 0 27
1986 0 24
1987 16 69
1988 16 88
1989 16 155
1990 16 152
1991 16 162
1992 16 141
1993 17 139
1994 17 145
1995 17 155
1996 17 160
1997 17 154
1998 17 160
1999 17 159
2000 29 165
2001 62 154
2002 75 193
2003 77 194
2004 84 223
2005 87 248
2006 96 271
2007 115 249
2008 115 266
2009 123 282
2010 123 234
2011 93 283
2012 110 276
2013 109 343
2014 110 275
2015 110 306
2016 108 292
2017 109 286
2018 107 235
2019 105 268
2020 88 249
2021 53 257
2022 55 262
2023 57 0
2024 50 0
2025 13 0
NOTE

Years distributed from 1984, nothing special (Table tbl-youngfishdbdbtime), this db does not use time periods lower than year.

Geography

Table 14: Geographical units in the young fish and smolt database
(a) Rivers (note that some labels seem to be duplicated in the database)
smolts young_fish
81 0 4
83 0 1
Åby älv 39 0
Age 18 0
Aģe 3 0
Agluona 0 13
Ähtävänjoki 0 2
Ahvenanmaa 0 7
Ahvenanmaa, Saaristo 0 4
Aitra 0 1
Akmena 0 25
Akmena-Dane 18 0
Akmena - Danė 2 0
Aland 0 137
Åland 0 6
Alantas 0 6
Amarnia 0 9
Amata 0 8
Ancia 0 7
Ančia 0 3
Anyksta 0 1
Armona 2 9
at sea 0 389
Aurajoki 0 97
Barta 40 1
Bārta 4 0
Bartuva 20 0
Bauda 0 18
Bebirva 0 8
Beke 0 1
Beste 0 10
Bezdone 0 10
Bezdonė 0 2
Blotnica 0 13
Błotnica 0 1
Bokenau 0 4
Bornholm 18 3
Brasla 0 11
Brazuole 0 17
Bražuole 0 1
Bražuolė 0 1
Bremena 0 4
Byske älv 39 0
Bystryi 16 0
Cirvija 0 4
Curau 0 1
Czarna Wda 0 19
Czerwona 0 14
Damshäger Bach 0 1
Darba 0 5
Daugava 24 77
Debosznica 0 8
Dratvainys 0 4
Dratvinys 0 6
Dratvuo 0 2
Dubysa 40 60
Duksta 2 20
Dūkšta 0 3
Egluona 0 2
Eleruona 0 1
Emån 38 0
Eurajoki 0 31
Ezeruona 0 2
Farver 0 2
Farver Au 0 7
Fiskarsinjoki 0 3
Funen 18 0
Gauja 45 93
Gauja (Vizla) 0 1
Gladyshevka 33 10
Grabuosta 0 11
Grimsnisau 0 8
Haaler Au 0 1
Habernis 0 9
Halikonjoki 0 4
Hanshagener 0 1
Hanshagener Bach 0 2
Hanshäger Bach 0 6
Hellbach 0 3
Hirvijoki 0 1
Hounijoki 0 7
Huttener 0 2
Huttener Au 0 4
Hüttener Au 0 2
Iijoki 0 174
Ilolanjoki 0 15
Ingarskila 0 1
Ingarskilajoki 0 2
Ingarskilanjoki 0 1
Irbe 45 0
Irtuona 0 6
Jägala 21 19
Jarubynas 0 1
Jevenau 0 1
Jukkola east 14 0
Jukkola middle 14 0
Jukkola west 14 0
Juodupis 0 10
Jura 20 47
Jūra 0 7
Jusine 2 12
Jusinė 0 3
Jutland 18 0
Juustilanjoki 0 1
Kaakamojoki 0 9
Kaberla oja 0 1
Kåge älv 18 0
Kalajoki 0 39
Kalix älv 39 0
Kälviänjoki 0 1
Karjaanjoki 0 25
Karvianjoki 0 106
Keila 25 0
Kello-oja 14 0
Kemijoki 0 111
Kena 1 32
Khabolovka 17 0
Kiiminkijoki 0 203
Kisko-Perniönjoki 0 5
Kisko-Perniönki 0 2
Kiskonjoki 0 2
Kiskonjoki-Perniönjoki 0 13
Kisupe 16 0
Klosterbach 0 7
Köhntop 0 7
Köhntop/Schiefe Möhn 0 2
Kohtla 0 2
Koivistonpuro 14 0
Koja, Letiza, Skervelis 0 1
Kokemäenjoki 0 105
Köppernitz 0 1
Korleputer Bach 0 1
Koseler 0 2
Koseler Au 0 7
Koskenkylänjoki 0 47
Koskenkylänjoki eli 0 1
Krazante 0 7
Kražantė 0 6
Kriesebyau 0 10
Kronsbek 0 10
Krusau 0 6
Kruunupyynjoki 0 6
Kuivajoki 0 47
Kulse 0 9
Kulšė 0 3
Kunda 25 0
Kuninkoja 0 1
Kymijoki 32 178
Kyröjoki 0 2
Kyrönjoki 0 27
Laajoki 0 25
Laihianjoki 0 3
Lakaja 0 8
Langballigau 0 8
Lange Rie 0 7
Lapinjoki 0 1
Lapise 0 6
Lapišė 0 3
Lapuanjoki 0 2
Lapväärtinjoki 0 76
Laukysta 0 18
Leba 0 78
Lestijoki 0 90
Liela Jugla 0 12
Lielā Jugla 0 1
Lielupe 0 17
Limingoja 0 6
Lindaubach 0 6
Lindaubach (Güderotter Au) 0 2
Linde 0 2
Liolinga 0 5
Lippingau 0 2
Ljungan 39 0
Lögde 39 0
Loiter 0 2
Loiter Au 0 16
Lomena 0 10
Loo 0 2
Loobu 25 26
Lososinka 14 0
Loviisanjoki 0 8
Luga 41 15
Luhnau 0 1
Lukne 0 3
Luknė 0 3
Luoba 0 7
Lupawa 0 42
Lusis 0 4
Maalahdenjoki 0 2
Maibach 0 7
Malinovka 14 0
Mäntsäläjoki 0 3
Maza Jugla 0 14
Melnichnyi 14 0
Melnsilupe 16 0
Mera 23 13
Merenkurkku 0 1
Merkys 0 9
Mildenitz 0 4
Minija 34 34
Minijos bas 0 1
Mišupis 0 1
Mlinovka 1 0
Mörrumsån 38 0
Mühlbach 0 1
Muke 0 4
Muse 2 30
Musė 0 3
Mustijoki 0 36
MV 0 13
Mynäjoki 0 20
Narva 0 16
Närvijoki 0 1
Nelma 18 0
Nemencia 2 3
Nemenčia 0 6
Neris 43 59
Neris B 0 2
Neva 19 13
Neveza 0 9
Notkopuro 14 0
Nova jogi 0 2
Odra 0 114
Olhavanjoki 0 13
Oravaistenjoki 0 2
Öreälv 39 0
Osterbek 0 6
Other 2 0
other rivers 2 0
others 8 0
Others 11 0
Oulujoki 0 123
Paimionjoki 0 22
Parnu 1 1
Pärnu 14 23
Parseta 0 93
Pasleka 0 34
Peipiya 0 2
Pelysa 0 8
Penttilan-oja 14 0
Perämeri 0 2
Perhojoki 0 15
Perhonjoki 0 59
Persoksna 2 15
Peršoksna 0 2
Peršokšna 0 2
Peršokšnos 0 1
Peschanaya 16 0
Peterupe 40 0
Pēterupe 5 0
Petrovka 18 0
Piasnica 0 10
Piehinkijoki 0 12
Pirita 26 13
Piteälven 13 0
Plastaka 0 15
Plaštaka 0 2
Polchow 0 9
Porvoonjoki 0 60
Pregola 18 0
Privetnaya 14 0
Prochladnaja 18 0
Pudisoo 0 16
Pulverbek 0 8
Purtse 16 49
Pyhajogi 0 18
Pyhäjoki 0 62
Raaseporinjoki 0 1
