overview
framrosetta.Rmd
library(framrosetta)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, unionframrosetta 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:
Adding stock or fishery label
Frequently we work with tables that use stock id or fishery id to
identify stocks or fisheries; while useful for programming, id numbers
are not the easiest to read. label_stocks() and
label_fisheries() use stock_id and
fishery_id to add human-readable stock and fishery names.
These functions are flexible (can manually specify the species or ), but
the simplest use-case is to label tables pulled from a fram database
with the framrosetta package, which works with default
arguments. Here is an example, using an artificial dataframe because we
cannot use framrsquared::fetch_table() in vignettes.
## create example data with random coho stock id, fishery ids, and landed catch
## We use
dat = stock_coho_fram[sample(1:nrow(stock_coho_fram), size = 5),] |>
dplyr::select(stock_id) |>
mutate(fishery_id = sample(1:200, size = length(stock_id), replace = TRUE),
landed_catch = runif(length(stock_id), min = 1, max = 1000))
# This makes a dataframe that could reasonably be output from framrsquared functions
dat
#> # A tibble: 5 × 3
#> stock_id fishery_id landed_catch
#> <dbl> <int> <dbl>
#> 1 173 102 875.
#> 2 151 111 176.
#> 3 204 47 35.2
#> 4 63 159 321.
#> 5 229 196 403.
## Not very human readable
## make the stock_id human readable
dat |>
label_stocks()
#> # A tibble: 5 × 4
#> stock_id stock_label fishery_id landed_catch
#> <dbl> <chr> <int> <dbl>
#> 1 173 Wash Late Wild UnMarked 102 875.
#> 2 151 Chehalis River Hatchery UnMarked 111 176.
#> 3 204 California Central Coast Wild Marked 47 35.2
#> 4 63 Deschutes River (WA) Wild UnMarked 159 321.
#> 5 229 Upper Fraser River Hatchery UnMarked 196 403.
## make both stock_id and fishery_id human readable
dat |>
label_stocks() |>
label_fisheries()
#> # A tibble: 5 × 5
#> stock_id stock_label fishery_id fishery_label landed_catch
#> <dbl> <chr> <int> <chr> <dbl>
#> 1 173 Wash Late Wild UnMarked 102 WA Area 8 Tr… 875.
#> 2 151 Chehalis River Hatchery UnMark… 111 WA Area 8D N… 176.
#> 3 204 California Central Coast Wild … 47 Willapa Bay … 35.2
#> 4 63 Deschutes River (WA) Wild UnMa… 159 Area 12C-12D… 321.
#> 5 229 Upper Fraser River Hatchery Un… 196 SEAK Northwe… 403.Searching for stock or fishery
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")
#> # A tibble: 2 × 5
#> species version_number fishery_id fishery_name fishery_title
#> <chr> <int> <int> <chr> <chr>
#> 1 COHO 1 5 Ca KMZ Spt KMZ Sport
#> 2 COHO 1 6 Ca KMZ Trl KMZ Troll
## Figure out which Coho fishery has id 50
fishery_search(50, "COHO")
#> # A tibble: 1 × 5
#> species version_number fishery_id fishery_name fishery_title
#> <chr> <int> <int> <chr> <chr>
#> 1 COHO 1 50 GryHbr Net Grays Harbor Estuary Net
## Find all the Chinook noocksack stocks
stock_search("nooksack", "CHINOOK")
#> # A tibble: 6 × 7
#> species stock_version stock_id production_region_number management_unit_number
#> <chr> <int> <int> <int> <int>
#> 1 CHINOOK 5 4 1 6
#> 2 CHINOOK 5 6 1 10
#> 3 CHINOOK 5 2 1 2
#> 4 CHINOOK 5 3 1 5
#> 5 CHINOOK 5 5 1 9
#> 6 CHINOOK 5 1 1 1
#> # ℹ 2 more variables: stock_name <chr>, stock_long_name <chr>
## Figure out which Chinook stock has id 21
stock_search(21, "CHINOOK")
#> # A tibble: 1 × 7
#> species stock_version stock_id production_region_number management_unit_number
#> <chr> <int> <int> <int> <int>
#> 1 CHINOOK 5 21 4 1
#> # ℹ 2 more variables: stock_name <chr>, stock_long_name <chr>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.
| 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.
| 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.
| 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.
| 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.
| species | stock_version | stock_id | production_region_number | management_unit_number | stock_name | stock_long_name | limiting_stock_name | limiting_stock_name_tamm |
|---|---|---|---|---|---|---|---|---|
| COHO | 1 | 1 | 1 | 1 | U-nkskrw | Nooksack River Wild UnMarked | NA | NA |
| COHO | 1 | 2 | 1 | 2 | M-nkskrw | Nooksack River Wild Marked | NA | NA |
| COHO | 1 | 3 | 1 | 3 | U-kendlh | Kendall Creek Hatchery UnMarked | NA | NA |
| COHO | 1 | 4 | 1 | 4 | M-kendlh | Kendall Creek Hatchery Marked | NA | NA |
| COHO | 1 | 5 | 1 | 5 | U-skokmh | Skookum Creek Hatchery UnMarked | NA | NA |
stock_coho_psc
Translating between Coho FRAM stock IDs and PSC IDs and names.
| 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.
| 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.
| 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.
| 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.
| 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.
| 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).
| 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.”) |