| TAF-package {TAF} | R Documentation |
Transparent Assessment Framework for Reproducible Research
Description
Functions to organize data, methods, and results used in scientific analyses. A TAF analysis consists of four scripts ('data.R', 'model.R', 'output.R', 'report.R') that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step.
Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, TAF is designed to have no package dependencies.
TAF forms a base layer for the [icesTAF](https://cran.r-project.org/package=icesTAF) package and other scientific applications.
Details
Initial TAF steps:
draft.data | draft DATA.bib file |
draft.software | draft SOFTWARE.bib file |
period | paste period string for DATA.bib |
taf.boot | set up data files and software |
taf.skeleton | create empty TAF template |
Running scripts:
clean | clean TAF directories |
clean.boot | clean boot directory |
make | run R script if needed |
make.all | run all TAF scripts as needed |
make.taf | run TAF script if needed |
msg | show message |
source.all | run all TAF scripts |
source.taf | 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 |
source.dir | read all *.R files |
taf.boot.path | construct path to boot folder |
taf.data.path | construct path to boot data 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 |
taf2html | convert TAF to HTML |
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 boot 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 |
read.bib | read metadata entries |
rmdir | remove empty directory |
taf.install | install package in TAF library |
taf.libPaths | add TAF library to search path |
taf.session | show session information |
taf.sources | list metadata entries |
unix2dos | convert line endings |
utf8.to.latin1 | convert file encoding |
Author(s)
Arni Magnusson and Colin Millar.
References
Development site: https://github.com/ices-tools-prod/TAF.
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.
Examples
## Not run:
taf.boot()
source.all()
## End(Not run)