Råne älv 39 0
Ratnycia 0 2
Rauna 0 2
Reda 0 60
Rega 0 82
Reppeliner 0 1
Reppeliner Bach 0 6
Rickleån 39 0
Riva 18 0
Roja 0 9
Rompotinpuro 14 0
Rosengartener 0 1
Rosengartener Beek 0 2
Saaristomeri 0 3
Saida 0 11
Saide 0 1
Saka 45 0
Salaca 45 4
Salcia 0 4
Saltuona 0 2
Saria 0 7
Sarios 0 1
Sata 0 7
Šata 0 1
Sausdravas 0 2
Sävarån 39 0
Schwartau 0 3
Schwastrumer 0 2
Schwentine 0 2
Schwinge 0 9
Sealand 18 0
Seleznevka 15 0
Selja 25 24
Selkämeri 0 5
Serga 16 0
Serksne 0 10
Šerkšnė 0 3
Sesuola 0 4
Šešuola 0 3
Sesuvis 0 14
Sešuvis 0 1
Šešuvis 0 1
SH 0 33
Siesartis 24 30
Siikajoki 0 72
Simo 39 0
Simojoki 0 84
Sipoonjoki 0 4
Sirvinta 4 26
Širvinta 0 6
Sista 18 0
Siuntionjoki 0 5
Siusis 0 10
Šiušis 0 2
Slupia 0 66
Smiltele 2 0
Smolyachkov 14 0
Spengla 0 4
Spolsau 0 4
Steinbek 0 4
Store 2 0
Strasburger Mühlbach 0 6
Strasburger Mühlenbach 0 2
Strikupe 0 1
Summajoki 0 50
Summanjoki 0 2
Sunija 0 15
Šunija 0 2
Sustis 0 2
Sventoji 59 65
Šventoji 0 10
Sventoji (Neris) 0 2
Sventoji B 20 10
Svetupe 18 0
Svētupe 3 0
Sysa 20 5
Taasianjoki 0 14
Temmesjoki 0 12
Tenenys 0 4
Terteboån 25 0
Tervajoki 0 5
Teuvanjoki 0 16
Toivola 14 0
Torne 39 0
Tornionjoki 0 172
Trave 0 18
Tvarkante 0 5
Ula 0 4
Ume/Vindel 39 0
Uniesta 0 9
Upyna 0 9
Urpalanjoki 0 1
Ushkovskii 16 0
Uskelanjoki 0 9
Uzava 40 1
Užava 5 0
Vaalimaanjoki 0 12
Vääna 25 0
Valgejogi 22 52
Valgejõgi 3 0
Valpperinjoki 0 5
Vanajogi 0 2
Vantaanjoki 0 130
Vasalemma 25 0
Vecpalsa 0 3
Vehkajoki 0 30
Veivirza 0 1
Velikaja 18 0
Venta 48 68
Verseka 0 1
Veskijogi 0 2
Viantienjoki 0 3
Viesvile 0 7
Vija 0 2
Vija, Vecpalsa 0 1
Vilnia 24 29
Virinta 9 36
Virojoki 0 6
Visete 0 5
Vistula 0 150
Vitrupe 45 0
Vizla 0 2
Vizla, Palsa, Vija 0 1
Voke 4 29
Vokė 0 5
Voronka 17 0
Vruda 0 13
Wallbach 0 8
Wallensteingraben 0 8
Warnow 0 7
Wehrau, Mühlenau, Reidsbek 0 1
Wieprza 0 68
Wolfsbach 0 8
Zalesa 0 7
Žalesa 0 2
Žalėsa 0 1
Zeimena 43 1
Zelenogorsky 14 0
Ziezmara 0 3
Žiežmara 0 3
Zvelsa 0 4
Zyba 0 3
(b) Duplicated values for name in ICES vocab
GUID Key Description LongDescription Modified Deprecated description0
41d3b782-c404-4029-9c59-5ccc0ae920da FI83004 Alhonoja NA 2023-07-11 FALSE Alhonoja
1a35a5f0-069a-4e71-a1c7-8ed1f886e293 FI83035 Alhonoja NA 2023-07-11 FALSE Alhonoja
92fa064c-2c1f-4108-a100-da74748008d9 DK0507 Ellebæk NA 2023-07-11 FALSE Ellebaek
f870f9d4-ac9a-46a0-a78d-f4341f2a94f6 DK1155b Ellebæk NA 2023-07-11 FALSE Ellebaek
cec6fbe3-a563-4846-9478-472f3f83777e FI16000 Koskenkylänjoki NA 2023-07-11 FALSE Koskenkylanjoki
9a0ed388-775c-4a01-a1cd-3af13b5385eb FI84055 Koskenkylänjoki NA 2023-07-11 FALSE Koskenkylanjoki
d9f7cc5d-b4b8-4b49-96fe-df2548525fd0 DK0744c Pomlerende NA 2023-07-11 FALSE Pomlerende
2f80e1ab-476e-444f-9e2f-9813efe5002f DK0748 Pomlerende NA 2023-07-11 FALSE Pomlerende
b8d456d6-1b36-4d5a-9a1c-afea66393979 DK0110 Risebæk NA 2023-07-11 FALSE Risebaek
9681b8dc-18d2-4c6a-ae9e-9b37244d52df DK0127 Risebæk NA 2023-07-11 FALSE Risebaek
70ee765f-9d3d-403b-8282-378632dea293 FI82062 Ruonanoja NA 2023-07-11 FALSE Ruonanoja
4a9e3458-8ae2-41c2-a6c1-df903bebe81d FI84136 Ruonanoja NA 2023-07-11 FALSE Ruonanoja
719312c8-ebdb-48d1-9179-f23cb01e6f9b FI82008 Storträsket NA 2023-07-11 FALSE Stortrasket
e073e339-2dde-4651-9f03-71a0fdf65aff FI83094 Storträsket NA 2023-07-11 FALSE Stortrasket
699f678a-96e2-4eff-8fe3-886e5e1253b9 FI81037 Storängsbäcken NA 2023-07-11 FALSE Storangsbacken
3f4725d1-24b3-42a5-af71-9f8745c78e2b FI81075 Storängsbäcken NA 2023-07-11 FALSE Storangsbacken
4c875927-fabb-408e-aab8-2055c8d85822 DK0134 Vasebæk NA 2023-07-11 FALSE Vasebaek
b804f016-7ed6-4e09-ad7f-631492cabd4e DK0528 Vasebæk NA 2023-07-11 FALSE Vasebaek
(c) Rivers with more than one ICES division
more_than_1_ICES_div
Eurajoki 2
Fiskarsinjoki 2
Karjaanjoki 2
Kyrönjoki 2
Mynäjoki 2
Nelma 2
Pärnu 2
Pregola 2
Prochladnaja 2
Sealand 2
Valpperinjoki 2
Venta 2
Wallensteingraben 2
Bornholm 3
Laajoki 3
at sea 4
(d) Table for values corresponding to more than one ICES division
200 22 22-23-24 24 24-25 25 26 28 29 30 31 32
at sea 0 0 0 0 0 0 0 0 95 73 79 142
Bornholm 4 0 0 0 14 3 0 0 0 0 0 0
Eurajoki 0 0 0 0 0 0 0 0 3 28 0 0
Fiskarsinjoki 0 0 0 0 0 0 0 0 1 0 0 2
Karjaanjoki 0 0 0 0 0 0 0 0 2 0 0 23
Kyrönjoki 0 0 0 0 0 0 0 0 0 24 3 0
Laajoki 0 0 0 0 0 0 0 0 4 20 1 0
Mynäjoki 0 0 0 0 0 0 0 0 5 15 0 0
Nelma 0 0 0 0 0 0 17 0 0 0 0 1
Pärnu 0 0 0 0 0 0 0 36 0 0 0 1
Pregola 0 0 0 0 0 0 17 0 0 0 0 1
Prochladnaja 0 0 0 0 0 0 17 0 0 0 0 1
Sealand 4 0 14 0 0 0 0 0 0 0 0 0
Valpperinjoki 0 0 0 0 0 0 0 0 1 4 0 0
Venta 0 0 0 0 0 0 3 113 0 0 0 0
Wallensteingraben 0 6 0 2 0 0 0 0 0 0 0 0

