TAF-package: Transparent Assessment Framework for Reproducible Research

In TAF: Transparent Assessment Framework for Reproducible Research

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)

TAF documentation built on March 31, 2023, 6:51 p.m.