Package 'framrosetta'

Lookup table for Chinook stock IDs from BkFRAM to normal FRAM

Description

This table is based on Chinook stock tables from pre-season 2024. Additional stock may be added in the future (splitting out stock aggregates). The 'bk_lookupfun_chin()' function accommodates this.

Usage

bk_lookup_chin

Format

A data frame with 116 rows and 3 columns:

stock_name_bk

Stock name

bk_stock_id

Stock ID in the BackwardsFRAM table

stock_id

Stock ID anywhere else in FRAM and TAMM

Source

2024 Pre-Season Chinook DB.mdb

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Generate Chinook bk_fram look-up table

Description

At present the FRAM databases use a differents stock_id numbering system in the BackwardsFRAM table than everywhere else. The dataframe 'bk_lookup_chin' provides a lookup table based on the stocks used in Preseason 2024. However, we are working to modify FRAM to support splitting Chinook stock aggregates, which will lead to increased numbers of StockIDs. 'bk_lookupfun_chin' provides an appropruate lookup table based on the 'max_stock' argument, either returning ‘bk_lookup_chin' (if max_stock is not provided or doesn’t exceed the stocks in 'bk_lookup_chin') or extending the dataframe with new stock ids based on the numbering conventions of the bk_stock_id.

Usage

bk_lookupfun_chin(max_stock = NA)

Arguments

max_stock

Positive integer representing the largest *Normal* stock id (stock ids outside of the BackwardsFram table). As of Preseason 2024, there are 78 stocks; splitting stocks might increase this (e.g. 80, 82, 84). Defaults to NA.

Value

Tibble of lookup table. '$stock_name_bk' gives numan-readable stock names; '$bk_stock_id' gives the "StockID" used in backwards FRAM; '$stock_id' gives the StockID used everywhere else. NAs in '$stock_id' correspond to "totalled" stocks, which are used in backwards FRAM and nowhere else.

Examples

temp = bk_lookupfun_chin(80)
tail(temp)

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Chinook fishery information

Description

Mapping of fishery_id to fishery name for Chinook salmon, taken from the 'Fishery' table of the Chinook FRAM database.

Usage

fishery_chinook_fram

Format

A data frame with 74 rows and 5 columns:

species

Species name

version_number

fishery_id

Chinook fishery id number in FRAM

fishery_name

Chinook fishery name in FRAM

fishery_title

consistent and more human readable version of 'fishery_name'

Source

2024 Pre-Season Chinook DB.mdb

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Coho fishery information

Description

Mapping of fishery_id to fishery name for Coho salmon, taken from the 'Fishery' table of the Coho FRAM database.

Usage

fishery_coho_fram

Format

A data frame with 198 rows and 5 columns:

species

Species name

version_number

fishery_id

Coho fishery id number in FRAM

fishery_name

Coho fishery name in FRAM

fishery_title

consistent and more human readable version of 'fishery_name'

Source

2024NOF_CohoFRAMdatabase_distribution.mdb

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Coho fishery information (PSC)

Description

Mapping of FRAM fishery_id to PSC fishery ID and name for Coho salmon, based on the AnnualReport R package.

Usage

fishery_coho_psc

Format

A data frame with 197 rows and 5 columns:

species

Species name

fram_fishery_id

Fishery ID in FRAM

psc_fishery_id

Corresponding ID for the psc fishery

psc_group_code

psc_fishery_name

Name of PSC fishery ID for the psc fishery

psc_fishery_order

Source

https://github.com/PSC-CoTC/AnnualReport

---

Search through fishery and stock lookup tables.

Description

Search through fishery and stock lookup tables.

Usage

fishery_search(pattern, species)

stock_search(pattern, species)

Arguments

pattern	Character string of pattern to search for, case insensitive. If numeric instead, function will return the row with the corresponding stock or fishery ID.
species	"CHINOOK" or "COHO" (or lowercase permutations)

Examples

fishery_search("kmz", "COHO")
fishery_search(50, "COHO")
stock_search("nooksack", "CHINOOK")
stock_search(21, "CHINOOK")

---

Add 'fishery_label' column to describe fisheries of dataframe

Description

Streamlined version of using 'left_join', 'rename', and 'relocate' to add human-readable text to a dataframe with fishery_id or similar columns. Automatically detects species and 'fishery_id' column; user can specify species or alternative name for fishery_id column if needed.

Usage

label_fisheries(.data, species = NULL, fisheries_col = "fishery_id")

Arguments

.data	Dataframe containing 'fishery_id' column (or analogous column with different name specied by 'fisheries_col' argument)
species	character atomic identifying either "CHINOOK" or "COHO" (or variations of those). Defaults to 'NULL'; only needed if '.data' does not have species defined as an attribute. Tables read from a fram database using 'framrsquared' package automatically have appropriate species attribute.
fisheries_col	character atomic identifying the column treated as containing fishery_id values Defaults to 'fishery_id'.

Value

Data frame with additional column 'fishery_label'

Examples

## create example data
dat = data.frame(fishery_id = sample(1:73, size = 10, replace = TRUE))
## Add fishery label
dat |> label_fisheries(species = "CHINOOK")

---

Add 'stock_label' column to describe fisheries of dataframe

Description

Streamlined version of using 'left_join', 'rename', and 'relocate' to add human-readable text to a dataframe with stock_id or similar columns. Automatically detects species and 'stock_id' column; user can specify species or alternative name for stock_d column if needed.

Usage

label_stocks(.data, species = NULL, stocks_col = "stock_id")

Arguments

.data	Dataframe containing 'stock_id' column (or analogous column with different name specied by 'stocks_col' argument)
species	character atomic identifying either "CHINOOK" or "COHO" (or variations of those). Defaults to 'NULL'; only needed if '.data' does not have species defined as an attribute. Tables read from a fram database using 'framrsquared' package automatically have appropriate species attribute.
stocks_col	character atomic identifying the column treated as containing stock_id values Defaults to 'stock_id'.

