icesTAF-package: 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.

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

Running scripts:

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

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

Plots:

Example tables:

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

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.