Package 'icesDatras'

Title: DATRAS Trawl Survey Database Web Services
Description: R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database <https://datras.ices.dk/WebServices/Webservices.aspx>.
Authors: Colin Millar [aut, cre], Cecilia Kvaavik [aut], Adriana Villamor [aut], Scott Large [aut], Arni Magnusson [aut], Vaishav Soni [ctb]
Maintainer: Colin Millar <[email protected]>
License: GPL (>= 2)
Version: 1.4.2
Built: 2024-09-16 04:46:55 UTC
Source: https://github.com/ices-tools-prod/icesDatras

Help Index

Check that a survey name is in the database

Description

Checks a survey name against a list of all survey names in the DATRAS database. If the name is not matched it puts up a message showing the available survey names.

Usage

checkSurveyOK(survey)

Arguments

survey

the survey acronym, e.g. NS-IBTS.

Value

logical.

See Also

checkSurveyYearOK and getSurveyYearQuarterList also perform checks against the DATRAS database.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
checkSurveyOK(survey = "ROCKALL")
checkSurveyOK(survey = "NOTALL")

## End(Not run)

Check that a survey and year combination is in the database

Description

Checks a year and/or survey name against a list of all survey year combinations in the DATRAS database. If the combination is not matched it puts up a message showing the available options.

Usage

checkSurveyYearOK(survey, year, checksurvey = TRUE)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
checksurvey

logical, should the survey name also be checked.

Value

logical.

See Also

checkSurveyOK and checkSurveyYearQuarterOK also perform checks against the DATRAS database.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
checkSurveyYearOK(survey = "ROCKALL", 2015)
checkSurveyYearOK(survey = "ROCKALL", 2000)
checkSurveyYearOK(survey = "NOTALL", 2000)

## End(Not run)

Check that a survey, year and quarter combination is in the database

Description

Checks a quarter and/or year and/or survey name against a list of all survey year quarter combinations in the DATRAS database. If the combination is not matched it puts up a message showing the available options.

Usage

checkSurveyYearQuarterOK(
  survey,
  year,
  quarter,
  checksurvey = TRUE,
  checkyear = TRUE
)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.
checksurvey

logical, should the survey name also be checked.
checkyear

logical, should the year also be checked.

Value

logical.

See Also

checkSurveyOK and checkSurveyYearOK also perform checks against the DATRAS database.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
checkSurveyYearQuarterOK(survey = "ROCKALL", 2015, 3)
checkSurveyYearQuarterOK(survey = "ROCKALL", 2015, 1)
checkSurveyYearQuarterOK(survey = "ROCKALL", 2000, 1)
checkSurveyYearQuarterOK(survey = "NOTALL", 2000, 1)

# be careful of unexpected results with checksurvey and checkyear!
checkSurveyYearQuarterOK(survey = "NOTALL", 2000, 1, checksurvey=FALSE)

## End(Not run)

Get Age-Based Data

Description

Get age-based data such as sex, maturity, and age counts per length of sampled species.

Usage

getCAdata(survey, year, quarter)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.

Value

A data frame.

Author(s)

Colin Millar.

See Also

getDATRAS supports querying many years and quarters in one function call.

getHHdata and getHLdata get haul data and length-based data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
cadata <- getCAdata(survey = "ROCKALL", year = 2002, quarter = 3)
str(cadata)

## End(Not run)

Get Catch Weights

Description

Calculate the total reported catch weight by species and haul.

Usage

getCatchWgt(survey, years, quarters, aphia)

Arguments

survey

the survey acronym e.g. NS-IBTS.
years

a vector of years of the survey, e.g. c(2010, 2012) or 2005:2010.
quarters

a vector of quarters of the year the survey took place, e.g. c(1, 4) or 1:4.
aphia

a vector of Aphia species codes defined in the WoRMS database, e.g. c(126436, 1264374).

Value

A data frame.

Note

The icesVocab package provides findAphia, a function to look up Aphia species codes.

