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overview

framrosetta.Rmd

framrosetta was developed to store the various lookup tables/mappings necessary to work with FRAM data, or to link other data (TOCAS, WAFT, PSC stock and fishery identities) to FRAM tables or vice versa. Most tables in FRAM identify stock and fisheries by id numbers, but we often want to present figures or analyses using names (or we need to filter to a specific fishery or stock of interest, and we have the name but not the id).

Key functions:

To identify a stock or fishery from an ID number, or to find the stock or fishery ID based on the name, framrosetta includes two search functions. fishery_search takes either a fishery ID number or a full or partial name and returns a tibble summarizing all fisheries that match; stock_search does the same for stocks. In both cases, the species argument must be provided to determine if the function should return the relevant "CHINOOK" or "COHO" fisheries / stocks. The pattern argument can take regular expressions, and is case insensitive.

## Figure out the coho fishery ids for the kmz fisheries
fishery_search("kmz", "COHO")
#>   species version_number fishery_id fishery_name fishery_title
#> 5    COHO              1          5   Ca KMZ Spt     KMZ Sport
#> 6    COHO              1          6   Ca KMZ Trl     KMZ Troll
## Figure out which Coho fishery has id 50
fishery_search(50, "COHO")
#>    species version_number fishery_id fishery_name            fishery_title
#> 50    COHO              1         50   GryHbr Net Grays Harbor Estuary Net
## Find all the Chinook noocksack stocks
stock_search("nooksack", "CHINOOK")
#>    species stock_version stock_id production_region_number
#> 1  CHINOOK             5        4                        1
#> 2  CHINOOK             5        6                        1
#> 38 CHINOOK             5        2                        1
#> 40 CHINOOK             5        3                        1
#> 41 CHINOOK             5        5                        1
#> 77 CHINOOK             5        1                        1
#>    management_unit_number  stock_name                stock_long_name
#> 1                       6 M-NK Sp Hat   Marked Nooksack Spr Hatchery
#> 2                      10 M-NK Sp Nat    Marked Nooksack Spr Natural
#> 38                      2   M-NkSm FF    Marked Nooksack/Samish Fall
#> 40                      5 U-NK SP Nat  UnMarked Nooksack Spr Natural
#> 41                      9 U-NK Sp Hat UnMarked Nooksack Spr Hatchery
#> 77                      1   U-NkSm FF  UnMarked Nooksack/Samish Fall
## Figure out which Chinook stock has id 21
stock_search(21, "CHINOOK")
#>    species stock_version stock_id production_region_number
#> 49 CHINOOK             5       21                        4
#>    management_unit_number stock_name           stock_long_name
#> 49                      1  U-MidPSFF UnMarked Mid PS Fall Fing

Table summaries

framrosetta contains the following tables for translating FRAM fisheries, stocks, and areas to other fishery data or human readable formats:

rmis_fram

Translating between FRAM and RMIS.

knitr::kable(head(rmis_fram, 5))
psc_code fishery_id fishery_name gear
2F 29FW 169 Fraser Spt 40
2F 29FW 169 Fraser Spt 41
2F 29FW 169 Fraser Spt 42
2F 29FW 169 Fraser Spt 43
2F 29FW 169 Fraser Spt 44

tocas_fram

Translating between FRAM and TOCAS.

knitr::kable(head(tocas_fram, 5))
fisher_type gear disposition catch_area fishery_id fishery_name
1 41 C&SF 1 34 A1-Ast 41
1 41 COMM 1 34 A1-Ast 41
1 41 ORGN 1 34 A1-Ast 41
1 41 TEST 1 34 A1-Ast 41
1 41 TKHM 1 34 A1-Ast 41

waft_fram

Translating between WAFT and FRAM.

knitr::kable(head(waft_fram, 5))
fisher_type gear disposition catch_area fishery_id fishery_name
1 41 C&SF 01 34 A1-Ast 41
1 41 COMM 01 34 A1-Ast 41
1 41 ORGN 01 34 A1-Ast 41
1 41 TEST 01 34 A1-Ast 41
1 41 TKHM 01 34 A1-Ast 41

stock_chinook_fram

Translating between Chinook stock IDs and human-readable names.

knitr::kable(head(stock_chinook_fram, 5))
species stock_version stock_id production_region_number management_unit_number stock_name stock_long_name
CHINOOK 5 4 1 6 M-NK Sp Hat Marked Nooksack Spr Hatchery
CHINOOK 5 6 1 10 M-NK Sp Nat Marked Nooksack Spr Natural
CHINOOK 5 8 2 2 M-Skag FF Marked Skagit Summer/Fall Fing
CHINOOK 5 10 2 6 M-SkagFYr Marked Skagit Summer/Fall Year
CHINOOK 5 12 2 10 M-SkagSpY Marked Skagit Spring Year

stock_coho_fram

Translating between Coho stock IDs and human-readable names.

