Package 'icesASD'

Stock Advice and Scenarios Database Web Services

Description

R interface to access the web services of the ICES Stock Advice and Scenarios database.

Details

Get dataset:

getAdviceViewRecord	Get Advice Record
getCatchScenariosTable	Get Advice Catch Scenario Table
getCatchScenariosNotes	Get Advice Catch Scenario Table Footnotes

Author(s)

Colin Millar, Luca Lamoni, Carlos Pinto, Laura Petre, David Miller and Neil Maginis.

References

ICES Advice and Scenarios database: http://sg.ices.dk.

ICES Advice and Scenarios database web services: http://sg.ices.dk/webservices.aspx.

---

Download advice scenarios

Description

Download a zip file of a set of advice scenarios

Usage

adviceDownload(adviceKeys, dir = ".")

Arguments

adviceKeys	a vector of advice view ids.
dir	directory to download to.

Examples

## Not run: 
adviceDownload(c(1009, 1011, 1022))

## End(Not run)

---

Create The ASD Webservice URL

Description

utility to build a url with optional query arguments

Usage

asd_api(service, ...)

Arguments

service	the name of the service
...	named arguments will be added as queries

Value

a complete url as a character string

Examples

asd_api("hi", bye = 21)
asd_api("csquares", argument1 = 2021, argument2 = NULL)

---

Check catch scenario notes in a browser

Description

Check catch scenario notes in a browser

Usage

checkNotes(notes)

Arguments

notes

df of culumns element of catch scenario table

Examples

## Not run: 
data(scenarioNotes)
checkNotes(scenarioNotes)

## End(Not run)

---

Check catch scenario table in a browser

Description

Check catch scenario table in a browser

Usage

checkTable(columns, rows, values)

Arguments

columns	df of culumns element of catch scenario table
rows	df of rows element of catch scenario table
values	df of values element of catch scenario table

Examples

data(scenarioColumns)
data(scenarioRows)
data(scenarioValues)
checkTable(scenarioColumns, scenarioRows, scenarioValues)

---

Create the XML format for catch scenario data

Description

Create the XML format for catch scenario data

Usage

createASDxml(
  info,
  scenarioColumns,
  scenarioRows,
  scenarioValues,
  scenarioNotes
)

Arguments

info	details
scenarioColumns	details
scenarioRows	details
scenarioValues	details
scenarioNotes	details

Examples

## Not run: 
checkTable(col, rows, vals)

## End(Not run)

---

Get Advice Catch Scenario Table

Description

Returns the catch scenario table for the selected stock and year using the advice view web service.

Usage

get_catch_scenario_table(adviceKey, assessmentYear)

Arguments

adviceKey	integer value of stock adviceKey
assessmentYear	integer value of assessment year

Value

data.frame containing the catch scenarios table for the advice view record

References

https://sg.ices.dk/adviceview/AdviceList

Examples

get_catch_scenario_table(3056,2022)

---

Get Advice View Record

Description

Get Advice View Record

Usage

getAdviceViewRecord(stockcode = NULL, year = NULL, assessmentKey = NULL)

Arguments

stockcode	string value of the stock code you wish to look
year	integer value of assessment year
assessmentKey	integer value of SAG assessmentKey

Examples

catch_scenario_list <- getAdviceViewRecord()
head(catch_scenario_list, 3)

getAdviceViewRecord("bll.27.3a47de", 2021, 15609)

---

Get Any ASD Data

Description

This function combines the functionality of getListStocks, getFishStockReferencePoints, getSummaryTable and getStockDownloadData. It supports querying many stocks and years in one function call.

Usage

getASD(
  stock = NULL,
  year = NULL,
  assessmentKey = NULL,
  outputData = "table",
  purpose = "Advice"
)

Arguments

stock	a stock name, e.g. cod-347d, or cod to find all cod stocks, or NULL to process all stocks.
year	the assessment year, e.g. 2015, or 0 to process all years.
assessmentKey	the assessmentKey of the stock of interest.
outputData	the data you want to retrieve, either "table", "record", or "notes".
purpose	the purpose of the entry, options are "Advice", "Bench", "InitAdvice", default is "Advice".