See Also

getSurveyYearList, getSurveyYearQuarterList, and getDatrasDataOverview also list available data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getCatchWgt(survey = "ROCKALL", years = 2002, quarters = 3, aphia = 126437)

# look up specific species
aphia <- icesVocab::findAphia(c("cod", "haddock"))
cwt <- getCatchWgt(survey = "ROCKALL", years = 2002, quarters = 3, aphia = aphia)

## End(Not run)

Get CPUE per Age per Haul per Hour for a given Survey, year and Quarter

Description

Get CPUE per Age per Haul per Hour for a given Survey, year and Quarter

Usage

getCPUEAge(survey, year, quarter)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of interest, e.g. 1

Value

A data frame.

Author(s)

Adriana Villamor.

See Also

getHHdata and getCAdata get haul data and age-based data., and getIndices, and getCPUELength.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getCPUEperAge(survey = "NS-IBTS", year = 2018, quarter = 1)

## End(Not run)

Get CPUE per Length per Haul per Hour for a given Survey, year and Quarter

Description

Get CPUE per Length per Haul per Hour for a given Survey, year and Quarter

Usage

getCPUELength(survey, year, quarter)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of interest, e.g. 1

Value

A data frame.

Author(s)

Adriana Villamor.

See Also

getHHdata and getCAdata get haul data and age-based data., and getIndices, and getCPUEAge.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getCPUELength(survey = "NS-IBTS", year = 2018, quarter = 1)

## End(Not run)

Get Any DATRAS Data

Description

This function combines the functionality of getHHdata, getHLdata, and getCAdata. It supports querying many years and quarters in one function call.

Usage

getDATRAS(record = "HH", survey, years, quarters)

Arguments

record

the data type required: "HH" haul data, "HL" length-based data, "CA" age-based data.
survey

the survey acronym e.g. NS-IBTS.
years

a vector of years of the survey, e.g. c(2010, 2012) or 2005:2010.
quarters

a vector of quarters of the year the survey took place, i.e. c(1, 4) or 1:4.

Value

A data frame.

Author(s)

Scott Large and Colin Millar.

See Also

getHHdata, getHLdata, and getCAdata get haul data, length-based data, and age-based data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
hhdata <- getDATRAS(record = "HH", survey = "ROCKALL", years = 2002, quarters = 3)
hldata <- getDATRAS(record = "HL", survey = "ROCKALL", years = 2002, quarters = 3)
cadata <- getDATRAS(record = "CA", survey = "ROCKALL", years = 2002, quarters = 3)

## End(Not run)

Summarize Data Availability

Description

Evaluate a presence-absence table for each survey with '1' where there is data and '0' (printed as '.') otherwise.

Usage

getDatrasDataOverview(surveys = NULL, long = TRUE)

Arguments

surveys

a vector of survey names, or NULL to process all surveys.
long

whether tables should have year as row names (default) or column names.

Value

A list of tables.

See Also

getSurveyList, getSurveyYearList, and getSurveyYearQuarterList also list available data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getDatrasDataOverview(surveys = "ROCKALL", long = FALSE)

## End(Not run)

Get Flex File

Description

Get all information in HH plus estimates of Door Spread, Wing Spread and Swept Area per square km. Only available for NS-IBTS survey.

Usage

getFlexFile(survey, year, quarter)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.

Value

A data frame.

Author(s)

Adriana Villamor.

See Also

getDATRAS supports querying many years and quarters in one function call.

getHHdata get haul data

icesDatras-package gives an overview of the package.

Examples

## Not run: 
flex <- getFlexFile(survey = "NS-IBTS", year = 2020, quarter = 1)
str(flex)

# error checking examples:
flex <- getFlexFile(survey = "NS_IBTS", year = 2016, quarter = 1)
flex <- getFlexFile(survey = "NS-IBTS", year = 2030, quarter = 1)
flex <- getFlexFile(survey = "NS-IBTS", year = 2016, quarter = 6)

## End(Not run)

Get Haul Data

Description

Get haul data such as position, depth, sampling method, etc.

Usage

getHHdata(survey, year, quarter)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.

Value

A data frame.

Author(s)

Colin Millar.

See Also

getDATRAS supports querying many years and quarters in one function call.

getHLdata and getCAdata get length-based data and age-based data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
hhdata <- getHHdata(survey = "ROCKALL", year = 2002, quarter = 3)
str(hhdata)

# error checking examples:
hhdata <- getHHdata(survey = "NS_IBTS", year = 2016, quarter = 1)
hhdata <- getHHdata(survey = "NS-IBTS", year = 2030, quarter = 1)
hhdata <- getHHdata(survey = "NS-IBTS", year = 2016, quarter = 6)

## End(Not run)

Get Length-Based Data

Description

Get length-based information such as measured length, individual counts, and sub-factors of sampled species.