knitr::kable(head(stock_coho_fram, 5))
species stock_version stock_id production_region_number management_unit_number stock_name stock_long_name
COHO 1 1 1 1 U-nkskrw Nooksack River Wild UnMarked
COHO 1 2 1 2 M-nkskrw Nooksack River Wild Marked
COHO 1 3 1 3 U-kendlh Kendall Creek Hatchery UnMarked
COHO 1 4 1 4 M-kendlh Kendall Creek Hatchery Marked
COHO 1 5 1 5 U-skokmh Skookum Creek Hatchery UnMarked

stock_coho_psc

Translating between Coho FRAM stock IDs and PSC IDs and names.

knitr::kable(head(stock_coho_psc, 5))
species fram_stock_id psc_stock_id psc_stock_name
COHO 17 1 Skagit
COHO 18 1 Skagit
COHO 23 1 Skagit
COHO 24 1 Skagit
COHO 29 2 Stillaguamish

fishery_chinook_fram

Translating between Chinook fishery IDs and human-readable names.

knitr::kable(head(fishery_chinook_fram, 5))
species version_number fishery_id fishery_name fishery_title
CHINOOK 1 55 Tr 6B:9Net Tr Area 6B:9 Net
CHINOOK 1 56 A 10 Sport NT Area 10 Sport
CHINOOK 1 57 A 11 Sport NT Area 11 Sport
CHINOOK 1 58 NT10:11Net NT Area 10:11 Net
CHINOOK 1 59 Tr10:11Net Tr Area 10:11 Net

fishery_coho_fram

Translating between Coho fishery IDs and human-readable names.

knitr::kable(head(fishery_coho_fram, 5))
species version_number fishery_id fishery_name fishery_title
COHO 1 1 No Cal Trm No Calif Cst Terminal Catch
COHO 1 2 Cn Cal Trm Cntrl Cal Cst Term Catch
COHO 1 3 Ft Brg Spt Fort Bragg Sport
COHO 1 4 Ft Brg Trl Fort Bragg Troll
COHO 1 5 Ca KMZ Spt KMZ Sport

fishery_coho_psc

Translating between Coho FRAM fishery IDs and PSC IDs and names.

knitr::kable(head(fishery_coho_psc, 5))
species fram_fishery_id psc_fishery_id psc_group_code psc_fishery_name psc_fishery_order
COHO 1 18 Southern U.S. SOF All 17
COHO 2 18 Southern U.S. SOF All 17
COHO 3 18 Southern U.S. SOF All 17
COHO 4 18 Southern U.S. SOF All 17
COHO 5 18 Southern U.S. SOF All 17

timestep_chinook_fram

Translating between Chinook time-step IDs and human-readable names.

knitr::kable(head(timestep_chinook_fram, 5))
species version_number time_step_id time_step_name time_step_title
CHINOOK 1 1 Oct-Apr October-April
CHINOOK 1 2 May-June May - June
CHINOOK 1 3 July-Sept July - September
CHINOOK 1 4 Oct-Apr-2 October-April-2

timestep_coho_fram

Translating between Coho time-step IDs and human-readable names.

knitr::kable(head(timestep_coho_fram, 5))
species version_number time_step_id time_step_name time_step_title
COHO 1 1 Jan-Jun January - June
COHO 1 2 July July
COHO 1 3 August August
COHO 1 4 Septmbr September
COHO 1 5 Oct-Dec October - December

bk_lookup_chin

For Chinook only, the backwards FRAM algorithm uses a separate stock ID system that is hard-coded into FRAM. The underlying idea is that normally FRAM tracks two versions of each stock (marked and unmarked), or occasionally four versions of each stock (marked and unmarked). For part of backwards fram for Chinook, the algorithm separately handles the total number of fish across these versions of stock and the allocation of those fish into the two (or four) stocks. To do so, the algorithm creates a new stock id numbering system, with an additional “sum” stock for each of the pairs (or sets of four) marked/unmarked or marked/unmarked x hatch/natural stocks.

Unfortunately, this means that the BackwardFRAM table in any Chinook database has a StockID that does not match the StockID column in any of the other tables. framrosetta::bk_lookup_chin maps between the stock ids in the BackwardsFRAM table ($bk_stock_id) and the stock ids everywhere else ($stock_id).

knitr::kable(head(bk_lookupfun_chin, 5))
function (max_stock = NA)
{
if (!is.na(max_stock) & (!is.numeric(max_stock) | max_stock%%1 !=
0)) {
cli::cli_alert(“max_stock must be an integer.”)