R Observatory: Metrics for icesSAG version 1.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

icesSAG

1.6.2Package record

Stock Assessment Graphs Database Web Services

1packages dependsuggested by 1

7.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Colin MillarCRAN page ↗GitHub ↗Website ↗Issues ↗

R interface to access the web services of the ICES Stock Assessment Graphs database https://sg.ices.dk.

Changes in 1.6.2

Upload stock function updated and working.
icesDatsu is used in uploadStock() to check file format and validate the data before upload.

icesSAG 1.5.0 (2024-10-24)

Update all functions to point to new API.
Remove token authentication, and move to JWT tokens via icesConnect.
Introduce the use of caching for some functions to reduce API requests.
export GET and POST request functions.
Depreciate redundant graph functions (e.g. YSSBR).
New functions to set package options: sag_use_token() and sag_messages().
Link messages package option to quiet argument in get requests.
GetListStocks now accepts a stock and modifiedAfter arguments for additional server side filtering.

Show all changes in 1.6.2Hide the rest of the changes in 1.6.2

Remove file upload capability.

icesSAG 1.4.1 (2023-05-11)

bug fix for stockInfo() and documentation.

icesSAG 1.4.0 (2022-02-17)

add new function getCustomColumns().

icesSAG 1.3-8 (2019-10-29)

Display warning if stock name contains – and not -, and quietly fix.

icesSAG 1.3-7 (2019-05-14)

Allow upload to contiue if errors found by DATSU - gives warning, not error.
Add function to parse stock status table values due to change in web service XML data structure.
Fix name in upload format specification CatchLandingsUnits.

icesSAG 1.3-6 (2019-03-13)

Fixed bug in parsing of XML tables. Function now reads the WSDL data that is included as an internal data set (list of variable names)
Set all examples to dontrun
code now checked against lintr for consistent style

icesSAG 1.3-5 (2018-06-08)

added function getStockSourceData() to download the XML file that was origionally uploaded.

icesSAG 1.3-4 (2018-05-01)

added function getLatestStockAdviceList()
export print methods for sag.list and sag.data.frame for fishdata and fishinfo objects used to upload data.
improved personal access token logic
improved help documentation
Added StockCategory, Purpose, ModelType, ModelName to upload functions
Added filter for assessment Purpose in getSAG()
fixed bugs arising from changes to xml2 package
fixed bug arsing from change in ICES Datsu web service

icesSAG 1.3-2 (2017-05-06)

User sets SAG database access token in a ~/.Renviron_SG file.
Addressed non CRAN compliant behaviour: user must create .Renviron file themselves.

icesSAG 1.3-1 (2017-05-04)

Improved createSAGxml() internal data validation.

icesSAG 1.3-0 (2017-04-05)

Added function uploadStock() to upload data to SAG database via uploadXMLFile(). The functions readSAGxml() and createSAGxml() convert data to and from SAG XML upload format.
Added functions stockInfo() and stockFishdata() to prepare data for upload. Uploads require user access tokens, available from the main SAG website.
Added function getStockStatusValues() to get stock status table, and getYSBRSummaryTable() to get yield and SSB per recruit.
Added functions getSAG*Settings*() and setSAG*Settings*() to get and set graph settings. The function getSAGTypeGraphs() lists the SAG graph types.
Renamed findKey() to findAssessmentKey().

icesSAG 1.2-1 (2017-03-24)

Hotfix release to match changes in the underlying web service, regarding assessment keys.

icesSAG 1.2-0 (2016-12-05)

Added functions get*Graph() to fetch standard graph images, with a corresponding plot() method. The convenience function getSAGGraphs() fetches four commonly used graphs.
Added argument 'regex' to findKey().
Fixed bug in getSAG() when different column names appear in stock summaries and combine = TRUE.
Removed dependency on RCurl and XML by using base functions to download and parse data.

icesSAG 1.1-0 (2016-10-29)

Added function findKey() to look up a unique stock list key.
Added function getSAG() to import summary results and reference points, without finding a lookup key first.
Changed argument in functions getSummaryTable() and getFishStockReferencepoints() from 'year' to 'key'.
Improved XML parsing, so both leading and trailing white space is removed.
Improved XML parsing, so "" and "NA" is converted to NA.
Improved XML parsing, so data frame columns are automatically coerced to the appropriate storage mode (character, numeric, integer).

icesSAG 1.0-0 (2016-08-09)

Initial release, with functions getListStocks(), getSummaryTable(), and getFishStockReferencePoints().