Usage

getHLdata(survey, year, quarter, species)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.
species

the valid aphia code of the species to download, if NULL all species are included

Value

A data frame.

See Also

getDATRAS supports querying many years and quarters in one function call.

getHHdata and getCAdata get haul data and age-based data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
hldata <- getHLdata(survey = "BTS", year = 1993, quarter = 3, species = 105883)
str(hldata)

## End(Not run)

Get Survey Indices

Description

Get age based indices of abundance by species, survey and year.

Usage

getIndices(survey, year, quarter, species)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.
species

the aphia species code for the species of interest.

Value

A data frame.

Note

The icesAdvice package provides findAphia, a function to look up Aphia species codes.

See Also

getDATRAS supports querying many years and quarters in one function call.

getHHdata and getCAdata get haul data and age-based data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
haddock_aphia <- icesVocab::findAphia("haddock")
index <- getIndices(survey = "NS-IBTS", year = 2002, quarter = 3, species = haddock_aphia)
str(index)

## End(Not run)

Get Litter assessment output

Description

Get Litter assessment output by survey, year and quarter. The raw data are also included in this file.

Usage

getLTassessment(survey, year, quarter)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.
quarter

the quarter of the year the survey took place, i.e. 1, 2, 3 or 4.

Value

A data frame.

Note

The icesAdvice package provides findAphia, a function to look up Aphia species codes.

See Also

getDATRAS supports querying many years and quarters in one function call.

getHHdata and getCAdata get haul data and age-based data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
index <- getLTassessment(survey = "NS-IBTS", year = 2002, quarter = 3)
str(index)

## End(Not run)

Get a List of All Surveys

Description

Get a list of all survey acronyms.

Usage

getSurveyList()

Value

A character vector.

Author(s)

Colin Millar.

See Also

getSurveyYearList, getSurveyYearQuarterList, and getDatrasDataOverview also list available data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getSurveyList()

## End(Not run)

Get a List of Survey Years

Description

Get a list of all data years for a given survey.

Usage

getSurveyYearList(survey)

Arguments

survey

the survey acronym, e.g. NS-IBTS.

Value

A numeric vector.

Author(s)

Colin Millar.

See Also

getSurveyList, getSurveyYearQuarterList, and getDatrasDataOverview also list available data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getSurveyYearList(survey = "ROCKALL")

## End(Not run)

Get a List of Quarters

Description

Get a list of quarters available for a given survey and year.

Usage

getSurveyYearQuarterList(survey, year)

Arguments

survey

the survey acronym, e.g. NS-IBTS.
year

the year of the survey, e.g. 2010.

Value

A numeric vector.

Author(s)

Colin Millar.

See Also

getSurveyYearList, getSurveyYearQuarterList, and getDatrasDataOverview also list available data.

icesDatras-package gives an overview of the package.

Examples

## Not run: 
getSurveyYearQuarterList(survey = "ROCKALL", year = 2002)

## End(Not run)

DATRAS Trawl Survey Database Web Services

Description

R interface to access the web services of the ICES DATRAS trawl survey database.

Details

Exchange data:

getHHdata haul data
getHLdata length-based data
getCAdata age-based data
getDATRAS exchange data

Catch weights:

getCatchWgt catch weights

Survey indices:

getIndices survey indices

Overview of available data:

getSurveyList surveys
getSurveyYearList years
getSurveyYearQuarterList quarters
getDatrasDataOverview surveys, years, and quarters

Basic queries (thin web service wrappers):
getCAdata, getHHdata, getHLdata, getIndices, getSurveyList, getSurveyYearList, getSurveyYearQuarterList

Derived queries (combining web services with R computations):
getCatchWgt, getDatrasDataOverview, getDATRAS

Author(s)

Colin Millar, Scott Large, and Arni Magnusson.

References

ICES DATRAS database: http://datras.ices.dk.

ICES DATRAS web services: https://datras.ices.dk/WebServices/Webservices.aspx.