Value

A data frame (default) or a list if combine is TRUE.

Note

Only years with "Published" status are returned.

Author(s)

Luca Lamoni.

See Also

getListStocks

findAssessmentKey finds lookup keys.

icesSAG-package gives an overview of the package.

Examples

## Not run: 
# Example usage
getASD(stock = "cod.27.7e-k", year = 2023, outputData = "record")
# Example usage with assessmentKey
getASD(assessmentKey = 18719, outputData = "table")

## End(Not run)

---

Get Catch Scenarios Notes

Description

Get Catch Scenarios Notes for a given record

Usage

getCatchScenariosNotes(adviceKey)

Arguments

adviceKey

advice view id(s)

Examples

catch_scenario_note <- getCatchScenariosNotes(2814)
catch_scenario_notes <- getCatchScenariosNotes(c(2814, 2815))

---

Get Catch Scenarios Table

Description

Get Catch Scenarios Table for a given record

Usage

getCatchScenariosTable(adviceKey)

Arguments

adviceKey

advice view id(s)

Examples

catch_scenario_table <- getCatchScenariosTable(2814)
catch_scenario_tables <- getCatchScenariosTable(c(2814, 2815))

---

Catch Scenario Datasets

Description

Predefined colors that can be useful in TAF plots.

Usage

info

Format

List containing four entries:

stockCode	ICES fish stock code
AssessmentYear	assessment year
Purpose	assessment purpose
contact	contact person

Details

The data are an excerpt from ...

Source

ICES (2024).

---

Read a file in the ASD upload format

Description

Read a file in the ASD upload format, returning a list of metadata and data.frame

Usage

readAsdUpload(filename, format = FALSE)

Arguments

filename	the file path of the file to read
format	should the output be formatted into an easy to read table

Examples

#filename <- system.file("CatchScenarios_AdviceKey_3207.xml", package = "icesASD")
#asd <- readAsdUpload(filename)

---

Catch Scenario Datasets

Description

Predefined colors that can be useful in TAF plots.

Usage

scenarioColumns

Format

List containing four entries:

stockCode	ICES fish stock code
AssessmentYear	assessment year
Purpose	assessment purpose
contact	contact person

Details

The data are an excerpt from ...

Source

ICES (2024).

---

Catch Scenario Datasets

Description

Predefined colors that can be useful in TAF plots.

Usage

scenarioNotes

Format

List containing four entries:

stockCode	ICES fish stock code
AssessmentYear	assessment year
Purpose	assessment purpose
contact	contact person

Details

The data are an excerpt from ...

Source

ICES (2024).

---

Catch Scenario Datasets

Description

Predefined colors that can be useful in TAF plots.

Usage

scenarioRows

Format

List containing four entries:

stockCode	ICES fish stock code
AssessmentYear	assessment year
Purpose	assessment purpose
contact	contact person

Details

The data are an excerpt from ...

Source

ICES (2024).

---

Catch Scenario Datasets

Description

Predefined colors that can be useful in TAF plots.

Usage

scenarioValues

Format

List containing four entries:

stockCode	ICES fish stock code
AssessmentYear	assessment year
Purpose	assessment purpose
contact	contact person

Details

The data are an excerpt from ...

Source

ICES (2024).

---

Screen an ASD file and submit for QC checks

Description

In this web service the user can upload a file to be screen and validated by the VMS database. The service can be called using post and the file will have to be part of the body of the call. The user needs to be authenticated in order to call this service. This file can be later pushed to the database by the same user.

Usage

screen_asd_file(file, verbose = FALSE)

Arguments

file	file name of the file containing the data to screen
verbose	return verbose information about the POST request

Value

text message from the screening process

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