Question / ANSWERS WGBAST

  • Could you please confirm the duplicated values here (values with similar names) in Table 14.

Yes, there are dublicates (with minor differences in writing). Need to check river by river.

  • Why are some entries for some rivers corresponding to more than one area ?

No, there should not be such as long as the key value in ICES vocab will be used. River name (“Description”) don’t always specify the river because several rivers/brooks may have the same name.

River_category

Table 15: River categories in the young fish and smolt database
smolts young_fish
mixed 527 0
wild 860 0
NA 1091 7714

Age

Table 16: Age in the young fish database
(a) Age for smolts
SAL TRS
1s parr 0 8
(b) Age for young fish
SAL TRS
1s parr 253 379
1yr 552 673
1yr parr 424 438
2s 1 0
2s parr 83 184
2yr 903 1137
2yr parr 8 3
3s 0 1
3yr 21 158
alevin 153 325
eyed egg 77 221
fry 408 1312

Question WGBAST

  • What is the meaning of the different age categories ?
  • There are 9 lines in the smolts database who have a stage corresponding to 1s parr Are these caught in downstream traps ?

ANSWER WGBAST

In this you have smolts and parr corresponding to release of aquaculture raised salmons. 2sshould be replaced by 2 s parr. yr correspond to 1yr old smolt. 1 yr parr correspond to parr relase at 1 yr old. There are very few parr in hatcheries that will not have smoltified at 2 yr (2yr parr), most will smoltify at age 1 so that’s why the number are low. Fry correspond to alevins with the yolk sack.

Origin

Table 17: Origin in the young fish and smolt database
smolts young_fish
R 0 7705
W 2478 0
NA 0 9

Question / ANSWERS WGBAST

There are just 9 NA values, is this an error ?

NA are errors.

Type of smolt number estimation method

  1. Complete count of smolts.
  2. Sampling of smolts and estimate of total smolt run size.
  3. Estimate of smolt run from parr production by relation developed in the same river.
  4. Estimate of smolt run from parr production by relation developed in another river.
  5. Inference of smolt production from data derived from similar rivers in the region.
  6. Count of spawners.
  7. Estimate inferred from stocking of reared fish in the river.
  8. Salmon catch, exploitation and survival estimate.
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  1.000   3.000   3.000   3.469   4.000   8.000    8666 

WGBAST

  • NOTE There are character values, “na”, “n.e.”,“0,3”, “0 .1”
  • QUESTION There are missing values there … Is that correct ?
  • Need to look closer all cases to be able to evaluate

part III - TRUTTA electrofishing densities dataset

truttadens <- readxl::read_xlsx(file.path(datawd, "WGBAST_TRS_densities2024filled.xlsx"), sheet = "dane")[,1:9]
ttd <- janitor::clean_names(truttadens)
ttd <- ttd[!is.na(ttd$density_n_100m2),]

ttd %>%skim()
Data summary
Name Piped data
Number of rows 10129
Number of columns 9
_______________________
Column type frequency:
character 6
numeric 3
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
species 2 1.00 3 3 0 1 0
country 0 1.00 2 4 0 10 0
sub_div 0 1.00 2 5 0 13 0
main_river 53 0.99 3 28 0 522 0
river 1938 0.81 3 43 0 620 0
age 55 0.99 2 3 0 2 0

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
year 0 1.00 2011.85 7.94 1975 2007.0 2013.00 2019.00 2023.00 ▁▁▂▆▇
density_n_100m2 0 1.00 18.03 38.77 0 0.8 4.61 17.31 598.47 ▇▁▁▁▁
number_of_sites 680 0.93 2.56 4.44 1 1.0 1.00 3.00 190.00 ▇▁▁▁▁

Species

Table 18: Frequencies of species type in the trutta densities dataset
(a) Frequency of values
Var1 Freq
TRS 10127
NA 2
(b) Lines with missing value for species
species country year sub_div main_river river age density_n_100m2 number_of_sites
NA FI 2002 31 Torniojoki Äkäsjoki >0+ 9.10 9
NA PL 2023 24 Odra Drawa >0+ 1.46 5
NOTE WGBAST

Two values without species, we can correct while integrating

Country

Table 19: Countries in the trutta density dataset
country Freq
DK 394
EE 2560
FI 416
GER 1598
LT 341
LV 842
PL 359
RU 464
SE 2403
SE-S 752

Question WGBAST

  • GER should be DE

Yes

  • What is SE-S, it’s not a country how do we deal with this. Why is it needed ? Could we use some other column from the other datasets (as they will be in the joined database structure) ?

This is notation for the assessment unit southern Sweden. Should not be used as the country value.

Time

Table 20: Number of values per year and sheet in trutta density dataset
country Freq
1975 12
1976 16
1977 2
1978 12
1982 12
1983 22
1984 10
1986 6
1987 3
1988 10
1989 16
1990 11
1991 9
1992 33
1993 35
1994 41
1995 73
1996 104
1997 69
1998 86
1999 116
2000 154
2001 170
2002 176
2003 225
2004 301
2005 354
2006 342
2007 342
2008 414
2009 452
2010 386
2011 383
2012 459
2013 387
2014 412
2015 473
2016 373
2017 505
2018 558
2019 811
2020 543
2021 595
2022 560
2023 56
NOTE

Years distributed from 1975, nothing special (Table Table 20), this db does not use time periods lower than year.