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("icesSAG", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ices-tools-prod/icesSAG")

Development version from ices-tools-prod/icesSAG. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-icessag

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-icesSAG

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-icesSAG

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.2

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structured · mentions 1.6.2Citation fileNoWebsiteYes

Help pages: 22includes a package overview page
Examples that run: 20%4 run in a plain check · 16 never run
Exported functions with examples: 95%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 5%

How these are measured

Downloads

7.7K

CRAN downloads in the past year

Rank #6,261 · ~21/day · ~641/mo

Releases R versions

Daily download trend is not available in this view yet.

50930 days

1.4K90 days

7.7K1 year

Compare downloads with other packages →

Also on93 r2u2 autocran

How downloads are counted

Repository

ices-tools-prod/icessag ↗Organization: ices-tools-prod

14Stars

9Forks

112Open issues

1Open PRs

12Releases

423Commits

7Commit identities

423 commits · Last activity 2025-09-29 · 0% stars, 30d · Default branch at 1.6.6, ahead of CRAN 1.6.2 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 84%
Median days to close, 50 most recently updated closed issues: 124
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-24 · 122026-07-07 · 14

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/ices-tools-prod/icessag on 2026-10-21.

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2025-09-21

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing icesSAG adds 17 packages (12 with compiled code, 4.6 MB of source tarballs). Heaviest: openssl 1.1 MB, jsonlite 1.0 MB, rlang 766 KB.

Depends (1)

R >= 4.3

Imports (7)

httr xml2 icesConnect icesDatsu memoise cachem rlang

LinkingTo (0)

none

Suggests (2)

testthat icesVocab

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

icesTAF

Suggests, most downloaded first

knobi

How these are counted

Code & Tests

People & History

People (5)

Colin Millar

Author, Maintainer since 1.2-0 (2016)

Scott Large

Author

Arni Magnusson

Author · added in 1.2-0

Laura Andreea Petre

Author · added in 1.5.0

Carlos Pinto

Author · added in 1.3-1

Previously maintained by Scott Large (1.0).

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.6.2Latest
record
2025-05-03 · current release · diff ↗ ·
removed 2 exports
ices_get, ices_post

added 4 exports
sag_get, sag_post, uploadStock, writeSAGxml
R
R 4.5.0 released · 2025-04-11
1.5.0
record
2024-10-24 · diff ↗ ·
removed 5 exports
findKey, getStockSourceData, getTokenExpiration, getYSBRSummaryTable, uploadStock

added 5 exports
ices_get, ices_post, sag_api, sag_messages, sag_use_token
R
R 4.4.0 released · 2024-04-24
1.4.1
record
2023-05-11 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-02-17
1.4.0
record
2022-02-17 · diff ↗ ·
added 1 export
getCustomColumns
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-08-07
it requires archived package 'icesVocab'
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
unarchivedReturned to CRAN
2019-03-12
1.3-6
record
2019-03-12 · diff ↗ ·
added 3 exports
getStockDownloadData, getStockSourceData, getTokenExpiration

Show 13 earlier eventsHide 13 earlier events

archivedRemoved from CRAN
2019-03-05
requires archived package 'icesVocab'
1.3-4
record
2018-05-01 · diff ↗ ·
added 1 export
getLatestStockAdviceList
R
R 3.5.0 released · 2018-04-23
unarchivedReturned to CRAN
2017-05-07
1.3-2
record
2017-05-07 · diff ↗
archivedRemoved from CRAN
2017-05-06
policy violation
1.3-1
record
2017-05-04 · diff ↗ ·
added 1 export
setSAGSettingForAStock
1.3-0
record
2017-04-30 · diff ↗ ·
added 12 exports
createSAGxml, findAssessmentKey, getSAGSettingsForAStock, getSAGTypeGraphs, getSAGTypeSettings, getStockStatusTable, getStockStatusValues, getYSBRSummaryTable, readSAGxml, stockFishdata, stockInfo, uploadStock
R
R 3.4.0 released · 2017-04-21
1.2-1
record
2017-03-24 · diff ↗
1.2-0
record
2016-12-07 · diff ↗ ·
added 13 exports
findKey, getFishMortality, getFishingMortalityGraph, getFishingMortalityHistoricalPerformance, getLandingsGraph, getRecruitmentGraph, getRecruitmentHistoricalPerformance, getSAG, getSAGGraphs, getSSBHistoricalPerformance, getSpawningStockBiomassGraph, getYSSB, getstock_recruitment
1.0
record
2016-08-09
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-08-09
Total releases: 12 / 10 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3
Download size: 24 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("icesSAG")

Format

Millar, C., Large, S., Magnusson, A., Petre, L. A., & Pinto, C. (2025). icesSAG: Stock Assessment Graphs Database Web Services (Version 1.6.2) [Computer software]. https://doi.org/10.32614/CRAN.package.icesSAG

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for icesSAG version 1.6.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →