Functions to support the ICES Transparent Assessment Framework, to organize data, methods, and results used in ICES assessments.
Arni Magnusson and Colin Millar.
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 |
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.