Age

Table 21: Age in the trutta density dataset
age Freq
>0+ 4913
0+ 5161
NA 55

ANSWER WGBAST

Yes for Trutta the ages are divided between 0+ and older than 0+ which is a grouping of several ages.

Geography

Table 22: Geographical units in the trutta densities dataset
(a) Rivers (note that some labels seem to be duplicated in the database)
river Freq
Aapuajoki 10
Abava 14
Abuls 4
Äkäsjoki 68
Akmena 7
Akmenos - Danės basin 24
Älandsån 32
Ålsån 4
Alte Schwentine / Kührener Au UL 2
Althoefer 4
Althöfer Bach 7
Altja oja 66
Amata 46
Angerja oja 14
Angla kraav 4
Araka oja 2
Arakaoja 2
Audru jõgi 4
Augraben 10
Åvaån 44
Azika 14
Bach aus Bernstorf 4
Bach aus Blowatz 6
Bach aus Grundshagen 6
Bach aus Hanshagen 6
Bach aus Huckstorf 4
Bach aus Körchow 4
Bach aus Neu Karin 6
Bach aus Parchow 6
Bach aus Ravensberg 4
Bach aus Zapkendorf 4
Bach aus Zierow 4
Bach bei Karschau 2
Bach Bernstorf 4
Bachgraben 5
Bachgraben (Ryckgraben) 4
Bagge 2
Baltic - Šventoji basin 12
Barnitz 14
Bartuva 7
Bartuvos basin 24
Beke 12
Bergshamraån 42
Beste 10
Bienebek 2
Birkenmoorgraben 4
Björkån 24
Blowatzer Bach 1
Blykobbe 2
Bollhaegerfliess 4
Bollhäger Fließ 6
Böllhäger Fließ 1
Bollstaån 8
Bönälven 14
Borgforsälven 22
Börrumsån 44
Brændemølle å 7
Brandsau ML 4
Brandsau UL 8
Brasla 24
Brebowbach 10
Brüeler Bach 4
Buslovka 2
Buurdieksgraben 4
Byskebäcken 42
Bystryi 6
Carbäck 4
Carbäk 6
Chernaya 12
Ciecere 6
Curau 10
Damshäger Bach 7
Degerbäcken 46
Dingwatter Au 6
Drawa 2
Drwęca 12
Dubysa 7
Dubysos basin 24
Durbe 4
Edstabäcken 22
Eglupe 2
Egļupe 8
Ekeberger Au OL 2
Ekeberger Au UL 12
Emakraav 2
Enångersån 24
Eru kr. 2
Esgruser Mühlenstrom 4
Esna jõgi 2
Fällforsån 44
Farpener Bach 4
Farver Au 8
Farver Au OL 2
Farver Au Wald 2
Faule Trave UL 8
Fauler Bach 2
Fauler Bach/Plastbach 4
Flaruper Au 4
Gådeån 2
Gladyschevka 18
Glazupe 2
Glāžupe 10
Glomså 17
Goddestorfer Au 4
Goldbach 10
Gorohovka 4
Gösebek 2
Göwe 10
Graben aus Ahrendsee 9
Graben aus Thorstorf 2
Grimsau OL 4
Grimsau UL 12
Grinau OL 2
Grinau UL 2
Große Hüttener Au 10
Große Schierbek 4
Gumbölenjoki 16
Gusinaya 21
Häädemeeste jõgi 30
Haberniser Au 4
Habernisser Au 8
Hagbyån 38
Hagener Au 4
Haisterbek OL 4
Haisterbek UL 12
Hällkroksbäcken 6
Halmstadsbäcken 46
Hanshäger Bach 7
Harku oja 2
Harrijoki 14
Heilsau 2
Hellbach 11
Hernespuu oja 4
Höbringi oja 32
Hohenfelder Mühlenau 8
Hohler Bach UL 8
Holmbacher Graben 10
Hopfenbach (Brüeler Bach) 4
Hugraifsån 38
Humalaste jõgi 4
Huumosen-oja 4
Idbyån 20
Ikla pkr 2
Ina 16
Ingarskilanjoki 16
Inviksån 26
Isojoki 16
Jägala jõgi 48
Jämaja oja 26
Järveoja 4
Jaunupe 54
Jeksen Bæk 20
Johannisbek OL 8
Jūra 7
Jūros basin 24
Jyryjoki 12
Kääntöjoki 10
Kaberla oja 46
Kabli oja 2
Kadaka oja 20
Kagghamraån 46
Kaldamäe oja 12
Kana-oja 2
Kanan-oja 4
Kanaoja 2
Kangosjoki 57
Karepa oja 4
Käsmu oja 2
Katzbach 10
Keibu pkr 18
Keila jõgi 56
Kello-oja 6
Keräntöjoki 6
Khabolovka 14
Khrevitsa 2
Kiebitzbek 4
Kiljatu oja 2
Kirrin-oja 2
Kiruma pkr 20
Kiruma pkr ülemine haru 2
Kitkiöjoki 40
Klaasbach 4
Klappmarksbäcken 46
Kloostri jõgi 38
Klosterbach 7
Kluetzer Bach 4
Klützer Bach 6
Kobek 4
Koerchow 4
Koesterbeck 2
Köhntop 5
Kohtla jõgi 2
Kohtla oja 2
Koivistonpuro 6
Kolga jõgi 2
Kolga oja 38
Kolmårdsbäcken 44
Kongla oja 2
Koolimäe oja 4
Kopparviksbäcken 38
Köppernitz 11
Korge 2
Korģe 50
Körkwitzer Bach 1
Korleputer Bach 2
Korleputer Mühlbach 1
Kõrtsioja 12
Koseler Au 18
Koseler Au Ol / Graben II 10
Kossau ML 10
Kossau UL 8
Kossau unterhalb Tresdorfer See 2
Kösterbeck 10
Kramforsån 8
Kremper Au 8
Kremper Au Mündung 4
Kremper Au UL 8
Krieseby Au 2
Kriesebyau 10
Krohnhorster Trebel 4
Kronsbek-Aschau 8
Kronsbek - Aschau 14
Krusau 2
Kuivajõgi 14
Kulleån 46
Kumada 4
Kunda jõgi 64
Künnapõhja oja 2
Künnimaa oja 2
Kuokkalan 4
Küti oja 2
Kutsasjoki 10
Kuusalu oja 6
Kuusiku oja 2
Kvarnån 16
Kvarsebobäcken 34
Laagna oja 2
Lachsbach Wald 4
Lachsbach/Steinbach 14
Læså 2
Lähkma jõgi 4
Lahnajoki 12
Landsgraben UL 2
Langballigau 12
Lange Rie 7
Långträskån 2
Lehbekerau 2
Leipiöjoki 8
Leisi jõgi 22
Leivajõgi 28
Lemmejõgi 20
Lemovzha 26
Lencupe 4
Lenčupe 8
Leppoja 2
Lestijoki 11
Lētiža 12
Lētīža 6
Lielā Jugla 18
Ligatne 2
Līgatne 10
Ligeoja 24
Lilleå 22
Lindau 6
Linde 10
Lipping Au 8
Lippingau 10
Lippingau ML 4
Ljustorpsån 36
Loån 42
Lodmannshäger Bach 4
Lõhavere oja 2
Lohja oja 4