Value

Data frame with additional column 'stock_label'

Examples

## create example data
dat = data.frame(stock_id = sample(1:73, size = 10, replace = TRUE))
## Add stock information
dat |> label_stocks(species = "CHINOOK")

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Coho limiting stock

Description

Maps between the limiting stock of the Coho TAMM (e.g., 'Hood Canal Wild') and FRAM stock ids. Useful for summarizing impacts on stocks of concern.

Usage

limiting_stock_coho

Format

A tibble with 10 rows and 2 columns:

name

Name of the limiting stock

name_tamm

Exact match of limiting stock name in the TAMM

stock_id_vec

a list of numeric vectors, each containing all fram stock_id values for that TAMM limiting stock

#' @source 2024 Pre-Season Chinook DB.mdb

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Lookup table for FRAM to RMIS recoveries

Description

For more about the Regional Mark Information System (RMIS), see https://www.rmpc.org/.

Usage

rmis_fram

Format

## 'rmis_fram' A data frame with 225,390 rows and 4 columns:

psc_code

RMIS PSC Recovery Location

gear

Gear Code

fishery_id

FRAM fishery ID

fishery_name

FRAM fishery name

Source

<https://github.com/FRAMverse/framr/blob/master/xlsx/lu_coho.xlsx

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Chinook stock information

Description

Mapping of stock_id to stock name for Chinook salmon, taken from the 'Stock' table of the Chinook FRAM database.

Usage

stock_chinook_fram

Format

A data frame with 78 rows and 7 columns:

species

Species name

stock_version

stock_id

Chinook stock id number in FRAM

production_region_number

management_unit_number

stock_name

Chinook stock name in FRAM

stock_long_name

'stock_name' but more human readable

Source

2024 Pre-Season Chinook DB.mdb

---

Coho stock information

Description

Mapping of FRAM stock_id to FRAM stock name for Coho salmon, taken from the 'Stock' table of the Coho FRAM database.

Usage

stock_coho_fram

Format

A data frame with 78 rows and 7 columns:

species

Species name

stock_version

stock_id

Coho stock id number in FRAM

production_region_number

management_unit_number

stock_name

Coho stock name in FRAM

stock_long_name

'stock_name' but more human readable

limiting_stock_name

Identifier for which of the limiting stock names of the Coho TAMM (sheet '2') this stock contributes to, if any.

#'

limiting_stock_name_tamm

As 'limiting_stock_name', but exact match to name in TAMM.

Source

2024NOF_CohoFRAMdatabase_distribution.mdb

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Coho stock information (PSC)

Description

Mapping of FRAM stock_id to PSC stock id and psc stock names, based on the AnnualReport R package.

Usage

stock_coho_psc

Format

A data frame with 41 rows and 4 columns:

species

Species name

fram_stock_id

Coho stock id number in FRAM

psc_stock_id

Corresponding PSC stock ID

psc_stock_name

PSC stock name

Source

https://github.com/PSC-CoTC/AnnualReport

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Chinook timestep information stock information

Description

Mapping of timestep numbers to dates in the year, taken from the 'TimeStep' table of the Chinook FRAM database

Usage

timestep_chinook_fram

Format

A data frame with 4 rows and 5 columns:

species

Species name

version_number

time_step_id

id number for the time step

time_step_name

Span of each timestep. Timesteps start on the first of the month, and end on the last of the month. Note that 'Oct-Apr-2' is highlighting that timestep 4 runs from October of the current year to April of the NEXT year (equivalent to timestep 1 of the following year).

time_step_title

'time_step_name', but months are written out

Source

2024 Pre-Season Chinook DB.mdb

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Coho timestep information stock information

Description

Mapping of timestep numbers to dates in the year, taken from the 'TimeStep' table of the Chinook FRAM database

Usage

timestep_coho_fram

Format

A data frame with 5 rows and 5 columns:

species

Species name

version_number

time_step_id

id number for the time step

time_step_name

Span of each timestep. Timesteps start on the first of the month, and end on the last of the month.

time_step_title

'time_step_name', but months are written out consistently

Source

2024NOF_CohoFRAMdatabase_distribution.mdb

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Lookup table for FRAM to TOCAS

Description

Lookup table for FRAM to TOCAS

Usage

tocas_fram

Format

## 'tocas_fram' A data frame with 10,462 rows and 6 columns:

fisher_type

1 = Non-Treaty / 2 = Treaty

gear

Gear Code

dispostion

Dispostion. "COMM" = Commercial, "C&SF" = Ceremonial and Subsistence fishing, "ORGN" = , "Test" and "TEST" = Test fishery (?), TKHM = ??

catch_area

Catch area code, not zero-padded

fishery_id

FRAM fishery ID

fishery_name

FRAM fishery name

Source

<https://github.com/FRAMverse/framr/blob/master/xlsx/lu_coho.xlsx

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Lookup table for FRAM to WAFT

Description

Lookup table for FRAM to WAFT

Usage

waft_fram

Format

## 'waft_fram' A data frame with 10,462 rows and 6 columns:

fishery_type

1 = Non-Treaty / 2 = Treaty

gear

Gear Code

dispostion

Dispostion. "COMM" = Commercial, "C&SF" = Ceremonial and Subsistence fishing, "ORGN" = , "Test" and "TEST" = Test fishery (?), TKHM = ??

catch_area

Catch area code, zero-padded

fishery_id

FRAM fishery ID

fishery_name

FRAM fishery name

Source

<https://github.com/FRAMverse/framr/blob/master/xlsx/lu_coho.xlsx

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