TAF-package: Functions to Support the ICES Transparent Assessment...

Description Details Author(s) References

Description

Functions to support the ICES Transparent Assessment Framework, to organize data, methods, and results used in ICES assessments.

Details

Initial TAF steps:

draft.data draft DATA.bib file
draft.software draft SOFTWARE.bib file
period paste period string for DATA.bib
taf.bootstrap set up data files and software
taf.skeleton create empty TAF template

Running scripts:

clean clean TAF directories
make run R script if needed
makeAll run all TAF scripts as needed
makeTAF run TAF script if needed
msg show message
sourceAll run all TAF scripts
sourceTAF run TAF script

File management:

convert.spaces convert spaces
cp copy files
mkdir create directory
os.linux operating system
os.macos operating system
os.windows operating system
read.taf read TAF table from file
sourceDir read all *.R files
taf.library load package from TAF library
taf.unzip unzip file
write.taf write TAF table to file

Tables:

div divide column values
flr2taf convert FLR to TAF
long2taf convert long format to TAF
long2xtab convert long format to crosstab
plus rename plus group column
rnd round column values
sam2taf convert SAM to TAF
taf2long convert TAF to long format
taf2xtab convert TAF to crosstab
tt transpose TAF table
xtab2long convert crosstab to long format
xtab2taf convert crosstab to TAF

Plots:

lim compute axis limits
taf.colors predefined colors
taf.png open PNG graphics device
zoom change lattice text size

Example tables:

catage.long long format
catage.taf TAF format
catage.xtab crosstab format
summary.taf summary results

Administrative tools, rarely used in scripts:

clean.data clean bootstrap data
clean.library clean TAF library
clean.software clean TAF software
deps list dependencies
detach.packages detach all packages
dos2unix convert line endings
download download file
download.github download repository
file.encoding examine file encoding
get.remote.sha look up SHA code
is.r.package check if file is an R package
latin1.to.utf8 convert file encoding
line.endings examine line endings
rmdir remove empty directory
taf.install install package in TAF library
taf.libPaths add TAF library to search path
taf.session show session information
unix2dos convert line endings
utf8.to.latin1 convert file encoding

Author(s)

Arni Magnusson and Colin Millar.

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.


TAF documentation built on April 7, 2021, 5:06 p.m.