Loiter Au OL 14
Loiter Au UL 12
Loja 12
Longinoja 16
Loo oja 42
Loobu jõgi 62
Loode oja 20
Lorumupe 2
Lorupe 4
Lososinka 4
Lößnitz 8
Lübscher Mühlenbach 2
Lyckebyån 44
Mägara oja 38
Maibach 7
Malbäcken 46
Malda oja 2
Malenter Au ML 10
Malenter Au UL 10
Malinovka 24
Malliner Wasser 10
Männiku oja 40
Männiku(Kolga) jõgi 6
Marlower Bach 9
Maurine 11
Maza Jugla 4
Mazā Jugla 8
Mazupīte 8
Mechelsdorfer Bach 11
Melnichnyi 2
Melsted 2
Merasjoki 10
Meriküla oja 4
Mildenitz 10
Minijos basin 24
Mittlere Trave 18
Mittlere u Untere Trave 8
Moltenower Bach 6
Moltenower Bach (Beke) 4
Moraån 42
Motel 2
Motel3 2
Muehlenfliess 4
Mühlbach (Hohensprenz) 4
Mühlbach Hohensprenz 6
Mühlbach Strelasund 4
Mühlenau 4
Mühlenau, Flaßlandbek, Schmiedenau 6
Mühlenau, Mühlenbach 6
Mühlenbach Strelasund 1
Mühlenbach UL 6
Mühlenbach(Strelasund) 4
Mühlenfließ 7
Mühlenstrom 4
Mustajoki 16
Mustoja jõgi 66
Naamijoki 61
Nätraån 20
Navesti jõgi 2
Nebel 10
Nepste oja 2
Neris 7
Neris basin 24
Nessendorfer Mühlenau 8
Neu Karin 5
Nianån 18
Niinemäe peakraav 2
Nimetu oja Laugu küla juures 2
Nonnenbach 4
Notkopuro 2
Nõva jõgi 46
Nurmizupite 2
Nurmižupīte 8
Nuutri jõgi 16
Ogerna oja 2
Oitme oja 4
Oju pkr 10
Õngu jõgi 18
Örupsån 32
Osterbek 6
Ostpeene 4
Oxbek 12
Paadrema jõgi 4
Pada jõgi 58
Pähkla oja 2
Pähkla pkr 2
Pakajoki 69
Pålböleån 40
Panzower 4
Panzower Bach 7
Parchow 5
Parkajoki 2
Pärlijõgi 2
Pärnu jõgi 50
Paskapuro 6
Peezer Bach 13
Peipiya 2
Pennewitter Bach (in Teppnitzbach) 4
Pennu oja 2
Penttilan-oja 8
Perjatsi oja 2
Pērļupe 2
Peschanaya 8
Petrovka 8
Pidula nimetu oja 2
Pidula oja 30
Piirsalu jõgi 16
Pikasoo oja 2
Pikkmetsa jõgi 2
Pikku Vammeljoki 2
Pilkenbek 2
Pirita jõgi 52
Platenes kanāls 4
Poama oja 10
Poischower Muehlenbach 4
Poischower Mühlenbach 7
Polchow 7
Polevaya 6
Poolnõmme oja 2
Prandi jõgi 2
Prästbäcken 46
Priivitsa oja 20
Privetnaya 8
Pudisoo jõgi 58
Pühajõgi 42
Pulverbek 12
Punapea jõgi 30
Puro (Repino) 2
Purtse jõgi 42
Råån 46
Rabeler Scheidebach 2
Radebach 12
Radegast 8
Radunia 4
Raksupe 2
Raķupe 4
Ramlösabäcken 46
Randkanal 11
Ranna oja 4
Rannametsa jõgi 4
Råtjärnbäcken 44
Rauna 12
Raunis 18
Ravensberg 1
Recknitz 1
Reiu jõgi 8
Reppeliner Bach 7
Riežupe 2
Riguldi jõgi 44
Rihula oja 4
Rinda 10
Risängesbäcken 46
Risebergabäcken 42
Risti oja 18
Ritzerauer Mühlenbach 2
Rompotinpuro 6
Roschinka 10
Rosengartener Beek 6
Rosengartener Bek 7
Rotbaeck 4
Runtiņš 2
Saarjõgi 4
Saegebach 4
Sagader Bach 4
Sagarder Bach 1
Sägebach 6
Sälgträskbäcken 2
Salme jõgi 2
Saluån 42
Salzau 4
Sandhagen 4
Sargarder Bach 4
Sauga jõgi 4
Saula kr 2
Schmieden Au 8
Schwartau 14
Schwartau bis Barkauer See 10
Schwartau UL 8
Schwastrumer Au 6
Schwennau 2
Schwentine bei Klausdorf 10
Schwentine Zulauf Sibbersdorfer See 2
Schwinge 13
Seebach (Steinhagen-Rühn) 4
Sege å 46
Sehrowbach 8
Seleznevka 20
Selja jõgi 52
Selker Mühlenbach 4
Šepka 6
Serga 8
Sestra 2
Siesbek 2
Sikån 24
Sista 26
Själsöån 30
Skalupe 2
Skaļupe 8
Skärjån 18
Skeboån 34
Šķērvelis 10
Šķervēlis 8
Smiltelė Baltic sea 12
Smolyakov 2
Smörbäcken 46
Solka 30
Sõmeru oja 2
Sommerdorfer Mühlbach 4
Soonda oja 6
Sõreda oja 6
Sõtke jõgi 8
Stadtgraben 4
Steinau/bei Nusse 14
Steinhagen 4
Stenbitbäcken 14
Stepenitz 10
Strasburger Mühlbach 3
Straßburger MB 2
Strehlower Bach 10
Stridbäcken 46
Strikupe 2
Strīķupe 20
Strinneån 26
Stubberup bæk 20
Süderbeste 6
Svenskebæk 16
Šventosios basin 24
Svētupe 2
Swinow 13
Šyša 7
Šyšos basin 24
Taaliku pkr 24
Tammispea oja 8
Tarnewitzer Bach 7
Tążyna 4
Tchernaya 2
Tebra 30
Teetzlebener Mühlenbach 4
Tegelbek/Twisselbek 10
Tehumardi pkr 2
Tensfelder Au 10
Tensfelder Au OL/Schlamersdorfer Moorgraben 4
Teppnitzbach 4
Tessenitz 10
Testorfer Au 6
Thorstorf 1
Timmkanal 36
Tirtsi jõgi 30
Tiskre 2
Tjærbæk 21
Tohrstorfer Bach 4
Toivola 4
Tolkkijoki 14
Tolkuse oja 2
Tollense 6
Toolse jõgi 54
Torsbäcken 44
Tõrvajõgi 6
Tõrvanõmme oja 2
Tõstamaa jõgi 32
Tostarpsbäcken 46
Trave I 14
Treimanni oja 6
Treppoja 6
Trunnerupsbäcken 42
Tryssjöbäcken 44
Tuhala jõe suudmest 2 haruoja 8
Tuhala jõgi 6
Türisalu 2
Tuuraste oja 8
Tvärån 56
Twisselbek 2
Udria oja 6
Udriku oja 2
Uecker 2
Üecker 2
Ukhora 12
Ura jõgi 6
Uruste oja 2
Uschkovsky 10
Uuemõisa oja 2
Vääna jõgi 52
Vaidava 4
Vaidava jõgi 2
Vainupea jõgi 58
Vaive 18
Valdimurru oja 2
Valgejõgi 58
Valkla oja 38
Valtiojoki 44
Vanajõgi 18
