| Version: | 4.3.0 |
| Title: | Functions to Support the ICES Transparent Assessment Framework |
| Depends: | TAF (≥ 4.3.0) |
| Imports: | icesVocab (≥ 1.3.1), icesDatsu (≥ 1.2.1), icesSAG (≥ 1.6.2), jsonlite, rlang, icesConnect, httr |
| Description: | Functions to support the ICES Transparent Assessment Framework https://taf.ices.dk to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science. |
| License: | GPL-3 |
| URL: | https://taf.ices.dk, https://github.com/ices-tools-prod/icesTAF |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-09-02 10:12:50 UTC; arnim |
| Author: | Colin Millar [aut, cre] |
| Maintainer: | Colin Millar <colin.millar@ices.dk> |
| Repository: | CRAN |
| Date/Publication: | 2025-09-02 10:50:02 UTC |
Functions to Support the ICES Transparent Assessment Framework
Description
Functions to support the ICES Transparent Assessment Framework, to organize data, methods, and results used in ICES assessments.
Author(s)
Colin Millar and Arni Magnusson.
References
ICES Transparent Assessment Framework: https://taf.ices.dk.
To explore example TAF stock assessments, see the introductory video and tutorial.
The TAF Wiki provides additional help resources.
See Also
Useful links:
Make an Artifact File Entry
Description
Form and validate an artifact as an export from a TAF repository.
Usage
artifact(path, type = c("adhoc", "FLStock", "SAG"), ..., check = TRUE,
quiet = FALSE)
Arguments
path |
The relative path to a file to be added, e.g. "data/indices.csv". |
type |
the type of output, e.g. FLStock, SAG_upload |
... |
a list of metadata to be attributed to the entry. |
check |
logical, should the artifact be checked for validity? |
quiet |
logical, should the function be quiet? |
See Also
check.artifact write.artifacts
Examples
sag_file <- system.file("SAG", "sol_27_4.xml", package = "icesTAF")
sag <- artifact(sag_file, type = "SAG", check = FALSE)
sag
## Not run:
# to check the artifact, use:
sag <- artifact(tmpfile, type = "SAG")
# or
check.artifact(sag)
## End(Not run)
Check an Artifact File Entry
Description
Validate an artifact as an export from a TAF repository.
Usage
check.artifact(artifact, check.metadata = TRUE, check.type = TRUE,
quiet = FALSE)
Arguments
artifact |
an artifact object made using |
check.metadata |
logical, should the metadata be checked against the ICES Vocabulary database? |
check.type |
logical, should type specific artifact checks be run? |
quiet |
logical, should the function be quiet? |
Examples
## Not run:
sag_file <- system.file("SAG", "sol_27_4.xml", package = "icesTAF")
sag <- artifact(sag_file, type = "SAG", check = FALSE)
check.artifact(sag)
## End(Not run)
Get a List of TAF Artifacts
Description
Get a list of TAF artifacts and their metadata, i.e., all the FLStocks, SAG upload files, RCEF files, and other files uploaded to TAF.
Usage
get.artifacts(year = NULL, stock = NULL, ...)
Arguments
year |
the assessment year, e.g. 2015, default all years. |
stock |
a stock name, e.g. lin.27.5a, default all stocks. |
... |
arguments passed to |
Value
A data frame.
Author(s)
Colin Millar.
See Also
icesTAF-package gives an overview of the package.
Examples
## Not run:
artifacts <- get.artifacts(2023)
nshad_artifacts <- get.artifacts(stock = "had.27.46a20")
## End(Not run)
Various TAF Helper Functions
Description
These functions are called by user-level functions. The functionality is documented in the user-level functions.
See Also
icesTAF-package gives an overview of the package.
Read an Artifact File
Description
Read and validate an artifact file.
Usage
read.artifacts(file = "ARTIFACTS.json", check = TRUE)
Arguments
file |
the name of the artifacts file to read |
check |
logical, should the artifact be checked for validity? |
TAF Skeleton
Description
Create initial directories and R scripts for a new TAF analysis using a stock assessment created on stockassessment.org.
Usage
taf.skeleton.sa.org(path = ".", stockname, force = FALSE)
Arguments
path |
where to create initial directories and R scripts. The default is the current working directory. |
stockname |
The short-form name of a stock on stockassessment.org. |
force |
whether to overwrite existing scripts. |
Value
Full path to analysis directory.
See Also
taf.skeleton creates an empty generic TAF skeleton.
icesTAF-package gives an overview of the package.
Examples
## Not run:
taf.skeleton.sa.org(stockname = "WBCod_2021_cand01")
## End(Not run)
Build a SAG web service url
Description
utility to build a url with optional query arguments
Usage
taf_api(service, ...)
Arguments
service |
the name of the service |
... |
name arguments will be added as queries |
Value
a complete url as a character string
Examples
taf_api("hi", bye = 21)
taf_api("FLStocks")
Get a url
Description
Get a url, optionally using an ICES authentication token
Usage
taf_get(url, retry = TRUE, quiet = getOption("icesTAF.messages") %||%
FALSE, verbose = FALSE, content = TRUE,
use_token = getOption("icesTAF.use_token") %||% FALSE)
taf_get_cached(url, retry = TRUE, quiet = getOption("icesTAF.messages")
%||% FALSE, verbose = FALSE, content = TRUE,
use_token = getOption("icesTAF.use_token") %||% FALSE)
Arguments
url |
the url to get. |
retry |
should the get request be retried if first attempt fails? default TRUE. |
quiet |
should all messages be suppressed, default FALSE. |
verbose |
should verbose output form the http request be returned? default FALSE. |
content |
should content be returned, or the full http response? default TRUE, i.e. content is returned by default. |
use_token |
should an authentication token be sent with the request? default is the value of the option icesSAG.use_token. |
Value
content or an http response.
Functions
-
taf_get_cached(): cached version of taf_get
See Also
taf_api builds a SAG web service url.
icesTAF-package gives an overview of the package.
Examples
## Not run:
taf_get(taf_api("FLStocks"))
## End(Not run)
Post to a url
Description
Post to a url using an ICES authentication token
Usage
taf_post(url, body = list(), verbose = FALSE)
Arguments
url |
the url to post. |
body |
a list of named arguments to be sent as the body of the post request. |
verbose |
should verbose output from the http request be returned? default FALSE. |
Value
content of the http response.
See Also
taf_api builds a TAF web service url.
icesTAF-package gives an overview of the package.
Write an Artifact File
Description
Validate and write an artifact file.
Usage
write.artifacts(..., append = TRUE, check = TRUE)
Arguments
... |
a list of artifact objects made using |
append |
logical, should the new artifacts be appended to the existing file? |
check |
logical, should the artifact be checked for validity? |