Vanakubja oja 4
Vanka 10
Varja oja 2
Vasalemma jõgi 56
Vaskjõgi 2
Västanbäcken 45
Veån 24
Vecpalsa 14
Vedruka oja 20
Vejupite 2
Vējupīte 8
Velikaya 6
Venta basin 8
Verkaån 44
Vesiku oja 20
Veski jõgi 44
Veskioja 20
Vēždūka 2
Vidon 14
Vidon' 2
Viešviles basin 16
Vihterpalu jõgi 54
Vildoga 10
Virån 40
Virbupe 4
Vitsån 40
Vodja jõgi 2
Voka oja 4
Võlupe jõgi 10
Vorfluter Kronstrang 4
Voronka 22
Võsu jõgi 52
Vruda 22
Waidbach 8
Wallbach 7
Wallensteingraben 11
Warbel 4
Warnow 10
Wellspanger Au 10
Westpeene 2
WestPeene 4
WestPeene (hinter Malchiner See) 4
Wietingsbach 4
Wittbeck 5
Wolfsbach 7
Yukkola east 12
Yukkola middle 4
Yukkola west 2
Zarnow 17
Zarow 2
Žeimena 7
Žeimenos basin 24
Zelenogorsky 4
Ziddorfer Mühlenbach 4
Zielona Struga 12
Zierower Bach 5
NA 1938
(b) Rivers with more than one ICES division
more_than_1_ICES_div
Bachgraben 2
Beke 2
Brebowbach 2
Degerbäcken 2
Kopparviksbäcken 2
Kösterbeck 2
Maurine 2
Peezer Bach 2
Punapea jõgi 2
Randkanal 2
Sägebach 2
Schwinge 2
Själsöån 2
Stepenitz 2
Swinow 2
Trunnerupsbäcken 2
Veskioja 2
Zarnow 2
(c) Table for values corresponding to more than one ICES division
22 23 24 27 28 29 30 31 32
Bachgraben 1 0 4 0 0 0 0 0 0
Beke 10 0 2 0 0 0 0 0 0
Brebowbach 4 0 6 0 0 0 0 0 0
Degerbäcken 0 0 0 0 0 0 42 4 0
Kopparviksbäcken 0 0 0 4 34 0 0 0 0
Kösterbeck 8 0 2 0 0 0 0 0 0
Maurine 7 0 4 0 0 0 0 0 0
Peezer Bach 11 0 2 0 0 0 0 0 0
Punapea jõgi 0 0 0 0 0 8 0 0 22
Randkanal 10 0 1 0 0 0 0 0 0
Sägebach 5 0 1 0 0 0 0 0 0
Schwinge 1 0 12 0 0 0 0 0 0
Själsöån 0 0 0 4 26 0 0 0 0
Stepenitz 9 0 1 0 0 0 0 0 0
Swinow 1 0 12 0 0 0 0 0 0
Trunnerupsbäcken 0 40 2 0 0 0 0 0 0
Veskioja 0 0 0 0 12 8 0 0 0
Zarnow 15 0 2 0 0 0 0 0 0
(d) Table of main rivers
main_river Freq
Aarhus å 20
Åbyälven 50
Age 2
Aģe 28
Älandsån 32
Althöfer Bach 8
Altja oja 68
Amata 4
Angerja oja 2
Ångermanälven 50
Angla kraav 4
Araka oja 2
Arumetsa oja 2
Audru jõgi 4
Augraben 12
Åvaån 44
Bach aus Bernstorf 6
Bach aus Blowatz 6
Bach aus Grundshagen 6
Bach aus Hanshagen 6
Bach aus Körchow 4
Bach aus Neu Karin 8
Bach aus Parchow 8
Bach aus Ravensberg 4
Bach aus Thorstorf 2
Bach aus Zierow 6
Bach bei Karschau 2
Bachgraben 6
Bäk 2
Baltic - Šventoji basin 30
Barthe 1
Bartuva (Barta) 6
Bartuva(Barta) 6
Beke 16
Bergshamraån 42
Bienebek 2
Blowatzer Bach 3
Bollhaeger Fliess 8
Bollhaegerfliess 4
Bollhäger Fließ 8
Böllhäger Fließ1 1
Bollstaån 8
Bornholm 8
Bornholm area 38
Börrumsån 44
Brændemølle å 8
Brebowbach 6
Broendstrup Moelleaa 2
Brøndstrup Mølleå 16
Byskeälven 158
Bystryi 6
Carbäk 8
Czarna Wda 14
Damshäger Bach 4
Daugava 30
ec_02 6
ec_03 4
ec_07_a 4
ec_07_b 14
ec_08 4
ec_09 4
Elverdams Å 2
Elverdams Å st2 16
Emån 60
Enångersån 24
Eru kr. 2
Espoonjoki 17
Farpener Bach 5
Farver Au 8
Fauler Bach 4
Fauler Bach/Plastbach 4
ff_01 4
ff_04 2
ff_05_b 12
ff_06_b 6
ff_07 4
ff_08 4
ff_09_a 4
ff_09_b 10
ff_10 2
ff_16 2
Fruebæk 2
Fruerskov Bæk 10
Gådeån 2
Gätenbach 2
Gauja 290
Gladyschevka 19
Goldbach 8
Gorohovka 4
Göwe 8
Graben aus Ahrendsee 10
Graben aus Sandhagen 2
Graben aus Thorstorf 2
Gudenå 43
Häädemeeste jõgi 29
Habernisser Au 8
Hagbyån 38
Halleby å 7
Hällkroksbäcken 6
Hanshagener Bach (Ziese) 2
Hanshäger Bach 6
Harkenbaek 4
Harku oja 2
Haubach 2
Hellbach 45
Hernespuu oja 4
Höbringi oja 2
Hohen Sprenzer Mühlbach 2
Hohenfelder Mühlenau 8
Holmbacher Graben 8
Hopfenbach 2
Hörnån 46
Hugraifsån 38
Humalaste jõgi 2
Huumosen-oja 4
Idbyån 20
Ikla pkr 2
Inčupe 4
Indalsälven 40
Ingarskilanjoki 28
Inviksån 26
Irbe 22
Isojoki 34
Jägala jõgi 50
Jämaja oja 26
Järveoja 4
Kaberla oja 48
Kabli oja 2
Kacza 11
Kadaka oja 21
Kågeälven 38
Kagghamraån 46
Kaldamäe oja 2
Kalixälven 194
Karepa oja 4
Käsmu oja 2
Katzbach 8
Keibu pkr 18
Keila jõgi 57
Kello-oja 6
Khabolovka 17
Kiljatu oja 2
Kirrin-oja 2
Kiruma pkr 22
Ķīšupe 6
Kloostri jõgi 39
Klosterbach 9
Kluetzer Bach 4
Klützer Bach 6
ko_02 6
ko_10_a 2
ko_10_b 10
ko_10_c 8
ko_13 6
ko_15 4
ko_20 4
ko_23 4
Koerkwitzbach 4
Koesterbeck 2
Köhntop 4
Kohtla oja 2
Koivistonpuro 6
Kolding 2
Kolding Å 18
Kolga jõgi 2
Kolga oja 39
Kolmårdsbäcken 78
Koolimäe oja 4
Kopparviksbäcken 38
Köppernitz 13
Körkwitzbach 3
Körkwitzer Bach 1
Korleputer Bach 4
Korleputer Mühlbach 2
Kõrtsioja 2
Koseler Au 8
Kösterbeck 8
Kramforsån 40
Kremper Au 8
Krieseby Au 2
Kronsbek-Aschau 8
Kunda jõgi 65
Künnapõhja oja 2
Künnimaa oja 2
Kuokkalan 4
Küti oja 2
Kuusalu oja 6
Kuusiku oja 1
Laagna oja 2
Lāčupīte 8
Læså 16
Lange Rie 4
Leba 38
Leisi jõgi 22
Leivajõgi 2
Lemmejõgi 21
Lestijoki 34
Ligeoja 24
Linde 12
Lipping Au 8
Ljungan 18
Loån 42
Lögdeälven 146
Lohja oja 4
Lollikebaek 2
Lollikebæk 20
Lollikebæk_site 2 2
Lonaste 2
Loo oja 44
Loobu jõgi 66
Loode oja 21
Lososinka 4
Lößnitz 4
lue_01_c 8
lue_01_d 4
lue_02 2
lue_03_b 4
lue_03_c 14
lue_08 2
Luga 95
Lupawa 12
Lyckebyån 44
Mägara oja 6
Maibach 4
Malda oja 2
Malinovka 42
Malliner Wasser 6
Mankinjoki 16
Männiku oja 41
Männiku(Kolga) jõgi 6
Marlower Bach 11
Maurine 8
Mechelsdorfer Bach 11
Melnichnyi 2
Melnsilupe 2
Meriküla oja 4
Mildenitz 8
Moellebaek 2
Møllebæk 18
Moltenower Bach 8
Moraån 42
Mörrumsån 62
Motel 2
Motel3 2
mtr_01 8
mtr_02 12
mtr_03 2
mtr_04 4
mtr_07_a 12
mtr_07_b 4
mtr_08_a 6
mtr_09 14
mtr_10 10
mtr_14 2
mtr_15 8
mtr_18_a 2
mtr_19_a 10
mtr_19_c 2
Muehlenfliess 8
Mühlbach Hohensprenz 6
Mühlbach Strelasund 4
Mühlenbach (Strelasund) 2
Mühlenbach(Strelasund) 4
Mühlenfließ 8
Mühlenfliess 1
Mühlenfließ1 1
Mustajoki 16
Mustoja jõgi 68
Nätraån 20
Nebel 16
Nemunas 269
Nepste oja 2
Nessendorfer Mühlenau 8
Nianån 18
Nimetu oja Laugu küla juures 2
Notkopuro 2
Nõva jõgi 48
Nuutri jõgi 16
Nybroån 78
Odense Å 17
Odra 18
og_10 4
og_15 8
og_16_a 2
og_16_b 2
og_16_c 6
Ogerna oja 2
Oitme oja 4
Oju pkr 10
Õngu jõgi 18
Öreälven 56
Orzechowka 14
otr_12_b 4
otr_13_b 8
otr_13_c 8
otr_14 8
otr_15_b 14
otr_15_c 10
Paadrema jõgi 4
Pada jõgi 62
Pähkla oja 2
Panzower Bach 8
Pärnu jõgi 81
Parsęta 40
Peene 38
Peezer Bach 12
Peipiya 4
Penttilan-oja 8
Perjatsi oja 2
Peschanaya 8
Peterupe 2
Pēterupe 28
Petrovka 8
Piasnica 14
Pidula oja 46
Piirsalu jõgi 4
Pikku Vammeljoki 2
Pilsupe 8
Pirita jõgi 120
Piteälven 70
Pitragupe 10
Poama oja 10
Põduste 13
Põduste jõgi 2
Poischower Mühlenbach 6
Polchow 4
Polevaya 6
Poolnõmme oja 2
Prästbäcken 46
Priivitsa oja 21
Privetnaya 8
Pudisoo jõgi 60
Pühajõgi 76
Punapea jõgi 32
Puro (Repino) 2
Purtse jõgi 50
Råån 184
Rabeler Scheidebach 2
Radebach 10
Radegast 8
Randkanal 13
Råneälven 54
Ranna oja 4
Recknitz 28
Reda 38
Rega 28
Reiu jõgi 4
Reppeliner Bach 4
Rickleån 94
Riguldi jõgi 78
Rihula oja 4
Risti oja 17
Riva 2
Rīva 18
Roja 16
Rompotinpuro 6
Roschinka 5
Rosengartener Beek 6
Rosengartener Bek 11
Ryck 4
Ryckgraben 1
Sagader Bach 4
Sagarder Bach 2
Sagarder Bach1 1
Sägebach 6
Saka 28
Salaca 142
Salme jõgi 2
Saluån 42
Sargarder Bach 4
Sauga jõgi 4
Saula kr 2
Sävarån 184
Schmieden Au 8
Schwinge 10
Segeå 88
Sehrowbach 10
Seleznevka 38
Selja jõgi 54
Serga 8
Sestra 2
Siesbek 2
Sista 28
Själsöån 30
Skärjån 18
Skeboån 34
sl_03_b 4
sl_05_a 2
sl_05_b 12
sl_07 6
sl_08 4
sl_09_a 12
sl_09_b 10
sl_10_a 12
sl_10_b 14
sl_11 10
sl_12 6
sl_13 10
sl_15 10
sl_16 10
sl_17 6
sl_18_a 12
sl_18_b 4
Słupia 38
Smiltelė Baltic sea 18
Smolyakov 2
Sõmeru oja 2
Soonda oja 6
Sõreda oja 6
Sõtke jõgi 8
st_03_a 10
st_03_d 10
st_04 8
st_06 14
Stavids Å 18
Stavidså 2
Stepenitz 30
Stokkebæk 26
Storå 18
Storaa 2
Strasburger Mühlbach 4
Straßburger MB 2
Strehlower Bach 12
Stridbäcken 46
Svetupe 2
Svētupe 48
sw_01_a 10
sw_02 10
sw_05 2
sw_13_b 10
sw_21 4
sw_28 2
sw_35_b 10
sw_38 4
Swinow 12
Taaliku pkr 24
Tammispea oja 8
Tarnewitzer Bach 19
Tavelån 44
Teetzlebener Mühlenbach 4
Tehumardi pkr 2
Tessenitz 8
Testeboån 16
Timmkanal 49
Tirtsi jõgi 30
Tiskre 2
Toivola 4
Tollense 18
Toolse jõgi 56
Torneälven 104
Torniojoki 289
Torsbäcken 44
Tõrvajõgi 4
Tõrvanõmme oja 2
Tõstamaa jõgi 33
Trebel 4
Treimanni oja 6
Treppoja 6
Trunnerupsbäcken 42
Türisalu 2
Tuuraste oja 7
Udria oja 6
Uecker 4
Üecker 2
Umeälven 91
Ura jõgi 4
Uruste oja 2
Uschkovsky 9
utr_09 2
utr_10 14
utr_15 2
utr_16 2
Uuemõisa oja 2
Uzava 2
Užava 32
Vääna jõgi 54
Vainupea jõgi 60
Valgejõgi 62
Valkla oja 40
Vanajõgi 18
Vanakubja oja 4
Vantaanjoki 16
Vasalemma jõgi 58
Veån 24
Vejstrup Å 20
Velikaya 6
Venta 70
Venta basin 12
Verkaån 44
Vesiku oja 40
Veski jõgi 46
Veskioja 6
Vihterpalu jõgi 93
Villestrup å 39
Vindelälven 54
Virån 40
Vistula 32
Vitrupe 30
Vitsån 40
Voka oja 4
Võlupe jõgi 10
Voronka 24
Võsu jõgi 54
Waidbach 6
Wallbach 2
Wallensteingraben 13
Warnow 99
Westpeene 2
WestPeene 4
Wieprza 40
Wittbeck 3
Wolfsbach 8
Yukkola east 12
Yukkola middle 4
Yukkola west 2
Zagórska Struga 22
Zaķupe 8
Zarnow 12
Zarow 2
Zelenogorsky 4
Zierower Bach 6
Ziese 1
NA 53

Question / answers WGBAST

  • Would it be usefull to start from a full db of electrofishing data ?

Yes, I thing would be good. Like for SAL electrofishing data too.

  • Could you please confirm the duplicated values here (values with similar names) in Table 22.

Potentially dublicates, but several rivers/brooks may have the same name.

  • Do you have GIS information corresponding to those rivers ?
  • The gis information is available in national geographic data bases. For example the Finnish Environmental Institute host the data concerned.
  • Some values are ‘at sea’ what does it means ?

These are release to the marine water at the coast away from any river mouth (no imprinting to the river).

  • Why are some entries for some rivers corresponding to more than one area ?

by river names yes but not if key code is used

Question ICES

  • There are duplicated names in the ICES Vocab, is it the same rivers ? Do you have ways to separate the rivers (gis information) ?

ANSWER WGBAST : The key code of the ICES vocab separates the rivers, not the river names (“Description”).

part IV - Electrofishing dataset for Salmon

TODO

Get the dataset from WGBAST (Atso)

part V The model

Overview of the different types of data available for the different Baltic salmon stocks. The table also indicates for which stocks the current assessment methodology is estimating smolt abundance, spawner abundance and associated stock–recruit function. River categories: W=wild, M=mixed, R=reared. (source wgbast stock annex)

Salmon populations in Gulf of Bothnia and southern Sweden (AUs 1–4), eastern Main Basin (AU5) and Gulf of Finland (AU6) are assessed separately (ICES 2021).

Overview of the assessment methodology for Baltic salmon stocks. The results from five uppermost analyses provide informative prior probability distributions for the full life-history model. These priors become automatically updated by the information contained in the data and by the biological knowledge of the Baltic salmon life cycle used to build a full life-history model. PSPC=Potential Smolt Production Capacity. Note that smolt trapping data is available from more rivers than indicated in the figure. (source wgbast stock annex)
TODO

Look at the report

Mark recapture

Mark–recapture experiments combined with smolt trapping have been used in eleven rivers (Tornionjoki, Simojoki, Åbyälven, Rickleån, Sävarån, Ume/Vindelälven, Öreälven, Lögdeälven, Testeboån, Mörrumsån and Emån).

  • number of untagged fish caught by the smolt trap
  • the number of tagged smolts released upstream from the trap
  • number of recaptured tagged smolts.
  • different time intervals, like days, or annual totals
  • daily water level
  • water temperature data

Sea marking recapture

Schematic presentation of the mark–recapture model for Baltic salmon. The offshore driftnet and longline fisheries in the Baltic Main Basin are assumed to take place in October and December, respectively. During the migration to the spawning grounds, the salmon can be intercepted by the coastal driftnet fishery in May, the trapnet and gillnet fisheries in June and the river fishery in August (Michielsens et al., 2006a).(source wgbast stock annex)

Parameters

  • Kmaximum smolt production (K, i.e. the smolt production that would be obtained with an infinite number of spawners under the Beverton–Holt model). Lognormal distributions with median and coefficient of variation matching with the ones of exact distributions are used for approximation. K priors are river specific. They might change (data call specific values can be stored each year).
  • Individual expert judgement on the productivity of each rivers for :
    • chance for successfull spawing
    • habitat quality of parr area
    • smoltification age
    • mortality during migration
    • size of production area
  • the model produces a probabilistic justification for the expert views of salmon smolt production
    • parr density capacity (5 discrete classes from the poorest river in the Northern Baltic area to the best river in the Baltic).
    • pre-smolt density capacity (5 classes).
    • smolt production capacity.
  • Yearly smolt production for the rivers Tornionjoki, Simojoki, Åbyälven, Rickleån, Sävarån, Ume/Vindelälven, Öreälven, Lögdeälven, Testeboån and Mörrumsån.
  • Smolt abundance estimated forall other rivers in AU1-4 for which only parr density estimates are available, based on the hierarchical linear regression analysis
  • Mark–recapture analysis : independent estimates of relative parr density and smolt abundance in a form of statistics of posterior distributions. Medians and CV.
  • Maturation rates,
  • Natural mortality rates,
  • Mortality F [year, age, category, fishery]
    • where fishery is :
      • offshore driftnet
      • offshore longline
      • coastal driftnet
      • trapnet and gillnet
      • river fishery
    • And category is :
      • wild / hatchery raised
  • Annual yolk sack mortality,
  • Annual M74 yolk sack mortality
  • Stock recruitment posterior distribution
  • proportion of MSW (multi-sea-winter) spawners encountered in the rivers Tornionjoki, Kalixälven, Byskeälven, Ume/Vindelälven, Öreälven and Piteälven
  • model-predicted catches are raised by the proportions of smolts produced in assessment units 5 and 6 (not yet been included in the model) compared with the total smolt production of all units.
  • the relative occurrence of wild vs. reared salmon in catches
  • Sex ratio (annually changing) for multi-sea-winter salmon for Ume/Vindelälven
  • Sex ratio per stock (outside from Ume/Vindelälven)
  • egg/female per stock
  • … might have missed a lot of things !

References

ICES. 2021. “Stock Annex: Salmon (Salmo Salar) in Subdivisions 22–31 (Main Basin and Gulf of Bothnia) and Subdivision 32 (Gulf of Finland),” April. https://doi.org/10.17895/ices.pub.18623147.v1.
———. 2024. “Baltic Salmon and Trout Assessment Working Group (WGBAST).” ICES Scientific Reports. https://doi.org/10.17895/ICES.PUB.25868665.
 

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